AmberFFC, a flexible program to convert AMBER and GLYCAM force fields for use with commercial molecular modeling packages

Abstract.

A program for converting the different existing AMBER and GLYCAM force fields for use with commercial molecular modeling packages is presented, using the Molecular Simulations Inc. (MSI or Accelrys) software package as a case model. Called AmberFFC, the program creates AMBER and GLYCAM force field files suitable for use with the Accelrys molecular mechanics modules by transforming the amino acid, nucleotide, and monosaccharide topology databases and force field parameter files to the Accelrys file format. It is intended for any modeler who is interested in using the current AMBER and GLYCAM force fields with the Accelrys FDiscover and CDiscover programs. AmberFFC has been written entirely with the Perl programming language, making it highly flexible and portable. In order to compare the implementation of the force fields converted by AmberFFC in the Accelrys package with their corresponding execution in the AMBER software, and also to verify the efficiency of the AmberFFC program, results from single point energy calculations for 13 model molecules were obtained with the two programs. It is demonstrated that results obtained with the CDiscover and FDiscover modules compare well to those found using Sander_classic, thus showing that AmberFFC is a highly efficient program. Some energy differences between the AMBER and Accelrys software have been observed, and their origin has been characterized and discussed.