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, with either explicit water or generalized Born solvent models.
The AmberTools suite is free of charge, and its components are mostly released under the GNU General Public License (GPL). A few components are included that are in the public domain or which have other, open-source, licenses. The sander program now has the LGPL license. 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 Amber16 package builds on AmberTools16 by adding the pmemd program, which resembles the sander (molecular dynamics) code in AmberTools, but provides (much) better performance on multiple CPUs, and dramatic speed improvements on GPUs. Major new features include:
Semi-Isotropic Pressure Scaling (GPU)
Charmm VDW Force Switch (CPU, GPU)
Enhanced NMR Restraint support + R^6 averaging support (GPU)
Gaussian Accelerated Molecular Dynamics (CPU, GPU)
Support for external electric fields (CPU)
Expanded umbrella sampling support (GPU)
Constant pH supported with replica exchange along pH coordinate (GPU)
Support for gas phase MD (igb=6) (CPU, GPU)
Support and significant performance improvements for the latest Kepler, Maxwell and Pascal GPUs from NVIDIA.
One of the issues for machine learning models in helping understand structure activity relationships (SAR) is providing a nice chemist friendly visualisation. This excellent blog post provides a description of how to colour code the parts of molecules that are predicted to contribute to an activity.
I've been sent details of a couple of jobs and I thought I'd pass them on.
BIO – Cheminformatics Data Scientist (Stratified Medical)
We are looking for an experienced and innovative cheminformatician to make a significant contribution in influencing the drug discovery process by applying your expertise in chemical methods development and use of intelligent algorithms to chemical data. Working within the Biomedical Data R&D team, you will be required to bring your experience and ideas across a broad range of drug design areas.
Technical Expert Cheminformatics, (Syngenta, Jealotts Hill)
In this role, you will provide cheminformatics and mathematical modeling support to the computational chemistry platform in Chemical Research.
Cresset have just announced the release of Spark V10.4.
Spark finds biologically equivalent replacements for key moieties in your molecule. Whether your goal is R-group exploration, patent busting or scaffold hopping, your results will include structures you have thought of yourself, plus new structures that make chemical sense and are totally unexpected.
The new features include:-
- New Cresset reagent databases derived from eMolecules’ building blocks, replacing previous reagents based on ZINC, include availability information for every result
- New analysis of the conformation of every result using the Torsion Library method of Guba et al. that is based on an analysis of the Cambridge Structural Database (CSD)
- New configurable connection to external REST service for properties that enables you to add your own data and properties to the Spark experiment
- Improved Radial Plots to support enhanced multi-parameter optimization.