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ForceGen: atomic covalent bond value derivation for Gromacs

Nash, Anthony, Collier, Thomas, Birch, Helen L. and De Leeuw, Nora 2018. ForceGen: atomic covalent bond value derivation for Gromacs. Journal of Molecular Modeling 24 (1) , 5. 10.1007/s00894-017-3530-6

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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.

Item Type: Article
Date Type: Publication
Status: Published
Schools: Chemistry
Publisher: Springer
ISSN: 1610-2940
Date of First Compliant Deposit: 2 January 2018
Date of Acceptance: 14 November 2017
Last Modified: 02 Jan 2018 13:56
URI: http://orca-mwe.cf.ac.uk/id/eprint/107828

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