Macs in Chemistry

Insanely Great Science

Molecular modeling

LICHEM: Layered Interacting CHEmical Models


An update to LICHEM: Layered Interacting CHEmical Models has been published DOI

LICHEM is an open-source (GPLv3) interface between QM and MM software so that QM/MM calculations can be performed with polarizable and frozen electron density force fields. Functionality is also present for standard point-charge based force fields, pure MM, and pure QM calculations.

Available from GitHub

Note, On OSX machines, the SEDI, TEX, BIB, and CXXFLAGS variables will need to be modified.


GROMAC 2019 released


I just noticed GROMACS 2019 was released on Dec 31 2018.

GROMACS is one of the major software packages for the simulation of biological macromolecules. It is aimed at performing the simulation of large, biologically relevant systems, with a focus on both being efficient and flexible to allow the research of a number of different systems

Several important performance improvements

  • Simulations now automatically run using update groups of atoms whose coordinate updates have only intra-group dependencies. These can include both constraints and virtual sites. This improves performance by eliminating overheads during the update, at no cost.
  • Intel integrated GPUs are now supported with OpenCL for offloading non-bonded interactions.
  • PME long-ranged interactions can now also run on a single AMD GPU using OpenCL, which means many fewer CPU cores are needed for good performance with such hardware.

Release notes here


Workshop on Computational Tools for Drug Discovery


In many companies/institutions/universities new arrivals are presented with a variety of desktop tools with little or no advice on how to use them other than "pick it up as you along". This workshop is intended to provide expert tutorials to get you started and show what can be achieved with the software.

The tutorials will be given a series of outstanding experts Christian Lemmen (BioSolveIT), Akos Tarcsay (ChemAxon), Giovanna Tedesco (Cresset), Dan Ormsby (Dotmatics) Greg Landrum (Knime ) and Matt Segall (Optibrium), you will be able to install the software packages on you own laptops together with a license to allow you to use it for a limited period after the event.

Registration and full details are here.

Computational Tools Flyer


Samson documentation updated


I've mentioned Samson a couple of times and I noticed that the documentation has been updated. Documentation is a critical but often overlooked feature of software.

SAMSON is a novel software platform for computational nanoscience. Rapidly build models of nanotubes, proteins, and complex nanosystems. Run interactive simulations to simulate chemical reactions, bend graphene sheets, (un)fold proteins. SAMSON's generic architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. SAMSON is developed by the NANO-D group at INRIA, and means "Software for Adaptive Modeling and Simulation Of Nanosystems

Pasted Graphic


ConstruQt API


Just got details of an interesting service

ChemAlive ( would like to offer ConstruQt, its core molecular design tool based on quantum mechanics (QM), for trial.

Currently you can:

  • Transforms list of SMILES or InChI molecular designations into state-of-the-art 3D molecular structures in SD format
  • Manages the conformational space of the molecules with a robust shape searching algorithm
  • Generates all reasonable tautomeric forms of the molecule and prioritizes them by energy
  • Generates all diastereomeric forms of the molecules and differentiates them by energy
  • All molecules are stored in our unique database architecture making the calculations easily augmented and carried through to other processes

The last bullet point is worth noting, so don't submit anything confidential.


IGMPlot release 2.4


The new IGMPlot release 2.4, is available for download at . It provides chemists with a visual analysis of covalent and non-covalent interactions

Detailed installation notes are in the documentation (page 5).

IGMPlot is written in C++. It has been installed and tested on several platforms: computational centers (linux), MacOS, Windows10, and several compilers and versions (GNU, Intel, PGI), it can be compiled with or without OpenMP support

On MacOs machines, a sequential version of IGMPlot can be obtained with the Clang compiler. In the Makefile choose the options:

  • CppCompilerFamily=GNU
  • CppCompilerVersion=5andabove o OpenMP=NO
  • CC=g++

On MacOS machines, to leverage OpenMP multicore execution, you must install a gcc (g++) version different from the one provided within the compiler front end “Clang” which until now has not built-in support for OpenMP. You might install gcc with the command: ‘brew install gcc -- without-multilib’ (see for instance openmp-on-mac-os-x-10-11). This way, the compiler might be installed somewhere like /usr/local/Cellar/gcc/7.1.0/bin/g++-7. In this example, make sure the g++-7 command be available with your PATH and adjust the IGMPlot makefile accordingly (changing the g++ command with g++-7 for instance).

This link might also be useful OpenMP under MacOSX.



pywindow: Automated Structural Analysis of Molecular Pores


An interesting recent publication describes pywindow DOI a Python package for the analysis of structural properties of molecular pores (porous organic cages, but also MOFs and metallorganic cages).

Structural analysis of molecular pores can yield important information on their behavior in solution and in the solid state. We developed pywindow, a python package that enables the automated analysis of structural features of porous molecular materials, such as molecular cages.

Freely available on Github

Requires numpy, scipy, scikit-learn

A number of Jupyter notebook examples are provided

Example1: Structural analysis of a single molecule loaded from a file type. (multiple examples)
2: Structural analysis of a single molecule loaded from an RDKit Molecule object. (required RDKit)
Example3: Calculating an average molecule diameter.
4: Analysis of a MOF.
Example5: Analysis of a metal-organic cage.
6: Analysis of a periodic system containing several molecular pores that requires unit cell reconstruction.
Example7: Analysis of an MD trajectory containing single molecular pore.
8: Analysis of an MD trajectory containing periodic system with multiple molecular pores that requires unit cell reconstruction


iRASPA: GPU-accelerated visualisation software for materials scientists


Just came across this application and I thought it would be worth flagging, iRASPA is a GPU-accelerated visualization package aimed at material science. Molecular Simulation Journal. 44 (8): 653–676 DOI


iRASPA is a visualization package (with editing capabilities) aimed at material science. Examples of materials are metals, metal-oxides, ceramics, biomaterials, zeolites, clays, and metal-organic frameworks. iRASPA is exclusively for macOS and as such can leverage the latest visualization technologies with stunning performance. iRASPA extensively utilizes GPU computing. For example, void-fractions and surface areas can be computed in a fraction of a second for small/medium structures and in a few seconds for very large unit cells. It can handle large structures (hundreds of thousands of atoms), including ambient occlusion, with high frame rates.

Via iCloud, iRASPA has access to the CoRE Metal-Organic Frameworks database containing 4764 structures and 2932 structures enhance with atomic charges. All the structures can be screened (in real-time) using user-defined predicates. The cloud structures can be queried for surface areas, void fraction, and other pore structure properties.

iRaspa is written in Swift.


Open Force Field Consortium


The Open Force Field Consortium, an academic-industry collaboration designed to improve small molecule force fields used to guide pharmaceutical drug discovery.

The Consortium will develop an extensible, open source toolkit for constructing, applying, and evaluating force fields; produce and curate public datasets necessary to build high-accuracy biomolecular force fields; and apply these tools and datasets to generate improved force fields. Academic and industry partners work together to ensure its success.


MGMS Young Modellers’ Forum 2018


Molecular Graphics and Modelling Society Young Modellers’ Forum 2018.

To encourage young molecular modellers at the beginning of their careers, the MGMS invites PhD students who wish to present their work on any aspect of computational chemistry, cheminformatics, or computational biology at the 2018 Young Modellers’ Forum. Other members of the modelling community are are strongly encouraged to attend this event as it is your opportunity to see these talented young modellers and to assist us in the evaluation of the prizes. There is also the chance to discuss the talks afterwards in the pub

Abstract submission 5th October 2018

Date: Friday, 30th November, 2018 Venue: Room QA063, Queen Ann Court, The Old Naval College, Greenwich Location: Details of how to get to the campus can be found at


Amber 18 and AmberTools 18released


Amber is a suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active develpment community

Amber 18 ajor new features include:

  • Free energy calculations on GPUs
  • GPU support for 12-6-4 ion potentials
  • Domain decomposition for CPU-parallelism
  • Nudged elastic band calculations for pmemd (CPU and partial GPU implementation)
  • Constant redox potential calculations, to supplement constant pH simulations
  • Support and significant performance improvements for the latest Maxwell, Pascal and Volta GPUs from NVIDIA.
  • New pmemd.gem code for advanced force fields, including AMOEB

AmberTools 18 new features include

  • CUDA-enabled pbsa solver; extensions for membrane modeling with PB *lambda-dynamics method for constant pH simulations *packmol_memgen tool for building lipids and bilayers *New ("middle") integration algorithms in sander *Build tools based on CMake *Continued updates and extensions to cpptraj: *ability to obtain energies from snapshots of PME simulations *Pairlist and other speedups *improved scripting abilities

Instructions for installing Amber under Mac OSX are here

You will need to install gfortran, whilst you can download the binary it might be worth considering using Homebrew as described here


Review of MOE 2018.01


The 2018.01 release of Chemical Computing Group's Molecular Operating Environment (MOE) software includes a number of new features, enhancements and changes. I written a review that highlights a number of the features.


Read more here….


RDkit in Samson


I've posted about Samson a couple of times and it just keeps getting better and better.

SAMSON is a novel software platform for computational nanoscience. Rapidly build models of nanotubes, proteins, and complex nanosystems. Run interactive simulations to simulate chemical reactions, bend graphene sheets, (un)fold proteins. SAMSON's generic architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. SAMSON is developed by the NANO-D group at INRIA, and means "Software for Adaptive Modeling and Simulation Of Nanosystems.

A recent blog post highlights the use of RDKit in Samson.

In this post I will present you the RDKit-SMILES Manager module that I integrated in the SAMSON platform. As some of you know, RDKit is an open source toolkit for cheminformatics which is widely used in the bioinformatics research. One of its features is the conversion of molecules from their SMILES code to a 2D and 3D structures. Thanks to the new SAMSON Element, it is now possible to use these features in the SAMSON platform. SMILES code files (.smi) or text files (.txt) containing several SMILES codes can be read using the import button.

The new module allows you to import a file containing SMILES strings, generate 2D depictions, and by right-clicking on these images, you can open, generate the 3D structure in SAMSON or save the image as png or svg.


It is also possible to run substructure searching using SMARTS.


OMEGA v3.0.0 released


Conformational analysis is a critical component of molecular modelling and I've always viewed OMEGA from OpenEye as the standard to which all other software packages should be compared.

OMEGA's knowledge-based approach produces high-quality conformers, superior to those of many other methods. It has also been found to be the fastest of commercially available conformer generators. Benchmarking Conformer Ensemble Generators, Friedrich, N.-O. de Bruyn Kops, C. Fachsenberg, F. Sommer, K., Rarey, M. Kirchmair, J. J. Chem. Inf. Model. 2017, 57, 2719-2728. DOI.

OMEGA’s capability has been expanded for molecules containing large rings by adding a method specifically tuned to sample macrocyclic conformational space. The approach is based on a rewritten version of the original OMEGA distance geometry algorithm.


In this update support for macOS El Capitan (10.11), macOS Sierra (10.12), and macOS High Sierra (10.13) has been added.


MOE update 2018.01 released


The latest update to Chemical Computing Group's Molecular Operating Environment (MOE) software includes a variety of new features, enhancements

Windows XP (finally!) and macOS 10.6 have been removed from the list of officially supported platforms. Supported Windows platforms are Vista/7/8/10, and the minimum supported macOS is 10.7 (Lion).

Amber14:EHT Forcefield. The Amber14 parameter set is now supported in MOE. The new parameters consist of improvements to nucleic acids; otherwise, protein and small molecule parameters (and charges) are unchanged. The forcefield can be selected in the MOE | Footer.

TCR-MHC Protein Complex Database. A new MOE Project database containing T-Cell Receptor (TCR) – Major Histocompatibility Complex (MHC) x-ray structures has been added to MOE. The database can be accessed with MOE | Protein | Search | TCR-MHC | TCR-MHC which will launch the MOE Project Search panel.

Several applications have been parallelized to run in the moe -mpu environment:

  • Descriptor calculations with the SVL function QuaSAR_DescriptorMDB.
  • Energy minimization in the Database Viewer DBV | Compute | Molecule | Energy Minimize.
  • Conformational search using MDB input files in MOE | Compute | Conformations | Search.
  • Rotamer library generation with DBV | Compute | Build Rotamer Library.
  • Project database creation with the SVL run file dbupdate.svl and the scripts $MOE/bin/projupdate and $MOE/bin/projupdate.bat.

I plan to review the latest version of MOE in the near future.


SeeSAR version 7.2 released


SeeSAR has been updated.

Get fresh inspiration from this huge update of SeeSAR! We realized, on the one hand, that the functionality of the editor was growing and growing, making it more and more complicated to use. On the other hand, access to the full functionality of ReCore demands a different kind of user interface. So we "took the bull by the horns" and, akin to the editor, created the new Inspirator which you can use to do:

  • Core replacement This feature is the same but with a much improved UI. You are able to directly select and visualize the bonds that will be clipped to carve out a core fragment for replacement. The clipped bonds now remain in place (even while you define sphere constraints) up until you define a new query. Also the display of results is much enhanced, as you can see the new core fragments highlighted in 2D as well as in 3D. For reference, your query molecule stays visible as well.
  • Fragment linking and merging You may of course launch the Inspirator with more than just one molecule. In this case, you can define bonds to clip on different molecules, thereby requesting linker fragments that will connect the remaining pieces. Note that it is not mandatory to clip a terminal part of each molecule to create the query, you may replace a core part in one and connect it to another fragment at the same time.
  • Fragment growing This was possibly the most frequently requested functionality in ReCore: Cut just one bond and grow onto this bond using a fragment library of typical side chains. In this way, you can, for example, reach out to nearby subpockets. The new growing algorithm can very quickly scan through a (for now) ready-made library of typical fragments. You may of course define sphere constraints at the same time in order to target particular locations in the bi

You can download SeeSAR here and use it for free for 7 days.


GROMACS updated


The official release of GROMACS 2018 is now available.

GROMACS is one of the major software packages for the simulation of biological macromolecules.

Highlights from this update include:-

  • PME long-ranged interactions can now run on a single GPU, which means many fewer CPU cores are needed for good performance.
  • Optimized SIMD support for recent CPU architectures: AMD Zen, Intel Skylake-X and Skylake Xeon-SP.

  • The AWH (Accelerated Weight Histogram) method is now supported, which is an adaptive biasing method used for overcoming free energy barriers and calculating free energies (see

  • A new dual-list dynamic-pruning algorithm for the short-ranged interactions, that uses an inner and outer list to permit a longer-lived outer list, while doing less work overall and making runs less sensitive to the choice of the “nslist” parameter.
  • A physical validation suite is added, which runs a series of short simulations, to verify the expected statistical properties, e.g. of energy distributions between the simulations, as a sensitive test that the code correctly samples the expected ensemble.
  • Conserved quantities are computed and reported for more integration schemes - now including all Berendsen and Parrinello-Rahman schemes.


SeeSAR for Parallelized Fragment Growing & Pocket Exploration


I see that SeeSAR now supports a parallelized 'real' fragment growing.

SeeSAR is a software tool for interactive, visual compound prioritisation as well as compound evolution. Structure-based design work ideally supports a multi-parameter optimization to maximise the likelihood of success, rather than affinity alone. Having the relevant parameters at hand in combination with real-time visual computer assistance in 3D is one of the strengths of SeeSAR. Stimulating exploration with SeeSAR, we have embarked on pursuing a new cheminformatics compute paradigm of "Propose & Validate".


You can download SeeSAR here and use it for free for 7 days.


Predicting the Conformational Energy of Small Molecules


An interesting publication in JCIM, Atom Types Independent Molecular Mechanics Method for Predicting the Conformational Energy of Small Molecules, DOI.

We report herein our effort to incorporate lone pairs into our model to extend its applicability domain to any saturated small molecules. The developed model H-TEQ 2 has been validated on a wide variety of molecules from polyaromatic molecules to carbohydrates and molecules with high heteroatoms/carbon ratios.




FreeSASA is a command line tool, C-library and Python module for calculating solvent accessible surface areas (SASA).

The Read Me gives download, build and installation instructions, in addition it details how to build the Python interface.

Simon Mitternacht (2016) FreeSASA: An open source C library for solvent accessible surface area calculations. F1000Research 5:189. DOI


SAMSON, Software for Adaptive Modeling and Simulation Of Nanosystems


SAMSON is a novel software platform for computational nanoscience. Rapidly build models of nanotubes, proteins, and complex nanosystems. Run interactive simulations to simulate chemical reactions, bend graphene sheets, (un)fold proteins. SAMSON's generic architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. SAMSON is developed by the NANO-D group at INRIA, and means "Software for Adaptive Modeling and Simulation Of Nanosystems.


SAMSON has an open architecture which allows anyone to extend it - and adapt it to their needs - by downloading SAMSON Elements (modules). SAMSON Elements come in many flavors: apps, editors, controllers, models, parsers, etc., and are adapted to different application domains. SAMSON Elements help users build new models, perform calculations, run interactive or offline simulations, visualize and interpret results, and more. Add new SAMSON Elements to SAMSON straight from SAMSON Connect.

In the latest news Python scripting is coming to SAMSON 0.7.0. Most of the SAMSON API is now exposed in Python, and this will allow you to create models and run simulations, generate movies, perform analysis and reporting, etc., directly from scripts. Python will make it even easier to integrate and pipeline SAMSON and SAMSON Elements with well-known packages from diverse fields, e.g. TensorFlow, PyRosetta, RDKit, ASE, etc., to name a few


SeeSAR 6.1 released


SeeSAR 6.1 has been released, looking at the release notes there are a couple of useful additions.

  • Multiple protein alignment, Since version 5.6 it has been possible to load and work with multiple proteins. So far this feature could only be utilized with pre-aligned structures. Now you can do the 3D alignment in SeeSAR itself. The alignment is based on and optimized according to the superposition of related active sites. Therefore, once you have selected a binding site, just one click is all that is needed to superpose all related binding sites at once. Note that the superposition is limited to highly homologous proteins (>90% sequence identity).
  • SeeSAR/StarDrop interface. We have implemented a new function that greatly improves the interaction between the two software packages. Using the option in the molecule table toolbar, you may now transfer all (or the subset of favorite) molecules directly to StarDrop, which is launched automatically. This interface is supported in StarDrop starting with the recently released StarDrop version 6.4 and StarDrop now analogously supports launching and submitting data to SeeSAR. So it is in fact possible to transfer data back and forth and exploiting maximum synergy to make the best of both worlds. Note that this feature may require a few adjustments in your SeeSAR settings to become fully functional.
  • Shortcut to copy protein ligands. Usually among the first tasks after loading proteins is to copy the related protein ligands to the molecules table for further processing (docking, editing, re-scaffolding, etc.). Especially with multiple proteins this turned out to be a quite cumbersome procedure. Therefore we have implemented a shortcut function in the toolbar of the proteins tab to copy all protein ligands at once to the molecules table. Note that this function will copy all ligands irrespective of their position in relation to the common binding site that is used in the context of the molecules table. So some of the copied ligands may lie well outside the common binding site.

SeeSAR is a software tool for interactive, visual compound prioritization as well as compound evolution. Structure-based design work ideally supports a multi-parameter optimization to maximize the likelihood of success, rather than affinity alone. Having the relevant parameters at hand in combination with real-time visual computer assistance in 3D is one of the strengths of SeeSAR.



Schrödinger Updated


The Schrödinger small molecule discovery suite has ben updated. This looks to be a substantial update and is described in the video below.

Supported MacOS X 10.12 and Mac OS X 10.9 - 10.11

3D Support, Supported: Interlaced stereo via Zalman 3D Monitors


ADF Modeling Suite 2017


Just looking at the release notes for ADF2017 and support pages and a couple of things caught my eye.

The python distribution shipped with ADF was upgraded to python 3.5. Among others, new and updated modules include the iPython interpreter for easier development of python codes, a number of useful packages such as numpy 1.11.3 / scipy 0.18.1, ASE 3.13.0, matplotlib and RDKit 2016.09.

The Mac OSX version no longer requires XQuartz and is much faster in visualizing large systems.


ChemDoodle 3D v3 is available


It has been a little while but ChemDoodle 3D is out, and looking at the new features it was certainly worth the wait, this is a major upgrade!


New features in ChemDoodle 3D v3:

  • Faster and more advanced shaders for the most realistic graphics or captivating cartoon rendering. There are now 6 shaders to choose from.
  • Fully customizable and dynamic real-time shadow rendering.
  • Molecules can now be built using intuitive tools and a continuous running optimization (using the new Minimizer widget) to allow you to build accurate models and the specific conformations you desire. It is a lot of fun to physically interact with the structures you build!
  • New bond types, more aromatic ring representations, more cheminformatics functions.
  • Distances can now be measured between any combination of bond centers and atoms; previously only atoms were allowed. Visual specifications for all shapes can now be independently edited.
  • Fully customizable surfaces can now be built for selections of atoms.
  • Selector tools have been added, and you can now select objects by lasso and rectangular marquee.
  • Our interface engine is now fully implemented including drawing toolbars, widgets, autosaving, workspace control and more.
  • Style sheets (and scene settings files) can now be created, saved and loaded.
  • Quaternions can now be used for all rotations, instead of just X-Y axis rotation.
  • Full support for the new RCSB MacroZZmolecular Transmission Format.
  • A more advanced copy and paste system.
  • After effects are new multipass shader options that provide additional graphical effects. Blurring and outlining are currently available.
  • Outlines are now rendered for highlighted and selected objects.
  • Model settings in the Visuals panel in Preferences are now organized by model type.
  • A new Custom Element Color Set. Color choosers have been upgraded and now affect graphics in real time. Improved MacOS look and feel.
  • Added the last of the new element names recommended by IUPAC. Added more published van der Waals values.
  • Polishing, new icons, and performance improvements affecting just about every asproect of the product, from picking to animations to rendering and saving images.


ADF Modeling Suite 2017


I just got this message

We are proud to announce the 2017 release of the ADF Modeling Suite, with excellent contributions from our collaborators and the continued efforts of the SCM team in Amsterdam.

Exciting new features include

  • Many new NLO properties (TPA, THG, ...): Hu, Autschbach & Jensen
  • Constrained DFT with excited states: Ramos & Pavanello
  • LFDFT for d-d and d-f transitions: Ramanantoanina & Daul
  • CV-DFT for singlet-triplet excitations: Krykunov, Senn, Park & Seidu
  • Faster periodic response with TD(C)DFT, including 2D systems: Raupach
  • VCD analysis tools: Nicu

Reactivity & Analysis-

  • Latest xc functionals (SCAN, MN15-L, ....): interface to libxc 3.0
  • Special points, fat bands and improved pDOS analysis
  • GUI support for NEGF with BAND (Thijssen group, includes self-consistent NEGF, gate & bias potential, spin transport) and post-SCF DFTB-NEGF (Heine group)
  • FDE + local COSMO: Goez & Neugebauer
  • Reactivity descriptors from conceptual DFT and QTAIM: Tognetti & Joubert
  • Geometry optimization with SpinFlip in QUILD: Swart
  • Spin-polarization and l-dependency for DFTB: Melix, Oliveira, Rueger, Heine
  • Much faster periodic DFTB(+D) optimizations, latest parameters freely available
  • eReaxFF including explicit electrons: based on Islam, Verstraelen & van Duin
  • Controllable mass-scaling for force bias Monte Carlo ReaxFF: Bal & Neyts
  • Improved VLE, LLE, IDAC, kOW with reparameterized COSMO-SAC: Chen & Lin

GUI & Builders-

  • Quantum ESPRESSO: GUI interface & binaries
  • MOF builder and UFF4MOFsII: Coupry, Addicoat, Heine
  • Much faster visualization of large and periodic systems
  • Set up and visualize 'molecule gun' calculations with ReaxFF

For a more comprehensive list and details see:


ORCA 4.0 released


The latest update to ORCA has just been released.

The program ORCA is a modern electronic structure program package written by F. Neese, with contributions from many current and former coworkers and several collaborating groups. The binaries of ORCA are available free of charge for academic users for a variety of platforms. ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations.

New Features of Version 4.0:

New Methods:

  • Linear scaling DLPNO-CCSD(T) open shell. New restricted open-shell formulation
  • Linear scaling DLPNO-MP2 (RHF and UHF)
  • Linear scaling DLPNO-MP2-F12 (RHF)
  • Linear scaling DLPNO-CCSD(T) (the 2013 implementation is still available)
  • Linear scaling DLPNO-CCSD(T) local energy decomposition scheme
  • Linear scaling DLPNO-CCSD closed shell density
  • Linear scaling cluster in molecule (CIM): MP2, CCSD(T), DLPNO-CCSD(T)
  • Linear scaling DLPNO-NEVPT2
  • NEVPT2-F12
  • Updated interface to BLOCK 1.0
  • Closed shell EOM-CCSD energies
  • Closed shell STEOM-CCSD energies
  • Partial PNO-EOM-CCSD method for excited states
  • Partial PNO-STEOM-CCSD method for excited states
  • Mukherjee Mk-LPNO-MRCCSD(T)
  • Powerful iterative configuration expansion (ICE-CI) approximation to Full-CI
  • ICE-CI for large active space CASSCF calculations
  • MREOM-CCSD (also with SOC)
  • Fully internally contracted MRCI
  • Full TD-DFT energies and gradient for hybrid functionals
  • Super-fast approximate TD-DFT: sTDA/sTDDFT of Grimme and co-workers
  • PBEh-3c method of Grimme and co-workers

SCF, DFT and Hessian:

  • Large performance improvements for calculations with four center integrals
  • Improved performance with RI-J with conventionally stored integrals
  • Gradient for range separated hybrids
  • Gradient for range double hybrid functionals with meta GGAs
  • Gradient for range double hybrid functionals with range separated functionals
  • Gradient for RI-JK
  • Frequencies for range separated functionals
  • Stability analysis and automatic search for broken symmetry states
  • Local spin analysis
  • Fractional occupation number analysis (FOD) for detection of MR character

MDCI module:

  • All improvements for DLPNO methods as listed above
  • Closed shell EOM-CCSD energies
  • Closed shell STEOM-CCSD energies
  • Automatic closed shell STEOM-CCSD active space selection
  • EOM-CCSD(2) and STEOM-CCSD(2) approximations
  • EOM-CCSD transition moments
  • EOM/STEOM-CCSD core level excited states
  • ADC(2) and CC(2) methods (initial implementation)
  • Improved automatic frozen core handling
  • Core-correlation in automatic basis set extrapolation

AUTOCI module:

  • FIC-MRCI, CEPA/0 variant and DDCI3


  • Detailed tutorial showing CASSCF/NEVPT2 usage
  • Accelerated CI (ACCCI) a more efficient CI step for multi-root calculations
  • Automatic implementation of AbInitio ligand-field theory
  • Simplified generation of double-shell orbitals
  • Active space protection scheme and improved warnings
  • ICE-CI as CI solver for larger active spaces
  • Partially Contracted NEVPT2 with and without RI
  • Updated interface to BLOCK 1.0
  • DMRG-NEVPT2 for active spaces up to 20 orbitals
  • Magnetization and magnetic susceptibility
  • Printing of the wavefunction in terms of CSFs and spin-determinants
  • MREOM-CCSD (also with SOC)
  • Local spin analysis for CASSCF
  • Fragment decomposition of the spin-spin interaction
  • Cumulant approximation for NEVPT2
  • ACCCI as CIStep for FIC and DLPNO-NEVPT2
  • Explicitly correlated RI-FIC-NEVPT2 (NEVPT2-F12)


  • Full TD-DFT for hybrid functionals
  • Gradient for full TD-DFT with hybrid functionals
  • TD-DFT/TDA gradient with range separated functionals
  • ROCIS magnetic properties (hyperfine, g-tensor, ZFS tensor, MCD)
  • ROCIS-RIXS spectra
  • PNO-ROCIS for spectacular performance improvements
  • Super-fast approximate TD-DFT: sTDA/sTDDFT
  • Natural transition orbitals in TD-DFT and ROCIS


  • GIAO implementation for NMR chemical shifts. Various aproximations (RIJOCOSX, RIJK)
  • New Handling of basis set names. Now fully consistent with TurboMole def2-defaults (including ECPs) SARC basis sets separately available
  • New reading of basis sets and ECPs together
  • New correlation consistent basis sets added
  • New SARC basis sets for the lanthanides; good for correlated calculations
  • New ANO-RCC basis sets added
  • Improved frozen core handling in correlation calculations
  • Improved automatic auxiliary basis set generation
  • Corrections for low-frequency modes in thermochemistry
  • New and improved NBO interface
  • CPCM and improved SMD solvent models
  • Intrinsic atomic orbital (IAO) and bond orbital implementation
  • Improved performance in Boys localization
  • Updated and improved mapspc program
  • Atomic Mean Field (AMFI) spin-orbit coupling operators
  • EPRNMR works with range separated hybrid functionals
  • New molecular dynamics module


MOE updated


Chemical Computing Group have announced and update to MOE. The MOE 2016.0802 update contains a number of updates to the biomolecule modelling including improved hydrogen bond detection, and addition of a number of unnatural amino acids.

There have also been improvements to MOE/Web MOE/web. The MOE/web version compatibility check has been broadened. MOE/web license waiting has been improved. HTTPS authentication proxy server support has been improved.


Tinker Updated


The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22/CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable model, and the AMOEBA (2004, 2009, 2013) polarizable atomic multipole force field.

The TINKER package contains a variety of interesting algorithms such as: flexible implementation of atomic multipole-based electrostatics with explicit dipole polarizability, various continuum solvation treatments including several generalized Born (GB/SA) models, generalized Kirkwood implicit solvation for AMOEBA, an interface to APBS for Poisson-Boltzmann calculations, efficient truncated Newton (TNCG) local optimization, surface areas and volumes with derivatives, free energy calculations via the Bennett Acceptance Ratio (BAR) method, normal mode vibrational analysis, minimization in Cartesian, torsional or rigid body space, symplectic RESPA multiple time step integration for molecular dynamics, velocity Verlet stochastic dynamics, pairwise neighbor lists and splined spherical energy cutoff methods, particle mesh Ewald (PME) summation for partial charges and polarizable multipoles, a novel reaction field treatment of long range electrostatics, fast distance geometry metrization with better sampling than standard methods, Elber's reaction path algorithm, potential smoothing and search (PSS) methods for global optimization, Monte Carlo Minimization (MCM) for efficient potential surface scanning, tools for fitting charge, multipole and polarization models to QM-based electrostatic potentials and more....

TINKER 8 is a major new release of the Ponder Lab tool set for molecular mechanics and dynamics calculations. An important change in this new version is the switch from old-style common blocks to Fortran modules. Use of modules and greatly increased use of dynamic memory allocation means TINKER can now support very large molecular systems. TINKER 8 also implements improved OpenMP parallelization throughout many parts of the code. Additional big improvements include parallel neighbor list building and updating, and big reduction in iteration needed to converge AMOEBA polarization via an efficient PCG solver. Other changes from the previous TINKER version include new and updated force field parameter sets and numerous minor additions and bug fixes, many of them suggested by users of the package. Please note that as with prior new releases, version 8 is neither backward nor forward compatible with earlier versions of TINKER. In particular, older versions of parameter files should not be used with TINKER 8 executables and vice versa.


Maestro 11 training


A nice image from the Maestro 11 training session run by Schrödinger, it looks like there are a few more training sessions coming up also.


Maestro 11 is the portal to all of Schrödinger's computational technology – far more than just a user interface, Maestro 11 also helps researchers organize and analyze data.


Molecular Design Toolkit


The Molecular Design Toolkit is an open source environment that aims to seamlessly integrated molecular simulation, visualization and cloud computing. It offers access to a large and still-growing set of computational modelling methods with a science-focused Python API, that can be easily installed using PIP. It is ideal for building into a Jupyter notebook. The API is designed to handle both small molecules and large bimolecular structures, molecular mechanics and QM calculations.


There are a series of Youtube videos describing some of the functionality in more details, starting with this introduction.


ICM version 3.8-5


MolSoft have announced the release of ICM version 3.8-5.

  • Generate a 2D Interaction Diagram of a ligand with the binding pocket. The image is annotated with hydrogen bonds and interacting residues.
  • 3D ligand editor is a powerful tool for the interactive design of new lead compounds in 3D
  • ICMJS is a JavaScript/HTML5 viewer for 3D Molecular Graphics which does not require any plugin or installation.
  • Support for MMTF format. The Macromolecular Transmission Format (MMTF)
  • Support for Mac retina display
  • Add docking restraints by selecting atoms in the receptor
  • Updates to protein modelling, bioinformatics and cheminformatics

Full release notes are here


SeeSAR 5.4 released


There has been a new update to SeeSAR, this latest update brings.

2D molecule browsing - time to look at things from a different angle

While the molecule table offers great functionality for prioritizing compounds based on the data, it does not provide an overview of the molecules themselves. This release, however, sees the introduction of 2D molecule browsing. The table now offers two views - the one you already know and a 2D browser - flick between them using the switch below the table. Both views are always kept in sync so if you add a filter or sort etc. the 2D browser will show you the same result in the same order as the table. Also try expanding the table area to see how more molecules fit into the view.

Fantastic new 3D graphics features

This release also brings with it some great new 3D graphics improvements. As much as we all like visualising the binding site surface, it lay often times in the way… The binding site surface can now be switched to transparent allowing you to see through it and therefore making the analysis of the binding site and molecules within much more comfortable. Also, the feeling of depth in the 3D view has been improved to help orientation - a so-called "fog effect" fades out the protein and molecules that are further away to bring the foreground more into focus.

Persistent amino acid labels and better view of reference

So far, labels on binding site components unfortunately disappeared when browsing through different molecules in the table. Now amino acid, co-factor and water labels remain present if you change to a different molecule in the 3D view and even if you enter the molecule editor. The view of the reference compound has also been improved. For better visibility, the thickness of the bonds has been increased and instead of coloring the whole molecule in a uniform blue color, only the carbon atoms are colored blue so that hetero atoms can be distinguished more easily.

There is a review of an early version of SeeSAR here.


MOE 2016.08 released


Chemical Computing Group have just announced an update to MOE. This release has fixed a couple of Mac OSX 10.12 (Sierra) issues but also brings a host of new features.

  • MOEsaic: Web-Application for Ligand Analytics
  • Spectral Analysis for Structure Determination
  • Enhanced Protein Patch Analyzer
  • Integrated Antibody Project Database and Antibody Homology Modeler
  • Small Footprint MOE to Facilitate Large Scale Deployments
  • Physical and Virtual Rendering of Structures

A more detailed description of the new and enhanced features in MOE 2016.08 can be found at


APBS 1.5 released


The latest version of APBS includes several notable features and bug fixes. This release includes the addition of Poisson-Boltzmann Analytical-Method (PB-AM), Poisson-Boltzmann Semi-Analytical Method (PB-SAM) and the Treecode-Accelerated Boundary Integral Poisson-Boltzmann method (TABI). Additionally, we have made improvements to the build system and the system tests, as well as miscellaneous bug fixes.

APBS & PDB2PQR: Electrostatic and solvation properties from complex molecules. Solve the Poisson-Boltzmann and related equations to calculate solvation energies and electrostatic properties for analysis and visualization

APBS 1.5 changes

Binary releases may be found on GitHub and on SourceForge. New Features

  • Poisson-Boltzmann Analytical Method (PBAM, see Lotan & Head-Gordon) and Semi-Analytical Method (PBSAM, see Yap & Head-Gordon) integrated with APBS.
  • PBSAM is currently only available in the Linux and OS X distributions.
  • Examples are located with the APBS examples in the pbam/ and pbsam/ directories.
  • More information and documentation may be found in the PBAM and PBSAM sections of the APBS-PDB2PQR website.
  • Tree-Code Accelerated Boundary Integral Poisson-Boltzmann Method (TABI-PB) integrated with APBS.(See Geng & Krasny)
  • Examples are located with the APBS examples in the bem/, bem-pKa/, and bem-binding-energies/ folders
  • Included NanoShaper alternative to MSMS.
  • More information and documentation may be found in the Contributions section of the APBS-PDB2PQR website
  • Added binary DX format support to the appropriate APBS tools.
  • Test suite amended and expanded.
  • Removed hard-coded limitation to number of grid points used to determine surface accessibility.

Known Bugs / Limitations

  • PBSAM not building in windows due to C standard restrictions in the Microsoft compiler implementation.

Full details here


Open Source Molecular Modeling


A great publication on Open Source Molecular Modeling.

The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at

From toolkits to desktop applications a fantastic and comprehensive listing.


Pymol and very large PDB files. The Zika Cryo-EM structure as a case study


An interesting post on chemistry and computers, Pymol and very large PDB files. The Zika Cryo-EM structure as a case study. Always good to see people stress testing computational tools.




Facio is a free GUI for computational chemistry softwares (TINKER, MSMS, Firefly, Gamess, MOPAC and Gaussian).


Comments A Python Based Metal Center Parameter Builder, a python based metal center parameter builder, has been developed to build force fields for the simulation of metal complexes employing the bonded model approach.

Pengfei Li and Kenneth M. Merz, Jr., " A Python Based Metal Center Parameter Builder." J. Chem. Inf. Model., 2016, Accepted, DOI.

There is an excellent and very detailed online page describing the use of


BALL Project


BALL (Biochemical ALgorithms Library) is an application framework implemented in C++ that has been specifically designed to reduce development times in the field of Computational Molecular Biology and Molecular Modeling. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.

BALLView is BALL’s standalone molecular modelling and visualization application. Furthermore, it is also a framework for developing molecular visualization functionality.


It can be downloaded from here and requires

  • CMake >= 2.8.12
  • git
  • Python 2.7
  • Qt 5.4

Installation instructions for Mac OSX are here


PDB2PQR 2.1 released


A new version of PDB2PQR has been released.

APBS (Adaptive Poisson-Boltzmann Solver) and PDB2PQR are software packages designed to help you analyze the solvation properties of small and macro-molecules such as proteins, nucleic acids, and other complex systems

  • Added alternate method to do visualization using 3dmol.
  • Replaced the Monte Carlo method for generating titration curves with graph cut. See (If you prefer the Monte Carlo method, please use
  • Added compile options to allow for arbitrary flags to be added. Helps work around some platforms where scons does not detect the needed settings correctly.
  • Added a check before calculating pKa's for large interactions energies.

OSX binaries require OSX 10.6 or newer. The OSX binary is 64-bit.

Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res, 35, W522-5, 2007. DOI

Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res, 32, W665-W667, 2004. DOI


SeeSAR Updated


SeeSAR Version 4.2 just came out! The main new features are

  • You now control when the compute-intense Hyde-calculation runs, this means large sets of molecules can now be loaded, analyzed and processed (e.g. filtering, calculating properties) before the intensive affinity calculations are run.
  • Much improved version of grouping all poses of the same molecule

Version 4.2 comes with a load of minor improvements, particularly for the command line use. The full release notes are here.

Mail Attachment

I've been following this software since it was first released and there is a review here, every update brings useful features. It is well worth downloading the free 1 week trial to have a look at.


ADF Modeling Suite 2016


The ADF modelling suite has been a popular modelling package used in many areas of chemistry and materials science. SCM have recently announced an important update to ADF

Software for Chemistry & Materials (SCM) is an Amsterdam-based computational chemistry software company. Originally spinning out from the Vrije Universiteit as Scientific Computing & Modelling NV in 1995, the SCM team supports and develops the ADF Modeling Suite, centered around the flagship program Amsterdam Density Functional (ADF), which was originally developed in the 1970s in the theoretical chemistry department.

Key new features::

  • New XC functionals: range-separated hybrid HSE06, long-range corrected hybrids and new meta-GGAs
  • SM12 solvation model and Constrained DFT in ADF
  • Spectroscopy: excitations from CV(n)-DFT, fast TDDFT+TB and sTDDFT, X-ray emission, surface-enhanced ROA, new kernel for periodic TDDFT, vibrationally resolved spectra from TDDFTB, hole states in BAND
  • Improved robustness for SCC-DFTB, COSMO, periodic optimizations, new HF exchange scheme
  • Analysis: unrestricted and periodic energy decomposition (pEDA), Fukui functions, Natural Transition Orbitals
  • Reactivity, PES: Automated reaction pathways for ReaxFF trajectories, new Transition State search options, MECP, analytic lattice gradients
  • GUI: job chaining, multiple spectra, orbital interaction visualization
  • Scripting: ASE interface for all codes, scripting support for COSMO-RS, job chaining, extensions to FlexMD multi-scale dynamics
  • Parameters, databases: Quasinano15 including repulsive potentials for light elements, latest 3OB parameters, new parameter sets for ReaxFF, ionic liquids database COSMO-RS

Full release notes are here




iSpartan has been updated.

What's New in Version 1.4.6 Improved stability for iOS9 for Spartan'14 Parallel Suite (Serve)r users Enhanced charge labels in Sketch mode Increased electrostatic potential surfaces integrity

iSpartan is a versatile app for molecular modeling on the iPad, iPhone, and iPod Touch. The app allows any chemist fast and easy access to computational methods that have proven reliable for a large range of molecules.





Added NCIPLOT to the alphabetical listing of applications. NCI (Non-Covalent Interactions) is a visualization index based on the density and its derivatives. It enables identification of non-covalent interactions. NCIPLOT is available for download.

Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.


Erin R. Johnson, Shahar Keinan, Paula Mori-Sanchez, Julia Contreras-Garcia, Aron J. Cohen, and Weitao Yang, J. Am. Chem. Soc. 2010, 132, pp 6498-6506.
J. Contreras-Garcia, E. R. Johnson, S. Keinan, R. Chaudret, J-P. Piquemal, D. N. Beratan, and W. Yang. J. Chem. Theory Comput. 2011, 7, pp 625-632.


BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library


Sampling conformational space is a key requirement for several areas of ligand design in small molecule drug discovery. A recent paper BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library DOI describes a new conformational search method.

The project homepage provides a download, supports Mac OSX 10.4 or higher.


An early Christmas present from Chemical Computing Group


Chemical Computing Group have just released an up date to MOE, version 2015.10 includes:-

Protein-Protein Docking

  • Generate docked poses using FFT followed by all atom minimization
  • Define receptor and ligand sites to focus docking
  • Automatically detect antibody CDR sites

Integrated Alignment, Consensus and Superposition in the Sequence Editor

  • Manipulate multimeric protein sequences using split side-by-side Sequence Editor panes
  • Use dendrograms to visualize pairwise similarity, identity and RMSD relationships
  • Select residues based on plotted values using resizable sequence editor plots

Distributed Pharmacophore Searching

  • Run pharmacophore searches on a cluster directly from MOE GUI
  • Perform fast corporate database searches
  • Access multiple databases stored on a central server

Covalent Docking and Electron Density Docking

  • Use reaction-based organic transformations to covalently docking
  • Minimize ligand strain energy while maximizing ligand fit to electron density
  • Run docking through an enhanced streamlined scenario-based interface

Extended Hückel Descriptors and pKa Model

  • Compute molecular properties such as logP, logS and molar refractivity
  • Determine populations of ligand protonation states at a given pH
  • Calculate the pKa and pKb of small molecules

13C NMR Analysis

  • Apply QM conformation refinement to calculate 13C NMR shielding
  • Convert computed shieldings and predict 13C NMR chemical shifts
  • Compare computed chemical shifts to experimental shifts for structure determination

I'll write a review in the New Year.


BCL::Conf: small molecule conformational sampling using a knowledge based rotamer library


I just thought I'd flag a recent paper on sampling conformation space DOI.

The interaction of a small molecule with a protein target depends on its ability to adopt a three-dimensional structure that is complementary. Therefore, complete and rapid prediction of the conformational space a small molecule can sample is critical for both structure- and ligand-based drug discovery algorithms such as small molecule docking or three-dimensional quantitative structure–activity relationships.

The software is available from the MeilerLab home page


Protein-Ligand Interaction Profiler has been updated


The PLIP Protein-Ligand Interaction Profiler has been updated.

According to the Changelog


  • Support for DNA and RNA as ligands__
  • Detection of metal complexes with proteins/ligands, including prediction of geometry__
  • Extended result files with detailed information on binding site residues and unpaired atoms__
  • Support for zipped and gzipped files__
  • Rich verbose mode in command line with information on detected functional groups and interactions
  • Automatic fixing of common errors in custom PDB files
  • Refined binding site selection
  • Better overall performance
  • Initial test suite for metal coordination
  • Classification of ligands
  • Improves detection of aromatic rings and interactions involving aromatic rings
  • Single nucleotides and ions not excluded anymore as ligands
  • Generation of canonical smiles for complete (composite) ligands
  • Generation of txt files is now optional
  • Basic support for PDBQT files
  • Correct handling of negative chain positions of ligands
  • Improved check for valid PDB IDs
  • Fixes several bug

The web service includes all the updates and integrates BioLip for flagging biologically relevant interactions. Since ligand molecules (e.g., Glycerol, Ethylene glycol) are often used as additives (i.e., false positives) for solving the protein structures, not all ligands present in the PDB database are biologically relevant.




Polyphony is an open source software suite written in python. Its purpose is the superimposition free analysis and comparison of multiple 3D structures of the same or closely related protein molecules.

Absolute Requirements

python 2.6 or later, scipy, numpy, Biopython, especially the Bio.PDB module

Highly recommended

All following documentation assumes that you have these installed.

ipython , for interactive python scripting, matplotlib, for graph plotting, PyMOL, for interactive 3D visualisation. Open source version available on SourceForge

William R Pitt, Rinaldo W Montalvão and Tom L Blundell, BMC Bioinformatics, 2014, 15:324 doi


Lucas, Molecule viewer and editor


Lucas is a novel program for graphical display and editing of molecular systems. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus is able to visualise dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to reveal a geometrical feature or a physical quantity. The program is developed as a graphical interface for the MOLCAS program package, however its adaptive nature makes possible to use luscus with other computational program packages and chemical formats. All data files are opened via simple plug-ins which makes easy to implement a new file format in luscus. The easiness of editing molecular geometries makes luscus suitable for teaching students chemical concepts and molecular modelling.


Journal of Cheminformatics 2015, 7:16 [DOI](}

The source code is available on Sourceforge


Scientific Applications under Yosemite


I just thought I'd like to thank all those who contributed to the Scientific Applications under Yosemite web page, many users and developers contacted me either via email or in the comments section and they certainly added information about applications that I don't have access to.

To date the page has been viewed well over 10,000 times with readers from 188 different countries. Viewers spent an average of just under two minutes on the page and it still attracts 800 pages views a month.

Given that 75% of the visitors to the site are now using Yosemite I suspect most scientists have now made the transition and I won't be updating the page any more. Once again thanks for the contributions.


MOE updated


MOE2014.0901 Update is now available. MOE is a fully integrated molecular modelling and drug discovery software package.

MOE 2014.0901 updates:


Protein Builder

  • Option for AMBER residue name
  • Append/prepend multiple residue sequence specified by single-letter names Builder:
  • Added H’s inherit color if there is a consistent coloring in the residue

sddesc: New -smi:p option causes field headers to be written to the output ASCII file

Bug Fixes:

  • MOESVLRUNPATH now properly honored
  • Combinatorial Builder now honors different attachment point locations on the same R-group
  • Database Save As one entry per file mode now properly generates unique filenames
  • Dock Template Forcing batch file now correctly generated
  • Saved views in .moe files now properly restored
  • Auto-save when Database Viewer display attributes are changed can now be disabled to prevent changes to the database file modification date when only the display is changed and not the database content
  • SVL function Deprotonate now works properly
  • Various MOE Project and Project Database Update bugs
  • Various minor bug fixes

There are reviews of MOE available here

Moe:- Molecular modeling
Moe Update (Jan 2009):- Molecular modeling
Review of MOE (2009.10 release):- Molecular modeling
Moe Update (December 2010.10 release):- Molecular modeling
Moe Update (December 2011 release):- Molecular modeling
Moe Update (December 2012 release):- Molecular modeling




PDB2PQR 2.0 which is now available from

PDB2PKA as an alternative to PROPKA for calculating pH values used to protonate residues. This feature is EXPERIMENTAL. The libraries to make this feature available are included in the binary releases. They are NOT included in the source code and are not compiled with the rest of PDB2PQR. Improved web interface. NEW FEATURES

  • Improved look of web interface
  • Option to automatically drop water from pdb file before processing.
  • Integration of PDB2PKA into PDB2PQR as an alternative to PROPKA.
  • Support for compiling with VS2008 in Windows.
  • Option to build with debug headers.
  • PDB2PKA now detects and reports non Henderson-Hasselbalch behavior.
  • PDB2PKA can be instructed whether or not to start from scratch with –pdb2pka-resume
  • Can now specify output directory for PDB2PKA.
  • Improved error regarding backbone in some cases.
  • Changed time format on querystatus page
  • Improved error catching on web interface.

OSX binaries require OSX 10.6 or newer. The OSX binary is 64-bit.

For more information see APBS & PDB2PQR: Electrostatic and solvation properties from complex molecules.


MOE updated


The molecular modelling platform MOE 2014.09 has been updated, some of the new features in MOE include:

  • MOE Project for Organizing SBDD Data
  • Focused Protein and Antibody Libraries - Virtual Phage Display
  • Quantum Mechanical Refinement of Conformations and Energy Minimization
  • Template Forced Docking and Molecular Superposition
  • Non-natural Amino Acid Support for Protein and Peptide Design
  • Specialized Protein Family Databases and Search Interface

MOE is a software system designed to support Cheminformatics, Molecular Modelling, Bioinformatics, Virtual Screening, Structure-based-design and can be used to build new applications based on SVL (Scientific Vector Language).

There are several reviews of the previous versions of MOE here


SeeSAR Updated


a href="">SeeSAR version 1.6 has been released. It covers:

The ability to change the charge of an Atom (+/-) and to protect such change against ProToss (this is the automated protonation/tautomerism to optimize the overall H-bonding network) overwrite

Improved table: pM affinity, in/exclude multiple columns, the pose-specific context-menu, quick-find molecules including a 2D popup rendering, this can be very useful when trying to work out the structure from a 3D conformation.


There is a review of an early version of the software here


UCSF Chimera (version 1.10) is available


A new production release of UCSF Chimera (version 1.10) is available.

Platforms: Windows, Mac OS X (including Yosemite), Linux. This will be the last release to support OS X 10.6 and 10.7.

New since version 1.9: Protein contact maps color-coded by distance, PDB biounit and CATH domain web fetch, plotting all-atom and backbone RMSDs along sequence alignments (previously only alpha-carbon RMSDs), update to AmberTools 14, "vop scale" density map normalization, Modeller dialog allows specifying distance restraints, further implementation of the MultiDomain Assembler homology-modeling pipeline.

More details are given below; see release notes for the full list:

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.


FORECASTER, docking tool


I just got this email

Thank you for your collaboration in helping us to test the beta version of the FORECASTER Suite 2014. From your feedback and bug reports, we have now released the final version of the Suite. The files were updated and posted on the download page. Please send us any bugs that you might have not yet reported.

The FITTED docking tool was initially been developed as a suite of three programs: SMART (used to prepare the small molecules for docking), PROCESS (used to prepare the protein files for docking) and the docking program FITTED. More recently, these three programs together with several others have been integrated into a single package, namely FORECASTER.

More information can be found here


2014 release of the ADF modeling suite


The ADF modeling suite consists of the GUI, the powerful DFT codes ADF (molecules) and BAND (surfaces, bulk), the semi-empirical DFTB and MOPAC2012 modules, ReaxFF, and COSMO-RS. The binaries for the entire suite work out of the box, in parallel, on all popular platforms (Windows, Mac, Linux).

A summary of new features and improvements in the 2014 release:

  • lower-memory, better parallel SCF in ADF
  • significant speed-ups in DFTB and the periodic DFT code BAND (AO-based)
  • many-body dispersion functionals (Tkatchenko et al.)
  • conformer search, support for multiple configurations, spectra averaging
  • TD-DFTB and DFTB-NEGF, with electronic parameters for 87 elements
  • ReaxFF force field optimizer, Grand Canonical Monte Carlo
  • COSMO-SAC 2013-ADF parameters

CHARMM INterface and Graphics


You might want to have a look at a new website that I’ve just been sent details of.

CHARMMing contains an integrated set of tools for uploading structures, performing simulations, and viewing the results. In order to provide the best possible user experience, it incorporates a number of freely available tools such as JSmol for visualization and an automatic residue topology file (RTF) generator (GENRTF) which generates the necessary information for atoms and residues that are currently not supported by the CHARMM force fields. Below is a partial list of functionality that currently is incorporated into

  • A CHARMM tutorial that has been specifically designed for novice CHARMM users
  • PDB/CRD reader and input script generator
  • Integrated molecular graphics
  • Integrated simulation tools (i.e. minimization, solvation, dynamics)
  • Automatic topology generation

SeeSAR 1.4


SeeSAR from BioSolve-it has just been updated, SeeSAR is intended as an interactive tool for designing/improving ligands for drug discovery. This update includes an option to highlight the neighbouring atoms that lead to a particular hyde-score, in the example below the carbon in the ring that gets a pretty big red (unfavourable) score, can be explained by the Receptor desolvation penalty ascribed to the carbonyl oxygen. stereo hardware support (as a first step supporting the polarized-glass-type only), a screen shot feature, an option to move labels out of the way for a better view.


There is a review of SeeSAR here


OpenEye Toolkits Updated


OEToolkits 2014.Jun This release of the OpenEye toolkits is focused on stability and new platform support. The last release, 2014.Feb, was a major feature release introducing numerous new features. This release focused on fixing many bugs and improving the overall stability of the OpenEye toolkits.

There is still a major new feature being added in this release:

FreeForm API added to Szybki TK

Mac Users should note this release will be the last release to support OSX 10.7.


SeeSAR Update


I recently wrote a review of SeeSAR and one of my comments was:-

Unfortunately there is no 2D display of ligands in the ligand list so sometimes it can be difficult to keep track of modifications.

Well, in keeping with the “fast and agile” release plan a update is now available that includes a 2D display.


More information


A review of SeeSAR


SeeSAR is an interesting new product from BioSolve-it, it is intended as an interactive tool for designing/improving ligands for drug discovery. I’ve written a brief review that you can read here.


This is a really interesting application, it seems a little rough around the edges but the developers have released it early are very keen to get feedback. I found them very responsive and enthusiastic about getting the views of users involved in how the application evolves. I would certainly encourage people to download it and use the free trial period to give it a go, and provide them with feedback.

There are more software reviews here.


DOT added to alphabetical listing


DOT is a software package for docking macromolecules, including proteins, DNA, and RNA. DOT performs a systematic, rigid-body search of one molecule translated and rotated about a second molecule. The intermolecular energies for all configurations generated by this search are calculated as the sum of electrostatic and van der Waals energies. These energy terms are evaluated as correlation functions, which are computed efficiently with Fast Fourier Transforms. In a typical run, energies for about 108 billion configurations of two molecules can be calculated in a few hours on a few desktop workstations working in parallel.

Roberts, Victoria A. and Thompson, Elaine E. and Pique, Michael E. and Perez, Martin S. and Ten Eyck, L. F., (2013) "DOT2: Macromolecular docking with improved biophysical models" Journal of Computational Chemistry, Volume 34, Issue 20, pages 1743-1758, 30 July 2013 DOI:


UCSF CHIMERA has been updated


Version 1.9 of UCSF Chimera has been released.

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.

This looks to be an extensive update,

New features include

Multiple sequence alignment using Clustal Omega or MUSCLE web services. Building double-helical nucleic acids,"colorkey" command, "struts" command to reinforce structures for 3D printing, "vseries" volume series playback and processing options,more efficient save/restore of coordinates in sessions, Dynameomics amino acid rotamer library, WMV2 movie output, COLLADA export.




There is an interesting publication in the latest issue of Chemical Biology and Drug Design describing, Chem-Path-Tracker An automated tool to analyze chemical motifs in molecular structures DOI. This is a plugin for the molecular visualisation tool VMD that allows the user to highlight and reveal potential chemical motifs with a protein using only a few selections.


The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed Chem-Path-Tracker.

More details on the project page


RCSB mobile PDB viewer


The official PDB viewer has been updated


Amber 14 and Amber 14 Tools released


Version 14 of the Amber software suite has been released (There was no "unlucky" Amber13.)

  • Force fields: Amber has two new fixed-charge protein force fields, ff14SB and ff14ipq, a new modular lipid force field, Lipid14, and updates to nucleic acid and carbohydrate force fields.
  • Improved options for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.
  • A completely reorganized Reference Manual
  • QM/MM calculations can interface with a variety of external quantum chemistry programs, expanding the types of quantum models available
  • More features from sander have been added to pmemd for both CPU and GPU platforms, including performance improvements, and support for extra points, multi-dimension replica exchange, a Monte Carlo barostat, ScaledMD, Jarzynski sampling, explicit solvent constant pH, GBSA, and hydrogen mass repartitioning. Support is also included for the latest Kepler, Titan and GTX7xx GPUs.
  • Expanded methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms, and tighter integration with replica-exchange simulations, and a new absolute free energy method.
  • New facilities are present for using electron density maps (e.g. from cryo EM/ET experiments) as constraints, and to support rigid (or partially flexible) groups in simulations.

Amber Tools have also been updated.

Among the new features in AmberTools14:

  • The sander module, our workhorse simulation program, is now a part of AmberTools;
  • Greatly expanded and improved cpptraj program for analyzing trajectories;
  • new documentation and tools for inspecting and modifying Amber parameter files;
  • Improved workflow for setting up and analyzing simulations;
  • new capability for semi-empirical Born-Oppenheimer molecular dynamics;
  • EMIL: a new absolute free energy method using TI;
  • New Free Energy Workflow (FEW) tool automates free energy calculations (LIE, TI, and MM/PBSA-type calculations);
  • Completely reorganized Reference Manual

GTKDynamo:- Molecular modeling extension for PyMOL


GTKDynamo is free/open source software which, together with pDynamo, transforms PyMOL into a powerful interface for molecular modeling. The interface has been designed to facilitate determining reaction pathways in biological systems, specially using hybrid QC/MM (or QM/MM) methods.

Some capabilities include:

  • Pure QC simulations - ab initio and SMO.
  • Pure MM simulations - using AMBER, CHARMM or OPLS force fields.
  • Hybrid QCMM simulations.
  • Single point calculations.
  • Energy minimization.
  • Molecular dynamics.
  • Reaction coordinate scanning.
  • Umbrella sampling.
  • Reaction path calculations - using NEB.

GTKDynamo is available for download for linux and Mac platforms . Please, make sure that you have installed:

  • pDynamo
  • Matplotlib
  • Numpy / Pylab
  • Pymol 1.x
  • pyGTK
  • ORCA, ab initio calculations.


J. F. R. Bachega, L. F. S. M. Timmers, L. Assirati, L. B. Bachega, M. J. Field, T. Wymore. J. Comput. Chem. 2013, 34, 2190-2196. DOI:


3D stereo viewing on a Mac


A little while back I posted a comment on the Apple SciTech list asking about options for stereoscopic viewing of molecular modelling on a Mac.

Many thanks to those who contacted me directly, it seems there are a number who have suffered the trials and tribulations of trying to set up stereo viewing. I suspect the combination of different graphics cards, driver, emitters, special connectors, special glasses, program software, X11, operating system changes means that this is a real pain to coordinate support., something always seems to get "updated" breaking everything else.

Which is why this email from Stephan Keith caught my eye.

Let me tell you my solution.  It is not necessarily cheaper, but for me, a whole lot easier. I am a 3D software engineer, but I am seriously interested in stereoscopic 3D.  I program in C, OpenGL and GLUT. I became weary of all the glasses, buffers, nVidia cards that didn't really work, emitters ... the whole mess. What I do, now, is I write my OpenGL software to create a sidexside or top over bottom stereo display that takes up the entire screen. I then connect an HDMI connector to my LG Stereo 3D Television.  I turn on the Stereo3D, put on my RealD glasses.  The S3D is passive, not active, so I don't get the annoying flicker, and I don't have to worry about nVidia 3D glasses running out of power (most annoying, at what was $185 a pop). No special glasses, no emitters, no special code, no special connectors.  All .... Gone.

I thought I’d try this out, so armed with a copy of MOE a MacBook Pro and a mini display port to HDMI cable I headed down to PCWorld in Cambridge to try it out (many thanks to the people at PCWorld who were really helpful).

Passive 3D

I first tried out an LG ELECTRONICS 27MT93V LG MT93V . The first thing I’d say is that the set up was trivial, from connection to viewing a protein in 3D was only a couple of clicks. This gave a good impression of a 3D protein structure, both in stick display to see side-chains and in cartoon display to see the overall structure of the protein, colours were excellent. However I found that it was necessary to sit facing absolutely in the centre of the screen to get a good display, also if you move close to the screen then the 3D effect is lost and you get jagged line artefacts. This might not be an issue for a TV but if you paln to use it as a computer monitor I suspect it might be a deal-breaker. I suspect it would be difficult to sit alongside colleagues and have them all have a good 3D impression.

Active 3D

I then tried an active 3D display on a Samsung UE46F6800 46-inch Widescreen TV, this was much larger than I needed but I understand there are smaller models available. Once again setup was a breeze, this gave a good impression of a 3D protein structure, both in stick display to see side-chains and in cartoon display to see the overall structure of the protein, colours were excellent, and the brightness did not seem to be impacted at all by the active glasses. The 3D viewing was acceptable at a wide range of screen angles and distances and it should be possible to sit beside colleagues to discuss a project and all have a good 3D view.

I wear prescription glasses and I found the active glasses fitted comfortably over my glasses. They were also a lot more lightweight than I remember in the past. In the past active shutter glasses have been very expensive but prices have dropped significantly.

Personally I found the Active 3D much superior, especially if you planning to use this mainly as a computer monitor rather than a TV that you view from the comfort of your sofa.


PYMOL Updated


Whilst the update to PYMOL was announced as part of the Schrodinger update I thought it deserved a separate blog entry.


  • Greater user control over color settings Color settings can be set as hexadecimal, colors, or floats ( [1., 1., 1.])
  • New ‘focalblur’ command
  • New ‘callouts’ for scene annotations


  • Improved and extended Filter Wizard

  • New commands Retrieve bond properties with get_bond Load structures from PubChem by SID and CID codes with fetch
  • Improved PDB Loader graphical interface
  • Expanded documentation of settings
  • Access settings and properties from the iterate/alter commands via “s.” and “p.”
  • Improved labels to include customizable connectors to atoms, multiline labels, and more
  • Ability to select atoms by coordinates or by user-defined property
  • New selection keywords: metals, sidechain, backbone
  • CTRL-F to find objects or selections in the Object Menu Panel

    Bug Fixes

  • Dynamic measures now stored in session files

  • Sequence viewer colors fixed
  • Fixed inversion problem with ‘cealign’
  • Improved stability for shader-based rendering


  • New option to embed content within a PowerPoint file

  • Support PowerPoint PPTX file format
  • Improved installer
  • AxPyMOL control displayed as an “Add In” on the PowerPoint Ribbon
  • 32-bit and 64-bit Office Support
  • Embeddable presentation content
  • Initial support for MAE files
  • Shader-based rendering support for volumes and improved graphics
  • Many bug fixes

The compiled PYMOL binaries are available for paid download with different options for academic, industrial and non-profit.

In addition the source code is available for free download. Not all new features make it to the source code right away, but eventually all features will, usually within a few months


Schrodinger Small Molecule Drug Discovery Suite Updated


The Schrodinger Small Molecule Drug Discovery Suite was updated over the weekend, this is a major update that brings in a host of new features and improvements.

Maestro Graphical Interface

Improved flexible ligand superposition Additional graphics settings
Real-time antialiasing Real-time ambient occlusion, outlines, and cartoon shading effects Multivariate ranking in the Project Table
Simultaneously maximize or minimize up to four property values, and rank entries based on the optimization Date Created and Date Modified fields automatically generated in the Project Table Workspace responsiveness of atom labels is up to 2.5x faster Click and drag to rearrange atom, measurement, and adjustment labels in the Workspace Support for bond labels Installed scripts and Tools menu items now searchable in the Task Tree Significant improvements to the Property Calculation interface in the project facility
Simultaneously calculate multiple properties Additional 2D properties now available: AlogP, #Hbond acceptors, #HBond donors, #rotatable bonds, polar surface area, molar refractivity, and polarizability

Ligand Docking

Ligand efficiencies are now calculated from the DockingScore instead of the GlideScore Generate per-residue interaction energies in Virtual Screening Workflow (VSW) for visualization New server mode in Glide Ligand Designer enables near real-time interactive docking (Glide Ligand Designer Script)

Pharmacophore Modeling

Performance improvements to Phase database operations, including faster deletion and insertion of ligands Automatic restart of Phase database subjobs

Field-Based QSAR

Use QM-calculated fields in 3D QSAR (command line only; phasefqsar script)
fqsar script generates Jaguar input files for computing QM electrostatic fields for use in 3D QSAR

Molecular Dynamics

Monitor secondary structure elements over the course of the trajectory (Simulation Interactions Diagram; SID)

Quantum Mechanics

New interface to compute thermodynamic properties for reactions New faster TDDFT algorithm and graphical interface Compute Raman intensities Several improvements to the results script Jaguar pKa displays the computed pKa as an atom label by default Heat of formation graphical interface now supports bromine and iodine Improved numerical stability of the 1st and 2nd derivatives of the D3 correction Increased utility of script
Script acts on a group of isomers and skips structures with unique stoichiometries

Protein X-Ray Refinement

Optionally set hydrogen B-values

Workflows & Pipelining

Includes the latest version of KNIME (v2.9)
Many new features including a Send Email node and ability to save workflows under different names; see for a complete list of new features Use any Glide simulation option in the Glide Ligand Docking node Employ a specific template in the Prime Build Homology Modeling node Import ungrouped structures to PyMOL from Run PyMOL node

Job Control

Improved fault tolerance Improved handling of suspended jobs in queueing systems

There are also updates to the Biologics Suite and the Materials Science Suite.


MolSoft Releases ICM Version 3.8


MolSoft have announced that a new version of ICM is now available for download from the support site . A description of the key new features can be found on the news page and release notes. To help you get to know the new features we will be holding a free webinar next week (2/11) - we hope you can join us, please register here.

Some of the key new features include:

  • Anaglyph Stereo
  • MolSkin - high quality surface graphics
  • Movies from Slides
  • SCARE - induced fit docking
  • Fragment screening
  • MolScreen - >360 high quality fingerprint and 3D pharmacophore models
  • Blast search direct from the GUI
  • ToxScore - new score for drug reactivity and toxicity

Scripting Vortex 17 tutorial


In the tutorial Scripting Vortex 15 I showed how it is possible to create a contextual script for Vortex that downloaded a specific PDB file, then a FlexAlign Vortex script first identifies the structure column and then get the SMILES string of the selected molecule generates a 3D structure and uses Flex Align to do a one-shot flexalign between the ligand in the system in MOE, and the incoming ligand.

While this is useful if you have similar structures (perhaps analogues in a series) there will certainly be situations where it may be preferable to dock the new ligand into the binding site. The Scripting Vortex 17 tutorial describes how to achieve this.


MOE Update


Chemical Computing Group have just announced an update for MOE.

A patch update is now available for MOE 2013.08. This patch contains a series of important updates for better performance, s

In the MOE 2013.0801 patch update:

  • System Manager browsing speed-up for large systems
  • System Manager tag/group expansion only on Ctrl-click during browsing
  • Mac OS X NVIDIA graphics driver bug workaround
  • Mac OS X real-time ray tracing now supported by default on the new Intel Iris and Intel Iris Pro graphics cards
  • Bug fixes

Computational Chemistry Freeware


I recently came across this brilliant collection of software from Michel Petitjean

  • ARMS: Spatial Alignment with the RMS (Root Mean Square) method. (fixed pairwise correspondence)
  • ASV: Analytical calculation of van der Waals surfaces and volumes. (or any union of spheres)
  • CCCPP: Computes Cavites, Channels, Pores and Pockets in proteins.
  • CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules. (pairwise correspondence computed)
  • CYL: Minimal radius enclosing cylinder. Minimal radius circumscribed cylinder.
  • DIVCF: Selects by clustering major conformations of a molecule in a set of its conformers.
  • DOG: Docking Geometrically two molecules. (fixed pairwise correspondence)
  • GRD: Computation of the Radius and Diameter of a molecular graph. (computes also the topological shape index)
  • MCG: Optimal Partition (classification): numerical variables and non-euclidean spaces. The number of classes is computed.
  • POP: Optimal Partition (classification): categorical variables. The number of classes is computed.
  • POSE: Computes the RMSD between two ligand poses. No rotation translation is performed.
  • QCM: Quantitative Chirality Measure of a conformer (graph automorphisms enumeration included)
  • RADI: Computation of the Radius and Diameter of a spatial set. (computes also various other geometrical parameters)
  • VIRAPOPS: A forward simulator dedicated to rapidly evolved viral populations.

Binaries are available for MacOSX and Linux.


Anaglyph 3D now available in iMolview


I was just reading the end of year newsletter from [Molsoft] and I came across this interesting snippet.

MolSoft is excited to announce that Anaglyph 3D is now available to use in ICM and iMolview.

Sure enough the update on Dec 24th has this in the release notes.

Anaglyph stereo mode is added. (Set 'Stereo Type' to 'Anaglyph' in Tools menu) Any red-cyan 3D glasses will work in this mode.

There are a number of suitable glasses on Amazon 3D Red/Cyan Glasses

I think this is the first app to enable this sort of stereo viewing and it just underlines the strides that mobile platforms are making in scientific computing.

For science apps for iOS have a look at the mobile science page.




I noticed that CPMD a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. is now available on Crunchyard expanding the list of available Computational Chemistry packages. The following packages are also available. CP2K, LAMMPS, GAMESS, GROMACS , NWCHEM




Whilst there are a number of desktop applications that allow for the creation or editing of 3-dimensional chemical structures there are not as far as I am aware any tools for editing the 3D structure within a web page. CH5M3D uses a combination of HTML5 and javascript to interactively draw and edit 3-dimensional structures of small molecules.


The details are described in a recent publication Journal of Cheminformatics 2013, 5:46 DOI, it can be downloaded from Sourceforge, and you can try it out on the CH5M3D website.


CPMD added to alphabetical listing

I’ve added CPMD to the alphabetical listing of applications.

CPMD is an ab initio electronic structure and molecular dynamics (MD) program using a plane wave/pseudopotential implementation of density functional theory (DFT). It is mainly targeted at Car-Parrinello MD simulations, but also supports geometry optimizations, Born-Oppenheimer MD, path integral MD, response functions, QM/MM, excited states and calculation of some electronic properties.

Full installation instructions are available on the website together with the user manual and examples.

The examples can run effectively on an Intel Core i5 (2.53 GHz, OS/X) with 4 GB of available memory (most of tests require ca. 1GB, few more). Nonetheless, references have been generated on an IBM Blade power7 (with 8 mpi tasks and 1 OMP task per CPMD run) with 64 GB of available memory. Estimates of the execution time and memory requirements will be given based on this more performant setup.

CPMD capabilities

  • Works with norm conserving or ultrasoft pseudopotentials
  • LDA, LSD and the most popular gradient correction schemes; free energy density functional implementation
  • Isolated systems and system with periodic boundary conditions; k-points
  • Molecular and crystal symmetry
  • Wavefunction optimization: direct minimization and diagonalization
  • Geometry optimization: local optimization and simulated annealing
  • Molecular dynamics: constant energy, constant temperature and constant pressure
  • Path integral MD
  • Response functions
  • Excited states
  • Many electronic properties
  • Time-dependent DFT (excitations, molecular dynamics in excited states)
  • Coarse-grained non-Markovian metadynamics

CPMD is free for non-profit organisations.


SYBYL-X 2.1.1 released


SYBYL-X 2.1.1 is now available, the focus of this release is to extend the capabilities available via the standalone PYTHON interface to 3D-QSAR, which was introduced in SYBYL-X 2.1 earlier this year. The PYTHON API allows 3D-QSAR models (CoMFA, CoMSIA, and Topomer CoMFA) to be created and used for predictions outside of SYBYL-X.

  1. Hologram QSAR (HQSAR) is a now available via Python.  HQSAR has been successfully applied to generate predictive global QSAR models for on- and off-target effects and models for important ADME related properties; the HQSAR method employs 2D-substructural counts as descriptors.

  2. Similarity computations and similarity searches (UNITY 2D fingerprints) are now accessible via Python to support various workflows, such as lead expansion, lead hopping, and cluster analysis.


MOE 2013.08 Released


Chemical Computing Group have just announced the release of the latest update of MOE (Molecular Operating Environment).

General Updates

Extended Hückel Theory for Pharmacophore Discovery

  • Apply EHT strengths to identify and discover weak and strong interactions
  • Annotate non-standard interactions: halogen and CH bond donors
  • Score pharmacophore hits using sum of interaction energies

de novo Loop and Linker Modeler

  • Search and browse for de novo and knowledge-based loop candidates
  • Generate multiple loop conformations and score loop-loop interactions • Investigate linkers for fusion proteins and dual variable domains

Protein Alignments and Superpositions

  • Superpose protein structures independent of sequence
  • Apply new threading methodology for sequence to structure alignments
  • Align sequences and superpose structures using STOVCA criteria

Core System Enhancements (with 64-bit support) The default versions of MOE for Linux, Windows, and Mac OSX are now all 64-bit. The current release also includes 32-bit versions for each architecture.

  • Create additional data grouping level in System Manager
  • Handle large number of protein:ligand complexes in real-time
  • Colour database viewer text and cells by data values for enhanced analysis, Empty cells can be specially colored

Interface to Mogul from CCDC

  • Access a knowledge-based library of small molecule crystallographic data
  • Visualize histograms and statistics fo rbond angles, dihedrals and torsions • Ensure ligand conformation is consistent with the CSD

Solvent Analysis using 3D-RISM Enhancements

  • Calculate water densities on full protein or protein:protein interface
  • Accurate placement and stability prediction of water sites
  • Use3 D-RISM densities to validate water position in crystal structures

chEMBL Library. MOE's SD Pipeline Command Tools were used to generate fragments from Release 14 of the ChEMBL database of bioactive drug-like small molecules. The resulting database of conformations, chemblr14_frag.mdb, for approximately 830,000 fragments, suitable for Scaffold Replacement or combinatorial chemistry methodologies

Mac OS X Enhancements.

  1. OS X Dock Icon Enhancements. A new Dock menu, accessed by right-clicking (or control-clicking) the MOE Dock icon, allows for standard Mac OS X operations – Hide, Show, and Quit – across all open iterations of MOE. The Dock Menu also contains menu items in order for users to view the About panel bundled in MOE, as well as access the Preferences panel. Additionally, the Dock indicator light under the MOE Dock icon remains persistent after having launched a new instance of MOE, until all opened MOE instances have been closed. Users continue to be able to drag and drop compatible MOE documents (i.e. .pdb, .svl, etc.) onto the Desktop and/or Dock icons for direct opening in MOE.

  2. New Preferences Menu. A new Preferences panel allows for certain parameters to be set and/or changed graphically. These parameters include the defaults key and path to MOE, the current configuration of MOE (32- or 64-bit, or Auto-select), as well as a selection of common command line tags, with a custom section for inputting other command line options.

  3. Output Continuity. stdout and stderr received from MOE have been standardized to be displayed in a native panel in a scrollable text box.


Turning up the heat with Torch and Forge


Anyone involved in a drug discovery programme will be aware of the challenge presented by trying to visualise and explore structure-activity relationships (SAR), in particular visualising questions like :-

“What is the largest change that can be made whilst maintaining activity?”

Activity Miner from Cresset is a new tool designed to rapidly interrogate and decipher SAR in both Torch and Forge. Activity Miner is intended to help identify key elements of the SAR by starting from a set of aligned molecules and then automatically comparing them to each other.

Activity Miner1

More details are here


Scripting Vortex and MOE

One of the new features in the latest version of MOE from Chemical Computing Group is the Listener. The MOE socket listener provides an alternative to MOE/web for executing functions remotely on a running instance of MOE.

The script will download the associated PDB structures from the rcsb Protein Data Bank, put them into a database then start the browser. It may take a few seconds to download the structure; this does rely on MOE having the right proxy settings to access the internet (use the Java console to set them). You can now transfer this to MOE and amend the display to highlight the ligand.

The MOEflexalign script takes the SMILES string of the selected row generates a 3D structure and does a one-shot flexalign between the ligand in the system in MOE, and the incoming ligand.

It is probably easier to see this in action, if it appears rather small click on the YouTube icon in the bottom right corner of the video.

Full details are here


LeView: automatic and interactive generation of 2D diagrams for biomacromolecule/ligand interactions

The latest issue of Journal of Cheminformatics has an article describing Ligand Environment View; Journal of Cheminformatics 2013, 5:40 DOI a Java program that can be used to generate 2D representations of ligands and their environments and binding interactions from PDB entries. The application can be downloaded from here, the source code is also available.

The image below was generated from 3K83 the Crystal Structure Analysis of a Biphenyl/Oxazole/Carboxypyridine alpha-ketoheterocycle Inhibitor Bound to a Humanized Variant of Fatty Acid Amide Hydrolase.


It seems that whilst Hydrogen bonds are clearly defined pi-stacking interactions are not and in my brief experiments bonding to halogens was not detected 3GT3


QUACPAC v1.6 released

OpenEye have announced the release of QUACPAC v1.6. This release incorporates several improvements and some bug fixes.

The chemistry of molecular interactions is a matter of shape and electrostatics, but doing electrostatics poorly is worse than doing none at all; accurate charges are required. Even the best charge models are useless if protonation states are wrong. QUACPAC attempts to offer everything necessary to do charges correctly. It includes pKa and tautomer enumeration in order to get correct protonation states, partial charges using multiple models that cover a range of speed and accuracy, and electrostatic potential map construction and storage


  • molcharge now uses the -method parameter for selecting a charge model. All individual flags for charge models have been removed.
  • tautomers will now allow interconversion of [NH2+]= and [NH3+]-.
  • tautomers now has a -warts option. Enabling this options will number the output molecules with an @ symbol.
  • The default AM1BCC charge model in molcharge now lightly restrains the AM1 geometry optimization to the starting coordinates. This allows the important relaxation of bond and angle degrees of freedom while greatly reducing the potential to alter the molecule’s conformation away from its starting coordinates.
  • The AM1BCC charge models -method am1bccsym and -method am1bccspt in molcharge now symmetrize the partial charges over bond-topologically equivalent atoms, e.g. methyl hydrogens, in keeping with the original model. This is especially important with conformationally flexible molecules.
  • molcharge now has a .fail file to output molecules that do not charge correctly.
  • fixpka has been refined to reflect feedback from collaborators. In particular isoxazoles and oxadiazoles were added while pyrazoles and aryl sulfonamides were refined. Aryl sulfonamide refinement also incorporated changes based on newly obtained experimental data.


Overview of SCM tools

It is sometimes difficult to keep the website up to date with some of the software that I don’t use and so I was delighted when Fedor Goumans contacted me to highlight some of the updates at Scientific Computing and Modelling. While ADF is still SCM's most widely used program, SCM offers a comprehensive modelling suite consisting of several different tools.


I have written a brief overview here.

Here is a list of the reviews available.


VHELIBS, a validation helper for ligands and binding sites

The Validation HElper for LIgands and Binding Sites (VHELIBS) is software that aims to ease the validation of binding site and ligand coordinates for non-crystallographers. It is written in java and can be downloaded from github here. I have not tested it extensivey but on my cursory look it seems to work fine under Mac OS X, provided you have installed java.

Using a convenient graphical user interface, it allows one to check how ligand and binding site coordinates fit to the electron density map. VHELIBS can use models from either the PDB or the PDB_REDO databank of re-refined and re-built crystallographic models. The user can specify threshold values for a series of properties related to the fit of coordinates to electron density (Real Space R, Real Space Correlation Coefficient and average occupancy are used by default). VHELIBS will automatically classify residues and ligands as Good, Dubious or Bad based on the specified limits. The user is also able to visually check the quality of the fit of residues and ligands to the electron density map and reclassify them if needed.

To start the application simply double-click on the icon, and then enter a PDB code (or you can load a list from a file) the analysis takes a few mins so if you are planning to examine a list of structures you may want to set it running overnight. The results can then be examined in the viewer which is uses JMOL.


It all seems pretty intuitive. In the view above the ligand atoms are purple and the associated electron density red, the protein atoms are white and a dubious area of associated electron density is shown in yellow.

You can read more details here Journal of Cheminformatics 2013, 5:36 doi.


SYBYL-X 2.1 released

The latest update to SYBYL-X has been released, version 2.1 is only supported on 64-bit systems. In addition Python 2.4 is no longer supported, if you are using the latest Mac OS X then you should have Python 2.5.1. To check simply type python in a Terminal window.

chrismacbookpro:~ chris$ python
Python 2.5.1 (r251:54863, Nov 13 2007, 11:10:08) 
[GCC 4.0.1 (Apple Inc. build 5465)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

The major changes in SYBYL_X are a New Job Control System which replaces Netbatch, giving a consistent interface that is implemented across all of SYBYL-X modules. This is compatible with popular job queuing systems like Oracle Grid Engine, LSF, and Torque, and provides improved multi-processor support for key applications (Surflex-Sim, Surflex-Dock, Topomer Search, and UNITY).

There have also been updates to the Molecular Data Explorer (MDE) including:

  • Set 3D Viewer preferences for the display of proteins
  • Switch the structure viewing between the 3D Viewer and SYBYL’s main graphics window
  • Mark compounds in the 3D Viewer
  • Mark compounds in the Grid Viewer
  • Use a right-click menu in the Grid Viewer
  • Display a regression line and or unity line in a Scatter Plot
  • Tile Viewers in a grid
  • Set precision of column data
  • Save structures to a database
  • Export structures and associated column data to a MOL2 file
  • Copy a table

The Python QSAR functionality is now accessible outside of SYBYL as standalone Python scripts. Results of the Python jobs can be read into SYBYL using the new readXML expression generator. See $TA_LIB/python/lib/python2.7/site- packages/tripos/qsarutl/README for more information.

QSAR Project Manager enhancements include the ability to:

  • Modify names of structure sets and descriptor sets via a right-click menu
  • Rename and delete items in the Project Data list via a right-click menu


MOPAC speed improvements

The research group headed by Prof. Dr. Gerd B. Rocha at the Federal University of Paraiba, Brazil, has been successful in implementing a significant speedup. Two modifications have been made: many of the old, slower, operations have been replaced by the Intel Math Kernel Library, and sections of the code have been parallelized to take advantage of multi-threading. Details of the modifications can be found here

Times, in seconds, for a single-point calculation run on a 2 x 2.93 GHz 6-Core Intel Xeon with 16Gb of 1333 DDR3 memory chips Mac Pro computer, using 12 of the 24 threads

Species #atoms Current MOPAC2012 MOPAC 2012 with MKL MOPAC 2012 with MKL and multi-threading
Naphthalene 18 0.02 0.15 0.02
(H2O)573 1719 3,082.23 584.78 79.3
1G6X 1455 8,612.57 1,240.48 142.07
1RNB (Barnase) 2066 34,372.13 4,108.87 411.26

The improved MOPAC is available and can be downloaded from

In MOPAC, proteins can be modeled using the MOZYME technique, however, that technique is limited to closed shell RHF calculations. This means that proteins with free radical sites, excited state proteins, and proteins containing iron, chromium or other transition metal atoms should not be modeled using MOZYME. The new MOPAC reduces the computation time so that conventional MOPAC methods can now be used for many proteins. This means that it is now practical to use conventional MOPAC methods - RHF-CI and UHF - for modeling most of the smallerproteins, and by implication that it will be possible to model many systems that currently cannot or should not be modeled using MOZYME.


IQmol updated

The free open-source molecular editor and visualization package IQmol has recently been updated to include

  • Revamped molecular builder:
  • Add atoms, functional groups, EFPs and entire molecules
  • Extensive and extensible library of molecules and fragments
  • OpenGL shader support:
  • Allows greater configurablity of appearance
  • Users can add their own shaders.
  • ESP plotting from a Distributed Multipole Analysis (from Q-Chem output file)
  • Animation of molecular surfaces
  • SGE queue system support for remote submission


IQmol now has its own Youtube channel which contains some animations generated with IQmol.



ProDy is a free and open-source Python package for protein structural dynamics analysis. It is designed as a flexible and responsive API suitable for interactive usage and application development.

Structure analysis

ProDy has fast and flexible PDB and DCD file parsers, and powerful and customizable atom selections for contact identification, structure comparisons, and rapid implementation of new methods.

Dynamics analysis

  • Principal component analysis can be performed for heterogeneous X-ray structures (missing residues, mutations) mixed structural datasets from Blast search NMR models and MD snapshots (essential dynamics analysis)
  • Normal mode analysis can be performed using Anisotropic network model (ANM) Gaussian network model (GNM) ANM/GNM with distance and property dependent force constants

Bakan A, Meireles LM, Bahar I ProDy: Protein Dynamics Inferred from Theory and Experiments 2011 Bioinformatics 27(11):1575-1577 DOI


Molegro Virtual Docker Update

An update to the Molegro Virtual Docker has been announced. It includes new data analysis tools that are now available directly from within Molegro Virtual Docker. Some of the new features include:

  • New and powerful regression features: Support Vector Machine regression and Partial Least Squares
  • Classification using either K-Nearest Neighbors or Support Vector Machine classification
  • Automated fine-tuning of regression and classification model parameters
  • Spring-Mass Maps for visualization of high-dimensional data
  • Clustering of data sets and subset selection
  • Principal Component Analysis
  • Outlier Detection


OpenEye updates

OpenEye have announced updates to a couple of their products

OMEGA v2.5 is designed to produce high quality multi conformer databases.

Highlights from this release include: OpenMPI version 1.6 is supported on all platforms. The -mpinp and -mpihostfile flags are now used to run OMEGA and makefraglib in MPI mode. These new flags replace the oempirun script. PVM (parallel virtual machine) is no longer supported. An option has been added to allow hydrogen atoms in -OH, -SH, and amines to take part in conformational sampling. This new option can be enabled via the -sampleHydrogens parameter. By default, hydrogen atoms are not sampled. Now using -fixsmarts without -fixmol will rematch for every input structure. Previously, this would only match the first input structure and reuse that match for the rest of the calculation. Using both -fixsmarts and -fixmol will continue to match against the fixmol and use that match for the entire calculation.

EON v2.2. compares electrostatic potential maps of pre-aligned molecules and determines the Tanimoto measures for the comparison.

Highlights from this release include: OpenMPI version 1.6 is supported on all plafforms. The -mpinp and -mpihostfile flags are now used to run EON and makefraglib in MPI mode. These new flags replace the oempirun script. PVM (parallel virtual machine) is no longer supported. The default hitlist format has been changed from sdf to oeb for increased functionality and decreased filesize. The output format is adjustable with the -oformat parameter. Now SD tags are prefixed with EON_. The tags are optional with the -sdTags parameter. Additionally, any existing ROCS tags will not be removed because ROCS and EON tags no longer conflict


Running LigPlot+ under Mac OS X

I occasionally get asked to help with non-Mac applications and recently someone inquired about LigPlot+.

LigPlot+ is a graphical front-end to the LIGPLOT and DIMPLOT programs.

  • LIGPLOT - automatically generates schematic diagrams of protein-ligand interactions for a given ligand in a PDB file.
  • DIMPLOT - plots interactions across a selected protein-protein or domain-domain interface.

Whilst this application is supported under Windows and Linux there is no official support for Mac OS X, however since the GUI LigPlot is written in java and LIGPLOT is written in C there seems to be no reason why it should not run under Mac OS X and with a couple of tweaks it seems to run fine. Full details are here


Added to the list of Hints and Tips


Schrödinger Software Release 2013-1

Schrödinger have just announced the latest release of their entire suite of software programs, this covers tools for drug design, material science, biological modelling and general purpose modelling.

There are a huge number of new features and improvements in the small molecule drug discovery suite as well as Materials Science. However a couple of features caught my eye, pKa prediction for both rule-based and QM-based methods has been improved. Covalent ligand docking has been added and includes a variety of common docking chemistries. Improved pi-stacking interactions in docking. The molecular dynamics has been updated and now includes support for GPU-acceleration. The QM tools look to have been updated and the interface improved. ADME tools have been updated and in particular P450 site of metabolism has improved accuracy.

Predictive capabilities that can be applied across a wide range of chemical systems, including ,Reaction thermochemistry and reaction path exploration ,Rate constants for reactions and transport from transition state theory ,Validated models for calculating oxidation and reduction potentials, Accurate heats of formation and atomization energies for larger systems, Reliable properties for systems containing transition metals,Efficient calculation of electric field dependent properties,Prediction of vibrational and electronic spectra for complex systems,Multiple pre-defined calculation modes representing tested simulation parameters balancing speed and accuracy.

There has also been an update to PYMOL with improved rendering speeds and a couple of bug fixes.

This is certainly a great update and well worth having a detailed look at.


NWChem 6.3 released

An update to NWChem has been released with a host of new features.

NWChem 6.3 includes a new real-time, time-dependent density functional theory capability developed by Ken Lopata, EMSLs first William Wiley Distinguished Postdoctoral Fellow. This capability allows researchers to probe the ultrafast dynamical behavior of molecules and materials in response to an applied electric field.

With this release, researchers will for the first time be able to perform large scale coupled cluster with perturbative triples calculations utilizing the NVIDIA GPU technology. A highly scalable multi-reference coupled cluster capability will also be available in NWChem 6.3.

EMSL Computing greatly expanded NWChem 6.3 plane wave capability with access to a large set of density functional and pseudopotentials or effective potentials, and a more extensive suite of functionality for the projector augmented wave methodology.

Latest set of basis sets in the Basis Set Exchange have been added to the NWChem basis set library.In addition, NWChem 6.3 includes a new set of reaction path methodologies, tools for various spectroscopies including Python scripts to post-process UV/Vis and core spectra. Binaries are not yet available but the source code and instructions for compilation on a Mac are available are available. You will need Xcode and gfortran 4.6.2 from


AmberTools13 (released on April 22, 2013)

AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations (using NAB or mdgx), with either explicit water or generalized Born solvent models. It includes

NAB to build molecules; run MD or distance geometry, using generalized Born, Poisson-Boltzmann or 3D-RISM implicit solvent models. Antechamber and MCPB Create force fields for general organic molecules and metal centers, tleap a basic preparation program for Amber simulations. sqm semiempirical and DFTB quantum chemistry program. pbsa Performs numerical solutions to Poisson-Boltzmann models. 3D-RISM Solves integral equation models for solvation. mdgx Code for explicit solvent molecular dynamics simulations. ptraj and cpptraj Structure and dynamics analysis of trajectories. and amberlite Energy-based analyses of MD trajectories.

AmberTools is distributed in source code format, and must be compiled in order to be used. You will need C, C++ and Fortran90 compilers. The distribution contains a Reference Manual in pdf format.

New features include

  • Greatly expanded and improved cpptraj program for analyzing trajectories;
  • New options for PBSA calculations, including new solvers and dielectric models;
  • Updates to, including access through NAB of two new GB models;
  • New documentation and tools for inspecting and modifying Amber parameter files;


ADF2013 released

I just got an email from CCL highlighting the release of ADF2013.

SCM is proud to announce the 2013 release of the ADF modeling suite. We continue to improve and expand our software suite with the aid of our academic and industrial ADF authors and other partners. Several enhancements and new features have been implemented in our molecular Density Functional Theory (DFT) code ADF and its periodic DFT companion BAND. Our semi-empirical Density Functional based Tight-Binding (DFTB) module has been updated and we offer Dr. Stewart's latest MOPAC2012 module including the PM7 model. The parallelization of the reactive MD module ReaxFF from van Duin and co-workers has been improved considerably.

There is more information here


I also noted there is a free 30-day trial available

Fully functional versions of all modules of our 2013 release are available free of charge for a 30-day evaluation period. The programs may be run on any machine at your organization, with full support. Just fill out our Free Trial Form. Other questions? : e-mail us at


UnityMol games engine based molecular viewer

When you compare the amount of resources and effort that goes into computer games with the amount that is available for scientific software it is clear that the games industry wind hands down. It is not surprising therefore that some enterprising scientists are looking at leveraging games technologies to build new applications.

You can read more here Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges

The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In the molecular sciences, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists?

For an example application have a look at:-

UnityMol is a molecular editor, viewer and prototyping platform, coded in C# with the Unity3D game engine. It was developed by Marc Baaden's team at the LBT laboratory at the IBPC institute of CNRS in Paris. UnityMol includes HyperBalls designed to visualize molecular structures using GPU graphics card capabilities based on shaders (GLSL or Cg). UnityMol can currently read Protein Data Bank (PDB) files, Cytoscape networks, OpenDX potential maps and Wavefront OBJ meshes.


SAR Table updated

The SAR Table app has had the ability to match scaffolds to molecules for a while now, but as of the latest release (1.3.4) just submitted to the AppStore, it will be able to match more than one scaffold at once. The actual process of performing the scaffold match is provided by a webservice (

More details here.


OpenMM Updated

OpenMM has been Updated

OpenMM is a toolkit for molecular simulation. It can be used either as a stand-alone application for running simulations, or as a library you call from your own code. It provides a combination of extreme flexibility (through custom forces and integrators), openness, and high performance (especially on recent GPUs) that make it truly unique among simulation codes.



Smina is a fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.


Open Molecular Mechanics (OpenMM) workshop

This might be of interest.

Simbios invites you to join us at its next Open Molecular Mechanics (OpenMM) workshop.

Where:  Stanford University When:   March 26-29, 2013 Registration:  Free but required and spaces are limited. To register or for more information, visit

OpenMM ( is open-source software that enables molecular dynamics (MD) simulations to be accelerated on high performance computer architectures. It has demonstrated speed ups for both implicit solvent[1] and explicit solvent simulations[2] on graphics processing units (GPUs).  Its performance, openness, and extreme flexibility  via custom forces and integrators  make it truly unique among simulation codes.

A well-designed framework provides an application layer and a library, so that non-programmers can easily and quickly run MD simulations and develop custom algorithms on GPUs, while programmers are simultaneously able to integrate OpenMM cleanly into their own programs.

The workshop offers two tracks:  one for those who want to use OpenMM to run molecular dynamics simulations (no programming experience is needed), and another for programmers interested in integrating OpenMM into their own software.  

The last two days of the workshop are devoted to having the OpenMM team assist participants with their individual projects.   You can sign up for an instructional track, just the open working days, or both.  

OpenMM is supported by Simbios, an NIH National Center for Physics-Based Simulation of Biological Structures. To learn more about Simbios and its research and software tools, visit

[1] OpenMM accelerated code running on NVIDIA GeForce GTX 280 GPU vs.  conventional code with Amber9 running on Intel Xenon 2.66 GHz CPU. MS Friedrichs, et al., "Accelerating Molecular Dynamic Simulation on Graphics Processing Units," J. Comp. Chem., 2009, 30(6):864-872.

[2]Eastman, P. and Pande, V.S., Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit, J. Comp. Chem., 2010, 31(6):1268-1272.

There is a listing of GPU accelerated scientific applications here.


UCSF Chimera Version 1.7

UCSF Chimera Version 1.7 has been released. UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles.

New Tools:

  • APBS (Surface/Binding Analysis) — interface to Poisson-Boltzmann electrostatics calculations with APBS, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy
  • AutoDock Vina (Surface/Binding Analysis) — interface to single-ligand docking with AutoDock Vina, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy
  • Model/Refine Loops (Structure Editing) — interface to Modeller for building missing parts or refining existing parts (the former Model Loops tool only performed the latter and did not facilitate combining the refined and unchanged parts)
  • Notepad (Utilities) — allows entering descriptive text that can be saved along with sessions
  • PDB2PQR (Structure Editing) — interface to structure cleanup and charge/radius assignment with PDB2PQR, using either a web service provided by the National Biomedical Computation Resource (NBCR) or a locally installed copy


SZMAP v1.1.1 Released

OpenEye have announced that SZMAP 1.1.1 has been released. This is a bug fix release that repairs one major bug and several minor ones.

  • A rare but important bug in how the SZMAP application decides which apo grid points will be analyzed under certain circumstances has been fixed.
  • The metadata added to SZMAP output now includes the correct version number.
  • The position of points tested for stabilization by GAMEPLAN no longer differ slightly between different architectures.
  • Running GAMEPLAN from a directory containing the word "gameplan" works properly now.
  • The GRID_COMP utility now generates the appropriate subset of probe orientations for displacement operations.
  • The Water Orientation VIDA Extension now clearly identifies ligand or protein displacement entries in the selection pop-up menu.
  • The WaterColor VIDA Extension no longer switches the hypothesis molecule to wireframe when run while a hypothesis is selected in the list window.

SZMAP uses semi-continuum Poisson-Boltzmann electrostatics to map variations in solvent properties in a protein binding site. It identifies key waters, shows their interactions, compares them to the corresponding ligand atoms, and determines whether neighboring waters aid or hinder binding, giving insights into the role of water molecules in ligand binding. The included tool GAMEPLAN, suggests ways to modify ligand chemistry based on this understanding of water structure in the immediate environment of the ligand.



Fen Zi GPU-based MD simulations

Fen Zi (yun dong de Fen Zi = Moving MOLECULES) is a CUDA code that enables large-scale, GPU-based MD simulations. The code of Fen Zi is now available in Google Code at Any help or feedback is welcome!

Fen Zi currently includes: - NVT and NVE ensembles (NPT coming soon) - Force field: CHARMM force field, Flexible Water Models - Lennard-Jones interactions: Switching or shifting - Long distance electrostatic interactions: Ewald summation method and Reaction field - Solvent: Explicit or implicit model; TIP3; Flexible SPC/Fw water model - Exclusion lists for VDW and electrostatic interactions: NBXMod from 1 to 5 - Restraint potentials to probe the free energetic evaluation of processes - Shake/Rattle bond constraints for atom–atom bonds involving at least one hydrogen atom in the bonded pair

There is a listing of GPU accelerated scientific applications here.


MacMolPlt Updated

MacMolPlt is a cross-platform (Mac OS X, Linux and Windows) gui for preparing, submitting and visualizing input and output for the GAMESS quantum chemistry package. Features include a graphical molecule builder, GAMESS input generation, animation of output and visualization of molecules, normal modes, orbitals and other properties.


Version 7.4.4 update notes:

  • Fixed a seg fault when reading a single mode in a molplt file.
  • Fixed a bug related to fragement parsing.
  • Fixed a problem when deuterium was encountered. There is still not proper support for isotopes, but MacMolPlt should behave normally if they are encountered.
  • Modified MCSCF natural orbital parser for a recent change to GAMESS.
  • Added recent GAMESS coupled-cluster methods.
  • Added a parser for EOM-CC natural orbitals.
  • Added a parser for CAS-SCF diabatic molecular orbitals.
  • Cleaned up some potential 64 bit issues.


Dock Updated

DOCK is a suite of programs for molecular docking. In version 6.6 two new scoring functions are available: Grid-based footprint scoring and SASA-based scoring.

The MultiGrid Footprint Score calculates the pair-wise interaction energies over multiple grids.  Important receptor residues are initially identified with a reference ligand, and individual grids are generated to model such residues.

The SASA score calculates the percent exposure of a ligand, and the percentage of the hydrophobic portion of a ligand and the receptor that are buried in the pocket.

In addition, a symmetry corrected RMSD (Hungarian matching) method was added to facilitate pose reproduction studies.

Full information on what is new in DOCK 6.6


Restarting the lmgrd license server

I use Moe for molecular modeling work, this uses a license.dat file in each installed MOE root directory that must be updated with the contents that you have been given by CCG (either by hard copy or e-mail). You can use any ASCII text editor (I used BBEdit) to edit the file. The FlexLM license manager lmgrd must be configured and run. Usually this runs quietly in the background and needs little intervention, however I've found that on some occasions the server quits (perhaps after updates) and needs to be restarted. However since it is something I don't need to do regularly I always spend a while working out the exact syntax. So I created this short Applescript to restart the server. Each time MOE gets updated you need to change the folder path, and I’ve updated the details to reflect this.


Using ChemBioDraw with MOE

As I mentioned in my recent review of MOE 2012 there is now support for using Marvin as an external 2D chemical drawing package, but what happens if you want to use another drawing package? Well that is where Applescript comes to the rescue, using Applescript support for shell scripts and one line of SVL (scientific vector language) we can use ChemBioDraw as the external editor. Full details of the script are here.


The Applescript section contains more tutorials, scripts and resources.


A Review of MOE 2012

I’ve just finished a review of the latest version of MOE from the Chemical Computing Group.

There are a number of new features that will be of particular interest to Mac users and I’ve included a few tips for using Marvin as the external 2D chemical drawing package.


There is a collection of software reviews here.


MOE 2012.10 released


Integrated Protein Engineering Applications

  • Residue scanning to identify critical residues for affinity
  • Search for optimal mutations to modulate thermostability
  • Predict hydrophobic and electrostatic hot spots with the protein Patch Analyzer

Domain Motif Searching

  • Compare protein domains based on secondary structure elements
  • Search proteins for secondary structure sub-geometries
  • Identify similarities independent of sequence

Amber12:EHT: New Force Field for Biopolymers and Small Molecules

  • Amber12 parameters for proteins and nucleic acids
  • Extended Hückel Theory parameterization of small molecules
  • More precise treatment of resonance and substituent effects

Reaction-based Library Enumeration and Screening

  • New reaction engine combined with library enumeration or sampling
  • Sketch reactions or core/R-group libraries
  • Screen products with 2D or 3D filters (educts & products)

Usability Enhancements

  • Docked System Manager with control over surfaces
  • Undo, redo, keyboard shortcuts, configurable mouse, drag & drop, etc.
  • 2D sketcher integration with MOE Window


Cheminformatics tools

A great collection of freeware tools provided by Michel Petitjean

  • ARMS: Spatial Alignment with the RMS (Root Mean Square) method. (fixed pairwise correspondence)
  • ASV: Analytical calculation of van der Waals surfaces and volumes. (or any union of spheres)
  • CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules. (pairwise correspondence computed)
  • CYL: Minimal radius enclosing cylinder. Minimal radius circumscribed cylinder.
  • DIVCF: Selects by clustering major conformations of a molecule in a set of its conformers.
  • DOG: Docking Geometrically two molecules. (fixed pairwise correspondence)
  • GRD: Computation of the Radius and Diameter of a molecular graph. (computes also the topological shape index)
  • MCG: Optimal Partition (classification): numerical variables and non-euclidean spaces. The number of classes is computed.
  • POP: Optimal Partition (classification): categorical variables. The number of classes is computed.
  • POSE: Computes the RMSD between two ligand poses. No rotation translation is performed.
  • QCM: Quantitative Chirality Measure of a conformer (graph automorphisms enumeration included)
  • RADI: Computation of the Radius and Diameter of a spatial set. (computes also various other geometrical parameters)


Molegro Virtual Docker

CLC bio is pleased to announce a new release of Molegro Virtual Docker , an integrated platform for computational drug design available for Windows, Linux, and Mac OS X. Molegro Virtual Docker offers high-quality protein-ligand docking based on novel optimization techniques combined with a user interface experience focusing on usability and productivity.

New features in version 5.5:

  • A new 'Energy Maps' tool provides volumetric visualization of protein force fields. This makes it possible to understand why a compound interacts with a given receptor, and may provide insights on how to improve the binding.

  • We also added a new execution mode in the Docking Wizard: 'Run Docking in Multiple Processes'. This makes it possible to run medium sized jobs on a local machine, while utilizing multiple CPU cores and even multiple GPU graphics cards. For large jobs on multiple machines, Molegro Virtual Grid should still be used.

  • The ray-tracer has been improved to more closely match the live 3D view output. This makes it possible to create high resolution renderings of the 3D view.


OpenEye Toolkits have been released

OpenEye is pleased to announce that the OpenEye Toolkits v2012.Oct have been released. This release includes the C++, Python, and .NET versions of the Toolkits

C++ examples build system changed to CMake for all supported platforms: Linux, Windows, and OSX.

This is a new release of the OpenEye Toolkits with versions of the following libraries:

OEChem TK:1.9.0
OEDepict TK:2.0.4
OEDocking TK:1.1.3
Grapheme TK:1.0.4
GraphSim TK:2.0.3
Grid TK:1.4.1
Lexichem TK:2.2.0
MolProp TK:2.1.4
Omega TK:2.5.0
Quacpac TK:1.6.0
Shape TK:1.8.3
Spicoli TK:1.1.3
Szybki TK:1.7.2
Zap TK:2.1.4

Details of the changes to the individual libraries are here


MolSoft updates

MolSoft have also released a new version of the free desktop molecular viewer ICM-Browser and the ActiveICM plugin  for viewing fully interactive molecules in web browsers.


SparkV10 released by Cresset

Cresset have announced the formal release of sparkV10 the replacement for FieldStere.

  • Updated molecular mechanics force field that uses a single analogue nitrogen atom and updates the field patterns for many functional groups including aromatic halides
  • Added capability to read protein excluded volumes from pdb files
  • Added new cluster algorithms for clustering of results
  • Added option to edit reference molecules in the molecular editor
  • Added capability to manage columns in the results table
  • New optional module for scoring results using StarDrop models, this does not require access to a StarDrop server, simply place StarDrop model files in a directory and they automatically get used if you have the right  license.  The standard ADMET models that Optibrium have created are supplied but it works equally well with any models created by StarDrop.
  • Added fragment import option in database generator
  • Added capability to rescore all results against a 3D QSAR model using Forge or Torch
  • Added capability to search databases for a particular fragment or substructure
  • Added option to delete entire clusters from results
  • Added depth cue to 3D window
  • Added a GUI interface for selecting a portion of a molecule and writing command line arguments
  • Cleaner GUI with improved buttons

Users should note:-

SparkV10 completely replaces Cresset’s previous “FieldStere” application. If FieldStere is currently installed then it is recommended to uninstall the binary to avoid confusion over which application should be used to open FieldStere project files


Avogadro Updated

Avogadro is a free, open source, cross-platform molecular editor designed for flexible use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Packages are available for Windows, Linux and Mac OS X. The source code source is available under the GNU GPLv2.

This release highlights a great deal of new features, including a built-in crystal library, crystallographic editing, building slabs / surfaces with arbitrary Miller planes, support for Abinit (and soon Quantum Espresso), searching for IUPAC names in PubChem, custom atomic colors and radii, and much more.

See the Release Notes:

What does Avogadro do?

  • An intuitive "builder," including common fragments, downloading directly from PDB or PubChem, and peptide sequences
  • Innovative "auto-optimize" tool which allows you to continue to build and modify, during molecular mechanics optimization
  • Interfaces to many common computational packages
  • Designed to help both educational users and advanced research
  • Plugins that allow Avogadro to be extended and customized
  • Well defined public API, library and Python bindings for development
  • Embedded Python interpreter
  • Translations available in 19+ languages

For more information:


PyMOL now on iPad

Schrodinger have just announced the release of PyMOL on the iPad. It is a free download from the App Store. With the app you can:-

  • View 3D molecular structures, images, and PDFs
  • Search and download data from the PDB, PubChem, Dropbox, or your own custom server.
  • Intuitively interactive: rotate, pan, twist, zoom, center, and adjust clipping planes, with simple gestures
  • Select atoms, residues, molecules, chains, objects, etc. – just by tapping the screen
  • Easy-to-use visualization presets cover the majority of visualization needs such as bond representations and surfaces.
  • Distance calculations, structure alignments, anaglyph 3D, and much more



MOPAC12 released

MOPAC12 A practical quantum chemistry tool for modeling biological systems and co-crystals. MOPAC2012™ brings major improvements in the prediction of intermolecular interactions and hydrogen-bonding. This significantly improves geometries and energies of proteins, crystals, co-crystals, metal clusters, inorganics and other condensed phase systems. New PM7 method significantly improves intermolecular energies, providing increased accuracy for condensed phase chemistry.  PM7 can be applied to modeling enzyme reactions and predicting co-crystals.


SZMAP updated

SZMAP uses semi-continuum Poisson-Boltzmann electrostatics to map variations in solvent properties in a protein binding site. It identifies key waters, shows their interactions, compares them to the corresponding ligand atoms, and determines whether neighboring waters aid or hinder binding. The newly released tool GAMEPLAN, suggests ways to modify ligand chemistry based on this understanding of water structure in the immediate environment of the ligand.


  • The Water Orientation VIDA Extension has been completely rewritten to be easier to use and more feature-rich, making it simple to find key waters and understand their interactions. Each water site can be labeled by its energy, van der Waals energy, and degree of order. The 3D representation shows whether a site is disordered, an acceptor, a donor, or both. Individual waters can be exported for use elsewhere. The other extensions have also been improved.
  • A new command-line program called GAMEPLAN has been released. GAMEPLAN runs several quick SZMAP calculations and analyzes the results to examine how the existing ligand chemistry aligns with the pocket environment. It also produces hypotheses of ligand modifications to improve its affinity, based on the energetics of the water environment directly adjacent to the ligand.
  • SZMAP output has been simplified: sections are clearly identified, the water orientation data is less obtrusive, and an updated set of grids is produced (neutral difference free energy, van der Waals, order, and mask). The Watercolor VIDA Extension now sets contour levels to emphasize significant results.
  • The speed of SZMAP stabilization calculations for both grids and arbitrary coordinates has been increased. Results from an existing apo protein calculation can be re-used, speeding up calculations for a series of compounds and/or poses in a single binding site. The speed of stabilization calculations is improved by avoiding extra calculations on the isolated ligand.
  • It is now easy to produce SZMAP results for just the region in the apo pocket where water has been displaced by the bound ligand, clarifying the analysis of water in the apo protein.
  • The programs SZMAP and GAMEPLAN will check to make sure input files contain partial charges and explicit hydrogens to avoid wasting time on meaningless calculations when the input is incorrect.
  • Protein preparation is easier because PCH (which adds partial charges to molecules and separates protein from ligand) now provides more control over the process and can work around structures that contain unsupported elements. PCH can now split out waters into a separate file.


CORINA 3D structure generation

I’ve added CORINA to the alphabetical listing. CORINA is a fast and powerful 3D structure generator for small and medium sized, typically drug-like molecules. Its robustness, comprehensiveness, speed and performance makes CORINA a perfect application to convert large chemical datasets or databases.


YASARA Updates

YASARA has seen several updates since I last mentioned it, most recently the ability to display pi-pi and cation-pi interactions.


YASARA is powered by PVL (Portable Vector Language), a new development framework that provides performance way above traditional software . PVL allows you to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard computers. You can push and pull molecules around and work with dynamic models instead of static pictures.


iSpartan and iSpartan server

I was wondering when someone would use an iPad as the front-end to a fully featured modelling package running on a remote server, looks like Wavefunction have done a pretty impressive job with taking their sophisticated Spartan computational chemistry package from the desktop to mobile devices.

iSpartan creates molecules as familiar 2D sketches, directly converts these into 3D structures, and calculates low energy conformations. Atomic and molecular properties, NMR and infrared spectra, molecular orbitals and electrostatic potential maps are available from a 5,000 molecule subset of the Spartan Spectra and Properties Database (SSPD). The database may also be searched by substructure. Properties, spectra and graphical models of molecules in the SSPD subset are available for examination.

iSpartan Server is an available add-on to the iSpartan app. iSpartan Server installs on a Windows or Macintosh computer and converts iSpartan from an application whose primary utility is sketching molecules in 2D and visualizing them in 3D, into an open-ended molecular modeling research tool providing access to the full Spartan Spectra and Properties Database (SSPD), currently ~170,000 molecules) and to the computational engines used to produce the data in the SSPD. For molecules not included in the database, connection to iSpartan Server supports calculation of structures, properties, and spectra for all user generated molecules from iSpartan running on the iPad, iPhone, and iPodTouch.


There is a listing of science apps for iOS here


Posit Updated to v1.0.2

POSIT - Ligand guided pose prediction POSIT is designed to use bound ligand information to improve pose prediction. Using a combination of OpenEye approaches, including structure generation, shape alignment and flexible fitting, it produces a predicted pose whose accuracy depends on similarity measures to known ligand poses. As such, it produces a reliability estimate for each predicted pose.


The optimizer has been enhanced to produce better aligned structures in certain cases.


A memory leak in the optimizer was fixed, POSIT should now properly handle large streams of molecules. The -mcs flag is now turned off by default.  In some cases, the mcs was taking far too long for no real benefit in pose prediction.


Cresset Product Update

I was at the Cresset Science Meeting last week and heard about the plans to update their comprehensive suit of drug discovery and design computational tools.

Together with an interesting updates to the tools the suite has undergone something of a makeover, all of the software tools have be renamed using a “Fire” theme and refocussed to specific users needs rather than the software capabilities. The renaming will not be complete until September so in the interim the links on some of the download pages still point to the originally named application.

TorchV10lite is a free 3D molecule viewing, editing and drawing application that shows your molecules in 3D overlaid with field patterns generated using their proprietary field technology together with 2D structure and physicochemical properties. It is the replacement of FieldView.

TorchV10 is a powerful design and 3D SAR tool for medicinal chemists. It is used to take leaps in structural design by identifying compounds with similar fields but different 2D chemical structures while maintaining or improving biological activity. It is the replacement for FieldAlign and due for release very soon.

SparkV10 is a powerful way of generating novel and diverse structures for your project.  sparkV10 uses Cresset’s field technology to find biologically equivalent replacements for key moieties in your molecule, enabling you to find new structures in new chemical space. You can then use calculated physiochemical properties to filter and select the best designs. sparkV10 is the exciting replacement for FieldStere and due for release very soon.

The three applications above look to be intended for use by Medicinal Chemists whilst the remaining two applications are perhaps better suited to those more experienced in computational chemistry.

ForgeV10 takes advantage of Cresset’s patented ligand comparison method to align, score and compare molecules from a biological viewpoint, using the shape and electrostatic character of your molecules to create qualitative and quantitative 3D models of activity. forgeV10 combines FieldAlign and FieldTemplater in a single application,

BlazeV10 uses the shape and electrostatic character of known ligands to rapidly search large chemical collections for molecules with similar shape and electrostatic properties. It is installed and runs on a Linux cluster but is operated through a web-browser, enabling access from any platform and multiple locations.

Many molecular visualisation/modelling tools seem to assume the charge associated with an atom sits as a point at the centre of the nucleus, whilst this makes the computation easy it does not really reflect what the electrostatic surface really “looks like”. Cresset has pioneered the use of field point descriptors to give a more accurate description of the charge around an atom and to enable better comparisons and visualisation. This has been shown to be particularly important when trying to understand some molecular interactions such as Aryl-Aryl interactions or creating bioisosteric replacements.


Cresset now have an impressive suite of tools for drug discovery and I hope to review them in due course.



forgeV10 takes advantage of Cresset’s patented ligand comparison method to align, score and compare molecules from a biological viewpoint

It is designed to

  • Decipher complex SAR and communicate the results
  • Design better molecules based on predictions you can trust
  • Prepare detailed pharmacophores
  • Virtually screen 10 000 compounds on your desktop
  • Generate ADME and off target activity profiles.



New Additions to alphabetical listings

Added to alphabetical listing

ARP/wARP is a software project for automated protein model building and structure refinement. It is based on a unified approach to the structure solution process. It combines electron density interpretation using the concept of the hybrid model, pattern recognition in an electron density map and maximum likelihood model parameter refinement with REFMAC.

The REFMAC program can carry out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. There are options to use different minimization methods. (At the moment only CGMAT is active.) REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where "missing data" have been restored.

Toxtree is a full-featured and flexible user-friendly open source application, which is able to estimate toxic hazard by applying a decision tree approach. Toxtree could be applied to datasets from various compatible file types. User-defined molecular structures are also supported - they could be entered by SMILES, or by using the built-in 2D structure diagram editor.


IQmol molecular editor and viewer

IQmol is a free open-source molecular editor and visualization package. It offers a range of features including a molecular editor, surface generation (orbitals and densities) and animations (vibrational modes and reaction pathways).



Graphite - LifeExplorer

Just added to the alphabetical listing

Graphite - LifeExplorer is a tool for modelling DNA, the tool generates DNA along a Bézier curve, open or closed, allows fine-tuning of atoms' position and, most importantly, exports to PDB. This software allows to model in 3D assemblies of proteins and DNA. Its main feature is the capability to create 3D models of DNA in a highly intuitive manner. To date, the modeling and visualization tool allows to: - import PDB files - create isosurface of molecular object - highlight residues of interest - calculate distance between residues pairs - import and export in 3D formats - model DNA and export the result in PDB - visualize a 3D scene with Level of Detail - explore a scene with real-time ambient occlusion - import a file with x,y,z coordinates and convert it into a DNA representation.

You can see a it in action here


Chemkit added to alphabetical listing

Chemkit is an open-source C++ library for molecular modelling, cheminformatics, and molecular visualization.



Schrödinger Suite 2012 supports Mac OS X

It was recently announced that the Schrödinger Suite 2012 now supports Mac OS X, I don’t have many details other than those on the website. There is now a Mac OS X native version of Maestro 9.3, and PyMOL 1.5 supports Mac OSX 10.7, there is encrypted file transfer channel to clusters, including the Cloud (Linux and Mac only). There is also a Mac OS X native version of Canvas 1.5.

If anyone has more information please let me know.


AMBER 12 released

A new version of AMBER 12 and AMBER Tools 12 has been released, the main changes are:-

  • Force fields: Amber has a new fixed-charge protein force field, ff12SB, enchanced support for polarizable potentials and a new modular lipid force field Lipid11 designed to be compatible with the other pairwise additive AMBER force fields.
  • Expanded options for numerical Poisson-Boltzmann solvation calculations, including models for membrane systems and support for periodic systems.
  • An enchanced 3D-RISM integral equation model, using the Kovalenko-Hirata (and other) closure approximations, with a better treatement of aqueous electrolytes.
  • Improved ideas for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.
  • Simplified installation and automatic update support.
  • Semi-empirical quantum calculations can use d-orbitals, allowing the use of Hamiltonian models such as AM1/d and PM6.
  • QM/MM calculations can interface with a variety of external quantum chemistry programs, expanding the types of quantum models available.
  • More features from sander have been added to the pmemd code for both CPU and GPU, including Temperature Replica Exchange, Isotropic Periodic Sum, Accelerated Molecular Dynamics and support for various harmonic restraints based on the use of NMRopt on GPUs.
  • Expanded methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms, and tighter integration with replica-exchange simulations.
  • New facilities are present for using electron density maps (e.g. from cryo EM/ET experiments) as constraints, and to support rigid (or partially flexible) groups in simulations.

There are detailed instructions for installing AMBER 12 under MacOSX and building CUDA enabled AMBER 12.


SYBYL-X 2.0 release now available

SYBYL-X 2.0 release now available - with new Molecular Data Explorer, QSAR enhancements, and updates for Surflex-Sim and Surflex-Dock to make performing your CADD modeling studies more intuitive and efficient.   

The Molecular Data Explorer is a multi-component tool for molecular data analysis and visualization, and early testers tell us they obtain insights into their dataset in minutes that previously would have taken days.


New applications added to alphabetical listing

Open3DALIGN is a command-line molecular alignment tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is installed on the system while Open3DALIGN is being operated interactively, the setup of alignments can be followed in real time on PyMOL's viewport.

Open3DGRID is an open-source software aimed at high-throughput generation of molecular interaction fields (MIFs). Open3DGRID can generate steric potential, electron density and MM/QM electrostatic potential fields; furthermore, it can import GRIDKONT binary files produced by GRID and CoMFA/CoMSIA fields (exported from SYBYL with the aid of a small SPL script).

Open3DQSAR is an open-source tool aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs). Open3DQSAR can generate steric potential, electron density and MM/QM electrostatic potential fields.


ICM Update

MolSoft have announced the release of ICM version 3.7-2c.

New features include Atomic Property Fields APF is a 3D pharmacophoric potential implemented on a grid. APF can be generated from one or multiple ligands and seven properties are assigned from empiric physico-chemical components (hydrogen bond donors, acceptors, Sp2 hybridization, lipophilicity, size, electropositive/negative and charge).

The 3D ligand Editor is a powerful new tool for the interactive design of new lead compounds in 3D. It allows you to make modifications to the ligand and see the affect of the modification on the ligand binding energy and interaction with the receptor.

Use AQUASITES to design chemicals based on their ability to displace or keep water molecules inside the ligand binding site of proteins. The first step is to identify water binding sites and then the second step is to estimate the free energy of water displacement for a particular ligand(s).

Protein Modelling Inside ICM there are many features for homology modelling and loop modelling. This new option can be used if you have a gap in your protein and you want to find loops in the PDB which fit the gap.

"Pipe-able" Scripting in ICM. New options to pipe icm commands and scripts. Easy way to write pipe-able scripts (see $ICMHOME/molpipe/*.icm). Easy way to add parallelism to unix/mac ICM scripts: fork with pipe option ($ICMHOME\molpipe*.icm)


UCSF Chimera Updated to version 1.6

UCSF Chimera is a highly extensible, interactive molecular graphics program is available for MacOSX, both X-windows and native versions are available. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics

This is a major update and whilst some of the new features and tools are described below full details can be found at Note this will be the last release supporting Mac PowerPC platforms.

New Tools:

  • Animation (Utilities) under development, not fully functional, may change significantly — save/restore Chimera scenes
  • Cage Builder (Higher-Order Structure) — create polyhedral cages composed of hexagons, pentagons, and other polygons
  • Change Chain IDs (Structure Editing)
  • MultiFit (Volume Data) — simultaneous rigid fitting of multiple structures into density (uses RBVI web server running the program MultiFit from the Sali lab)
  • Palette Editor (Utilities) — create and choose palettes (series of colors and interpolation method; currently used for background color gradients)
  • Renumber Residues (Structure Editing)

    New Commands:

  • background — set background color(s) or image

  • changechains — reassign chain IDs
  • fitmap — command implementation of Fit in Map, plus features not available in that tool:
  • global search with random initial placement
  • sequential fitting of multiple different structures
  • symmetric fitting of copies of the same structure
  • invert — swap substituents
  • resrenumber — renumber residues
  • ibclass — set ribbon residue class: which atoms control ribbon path and which are hidden by ribbon
  • ribspline — set ribbon path method: B-spline or cardinal spline; control additional smoothing and “stiffness” of cardinal spline ribbon
  • scene — save and restore scenes, which include positions, display status and styles, labels, etc. (see also new tool: Animation)
  • zonesel — select atoms and/or surfaces within a cutoff distance of specified atoms and/or surfaces (this command allows defining zones by surfaces, whereas the standard command-line zone operators < and > refer to atoms only)


RESP ESP charge Derive version III.5

I just got this message.

I am pleased to announce the release of the program RESP ESP charge Derive version III.5 (or R.E.D. III.5) and its related tools (Ante_R.E.D.-1.5 and X R.E.D. III.5) available @ New features available: - Bug corrections and code cleaning, - Update of the Mini-HowTo & Tutorials, - Better handling of Gaussian, GAMESS and Firefly error messages, - Charge value rounding off errors automatically corrected at 10-6 up to 10-2 depending on the user choice, - Handling geometrical constraints in the P2N file format (geometry optimization using the Gaussian program), - Two new scripts for data submission in R.E.DD.B., - New version for the RESP program: version 2.2 with updated documentation. The R.E.D. III.5 tools are distributed under the GNU General Public License after a simple Register & Download procedure. The article describing the R.E.D. tools is available @ News about the latest developments of R.E.D. IV can be found @ Best regards, The q4md force field tools team

R.E.D. allows computational biologists involved in AMBER/GAFF, CHARMM, GLYCAM & OPLS force field based biological studies to automatically derive highly effective and reproducible charge values, and to build force field libraries for new molecules and molecular fragments.


Perspectives on the state and future of Computer aided molecular design

I just thought I’d mention that Journal of Computer-Aided Molecular Design commissioned some Perspectives on the state and future of the field to commemorate the journal's 25th anniversary and have made this content open access for a limited period.

Special Issue: The next 25 years: Commemorating the 25th anniversary of the Journal of Computer-Aided Molecular Design

There are some very interesting insights, well worth reading.


Have a read of Alpha shock by Mark A. Murcko • W. Patrick Walters

Sanjay toggled the telepresence feature on his iPhone (standard since IOS 27.2) and he and Paolo were instantly ‘‘together’’ examining a set of images from the virtual pharmacology study.


OMEGA updated

OMEGA v2.4.6 has been released. This is a major release with new features including an extension to the MMFF94 force field for three coordinated boron compounds. Designed for use with the large libraries required for computer-aided drug design, OMEGA rapidly generates multi-conformer structure databases.


OpenEye Applications added to listing

I was reading the announcements of new products from OpenEye and I thought I should update the listings.

AFITT from OpenEye is the only software to offer a fully automatic ligand fitting process that optimizes a real-space fit to density while keeping conformational strain to a minimum. It capitalizes on a combination of core technologies that OpenEye has developed, specifically conformer generation, shape potential, high quality small molecule structure minimization, and visualization. The key step, after finding the appropriate conformers and aligning them to density, is the implementation of a refinement that combines force field and shape potentials, via a series of adiabatic optimizations [1]. The AFITT distribution includes both a GUI and a collection of command-line applications.

BROOD is a software application designed to help project teams in drug discovery explore chemical and property space around their hit or lead molecule. BROOD generates analogs of the lead by replacing selected fragments in the molecule with fragments that have similar shape and electrostatics, yet with selectively modified molecular properties. BROOD fragment searching has multiple applications, including lead-hopping, side-chain enumeration, patent breaking, fragment merging, property manipulation, and patent protection by SAR expansion.

FILTER is a very fast molecular filtering and selection application. It uses a combination of physical property calculations and functional group knowledge to remove undesirable compounds before they enter experimental or virtual screening. Undesirable properties may include: toxic functionalities, a high likelihood of binding covalently with the target protein, interfering with the experimental assay, and/or a low probability of oral bioavailability.

QUACPAC provides pKa and tautomer enumeration in order to get correct protonation states. It also offers multiple partial charge models (including MMFF94 [1], AM1-BCC [2], and AMBER [3]) that cover a range of speed and quality in order to allow appropriate charging for every end use. QUACPAC's approach to tautomeric enumeration is to provide multiple tautomeric states rather than one "correct" tautomer. Subsequent downstream processes are then used to identify the appropriate tautomeric form.

SZYBKI optimizes molecular structures with the Merck Molecular Force Field, either with or without solvent effect, to yield quality 3D molecular structures for use as input to other programs. Since the chemistry of molecular interactions is a matter of shape and electrostatics, it is impossible to consider either without reasonable 3D molecular structures. SZYBKI also refines portions of a protein structure and optimize ligands within a protein active site, making it useful in conjunction with docking programs.



I just heard about a platform - FORECASTER - that includes programs for drug discovery and process chemistry, these include

  1. FITTED, a docking program
  2. PREPARE, PROCESS and SMART, programs that can prepare protein and ligand files automatically
  3. CONVERT, a program that converts 2D molecules to energy-minimized 3D molecules (adds hydrogens, generates tautomers and protomers)
  4. SELECT, a program that computes compound similarity, extracts focused highly diverse libraries or identifies analogues
  5. REDUCE, a program that filters using descriptors and functionnal groups
  6. REACT, a program that performs combinatorial chemistry in silico from user-defined chemical schemes
  7. IMPACTS, a sites of metabolism prediction program (CYP 450)
  8. ACE, a program that predicts the stereochemical outcome of reactions

All the programs are integrated into a new web-based graphical interface that allows complete automation of the different workflows. 

You can read more details here, Integrating Medicinal Chemistry, Organic/Combinatorial Chemistry, and Computational Chemistry for the Discovery of Selective Estrogen Receptor Modulators with Forecaster, a Novel Platform for Drug Discovery


MOE 2011 Review

I’ve just added a review of the latest version of MOE from Chemical Computing Group.


MOE 2011.10 released, Lion compatible

CCG have announced the release of MOE 2011.10. This includes a new license manager compatible with LIon.

Some of the new and enhanced features in MOE include:


Non-Bonded Interaction Visualization Model - Visualize halogen bonds, H-bonds, CH-X, proton- for interactive modeling - Calculate strengths using Extended Hckel Model - Display strengths and interactions in 2D Ligand Interaction Diagrams Sequence Editor Redesign - Wrapped view, zoom, chain name/tag, etc. - Synchronized coloring (% identity, similarity, Clustal X, RMSD) - Cut and paste for loop grafting, inserting linkers, filling gaps, etc. Combinatorial Build in Pocket - Add R-groups to one or more attachment points in 3D pocket - Apply 2D and 3D filters, refine in (flexible) pocket and score - Use Builder to scan fragments for interactive ligand optimization Analysis of Solvent in Binding - Calculate within minutes a solvent binding free energy map using 3D-RISM - Calculate water, salt and hydrophobe solvation densities in complex or apo receptor - Diagnose how well alternate groups take advantage of water upon binding Macromolecular System Preparation - Correct common problems in protein structures automatically - Browse alternate conformations, cap termini, build missing loops - Optimize hydrogen bond network by flipping residues and adjusting states GPCR Family Database and Alignment Tools - Identify and annotate transmembrane regions of GPCRs - Add alignment constraints to improve GPCR sequence alignments - Augment a database of GPCR crystal structures with in-house data


New major release of Molegro Virtual Docker

Molegro is pleased to announce a new major release of Molegro Virtual Docker, an integrated platform for computational drug design available for Windows, Linux, and Mac OS X. Molegro Virtual Docker offers high-quality protein-ligand docking based on novel optimization techniques combined with a user interface experience focusing on usability and productivity.

Major new features in version 5.0: -GPU-accelerated docking on CUDA supported hardware making it possible to screen drug-like compounds up to 30 times faster than using conventional CPU-based methods. The GPU implementation builds upon and extends the research described in the paper "GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution" ( -The new 2D Ligand Map provides an easy way to inspect and visualize protein-ligand interactions.

For more information, or to download a trial version, please visit our company website at:


Added Crystal

CRYSTAL program computes the electronic structure of periodic systems


OpenEye announce EON and ROCS updates

OpenEye has announced a couple of updates.


sdf2xyz2sdf is an open-source software aimed at converting SDF files into TINKER XYZ files (and vice versa) Read More...

QuantumBio Inc. and Chemical Computing Group, Inc. Announce the Release of the DivCon Discovery Suite for the Molecular Operating Environment (MOE)

 QuantumBio Inc., a leader in Structure-based and Fragment-based Drug Discovery solutions, based upon their next-generation linear-scaling quantum mechanics (QM) methods, has announced the release of DivCon Discovery Suite 5.0 for the Molecular Operating Environment (MOE) platform Read More...

SYBYL-X now on Mac (updated)

SYBYL-X now on Mac

Cresset Announces Academic Access Program

Cresset Announces Academic Access Program

ICM Update

Molsoft have announced an update to ICM.

UCSF Chimera updated

UCSF Chimera Version 1.5 has been released

APBS Updated

APBS is a software package for modeling biomolecular solvation. Read More...

Added VESTA to alphabetical listing

VESTA is a 3D visualization program for structural models and 3D grid data such as electron/nuclear densities. Read More...

Added OpenMM Zephyr

I’ve added OpenMM Zephyr to the alphabetical listing.


Added YASARA a high performance structure visualisation, modelling and simulation program to the alphabetical listing. Read More...


Publication describing validation of OMEGA a systematic, knowledge-based conformer generator. Read More...

Review of MOE (2009.10 release)

A review of the latest version of MOE.

VASP Tools

Tools for VASP users

Millsian Molecular modeling

A new molecular modeling package.

WebMo Update


AMBERTools 1.3 Available

AmberTools 1.3 is now available

UCSF Chimera Updated

A new production release of UCSF Chimera (version 1.4) is now available. Download is free for noncommercial use. The download includes full documentation and tutorials. Read More...

MOE updated

Chemical Computing Group Inc. (CCG) has just announced the general release of the 2009.10 version of the Molecular Operating Environment (MOE).   Read More...

APBS Update

Adaptive Poisson-Boltzmann Solver (APBS) -- Software for evaluating the electrostatic properties of nanoscale biomolecular systems Read More...

OpenMM released

Version 1.0beta of OpenMM has been released, a library which provides tools for modern molecular modeling simulation.

Turbomole Updated

Version (6.1) of Turbomole, one of the fastest and most stable quantum chemistry programs, has just been released. Read More...


R.E.D. allows computational biologists involved in AMBER/GAFF, CHARMM, GLYCAM & OPLS force field based biological studies to automatically derive highly effective and reproducible charge values, and to build force field libraries for new molecules and molecular fragments. Read More...

Zephyr Updated

OpenMM Zephyr is a freely available molecular simulation application with an easy-to-use graphical user interface and GPU-acceleration capabilities Read More...


SOMA2 is a web-based molecular modelling environment.

TINKER has been updated

The molecular modeling package TINKER has been updated (14 Aug)

AMMOS added

AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening) employs an automatic procedure for energy minimization of protein-ligands complexes Read More...

FITTED has been updated

FITTED has been updated to 2.6.1 and is available for download.


VMD Updated

The molecular visualisation program VMD has been updated

WebMo added

Added WebMo a front-end to a range of computational chemistry packages. Read More...

Another Application added

The PSI3 suite of quantum chemical programs is designed for efficient, high-accuracy calculations of properties of small to medium-sized molecules. Read More...

Balloon Updated

Balloon a tool for generating 3D structures has been updated. Read More...

New Applications Added

ORCA (quantum Chemistry), HADDOCK (Molecular Docking).

COSMOtherm now available on Mac

COSMOtherm is a program for the quantitative calculation of solvation mixture thermodynamics based on quantum chemistry. Read More...

PC Gamess/Firefly for Mac OS X

As of February 23, 2009, the PC GAMESSFirefly team is proud to announce the availability of the first official release of the PC GAMESS/Firefly package for Mac OS X/Intel platform Read More...

MOE Update

I’ve just written a review of the latest update to the molecular modeling and cheminformatics package MOE Read More...

Molecula Numerica

A new version of Molecula Numerica.


A few updates and news snippets

Added APBS

Added APBS to list of Max OS X applications. Read More...

Zodiac website

Just had word that the website for Zodiac has been updated, why not have a look


A new version of the advanced molecular editor Avogadro has been released. Read More...


Zodiac has been updated


A review of LigandScout


Updated MOE Review