Macs in Chemistry

Insanely Great Science

AMBER 11 has been released

AMBER 11 has been released

  • Force fields: Amber now supports most CHARMM fixed-charge force fields, including those with CMAP torsional potentials. There is also an updated version of GAFF, the general Amber force field for organic molecules.
  • A new parameterization of the generalized Born solvation model is available, optimized for peptides and proteins.
  • Expanded options exist for numerical Poisson-Boltzmann solvation calculations.
  • Solvation effects can also be estimated using a 3D-RISM integral equation model, using the Kovalenko-Hirata (and other) closure approximations.
  • There is improved integration with the Chimera visualization program, and with UCSF DOCK.
  • Simplified methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms.
  • Amber 11 includes a new implementation of the nudged elastic band model for finding low-energy pathways for conformational transitions, which can be used for only part of the system, or in explicit solvent simulations.
  • There are updated scripts for constant pH simulations and for MMPB/SA free energy calculations.
  • The "polar" version the isotropic periodic sum model has been added, along with its IPS-DFFT counterpart.
  • MD simulations using pmemd can take advantage of NVIDIA GPU cards to obtain significant speedups compared to traditional CPU codes.

Ordering Info
blog comments powered by Disqus