ForceGen: Atomic covalent bond value derivation for Gromacs
Loading...
Date
2018-01
Open Access Location
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Springer Berlin Heidelberg
Rights
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 structures of a small organic solvent, a naturally occurring protein crosslink derived from two amino acids following post-translational modification and the amino acid ligands of a zinc ion. We then derive Laplacian bond orders to understand how the resulting force values relate back to the quantum mechanical model. The parameterisation of the organic solvent, toluene, was verified using Molecular Mechanics simulations. The structural data from the simulation compared well with the quantum mechanical structure and the system density compared well with experimental values.
Description
Keywords
Gromacs, Force values, Laplacian bond order, Molecular dynamics, Hessian
Citation
Journal of Molecular Modeling, 2018, 24 (5), pp. 1 - 11