Paper Citing NAMD - Abstract
Crowley, Michael F.; Williamson, Mark J.; Walker, Ross C.
CHAMBER: Comprehensive Support for CHARMM Force Fields Within the AMBER Software
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 109:3767-3772, DEC 2009
The similarity of the AMBER force field's energy functional form with that of the CHARMM force field, gives the potential for direct translation of common bonding and nonbonding terms, along with their parameters, present in CHARMM topology and parameter files, with the intent of evaluation within the AMBER software; specifically the SANDER and PMEMD dynamics engines. To this extent, we have created a tool, CHAMBER, which can take a CHARMM protein structure file (PSF), coordinate file (COR) and associated forcefield files, and convert these to an AMBER topology file (prmtop) and associated coordinate file (inpcrd). CHAMBER opens a conversion route which enables the simulation of CHARMM parameterized models using AMBER's PMEMD engine; thus providing improved serial efficiency as well as parallel efficiency over large numbers of CPUs. Significant effort has been expended in ensuring a true representation of the CHARMM force field in AMBER providing energies and forces that are the same to the limits of machine precision. This software will be released in the upcoming version 1.3 of the free AMBERTools suite. (C) 2009 Wiley Periodicals, Inc. Int J Quantum Chem 109: 3767-3772, 2009
