ForceGen: atomic covalent bond value derivation for Gromacs.

ABSTRACT: A large number of crystallographic protein structures include ligands, small molecules and post-translational modifications. Atomic bond force values for computational atomistic models of post-translational or non-standard amino acids, metal binding active sites, small molecules and drug molecules are not readily available in most simulation software packages. We present ForceGen, a Java tool that extracts the bond stretch and bond angle force values and equilibrium values from the Hessian of a Gaussian vibrational frequency analysis. The parameters are compatible with force fields derived using the second order tensor of the Hessian. The output is formatted with the Gromacs topology in mind. This study further demonstrates the use of ForceGen over the quantum mechanically derived structur

SUBMITTER: Nash A 

PROVIDER: S-EPMC5719132 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature