ForceGen: Atomic covalent bond value derivation for Gromacs

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dc.citation.issue5
dc.citation.volume24
dc.contributor.authorNash A
dc.contributor.authorCollier TA
dc.contributor.authorBirch HL
dc.contributor.authorde Leeuw NH
dc.date.available2018-01
dc.date.issued2018-01
dc.description.abstractA 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.
dc.description.confidentialfalse
dc.format.extent1 - 11
dc.identifier.citationJournal of Molecular Modeling, 2018, 24 (5), pp. 1 - 11
dc.identifier.doi10.1007/s00894-017-3530-6
dc.identifier.eissn0948-5023
dc.identifier.elements-id397153
dc.identifier.harvestedMassey_Dark
dc.identifier.issn1610-2940
dc.publisherSpringer Berlin Heidelberg
dc.relation.isPartOfJournal of Molecular Modeling
dc.relation.replaceshttp://hdl.handle.net/123456789/11741
dc.relation.replaces123456789/11741
dc.relation.urihttps://link.springer.com/article/10.1007/s00894-017-3530-6
dc.subjectGromacs
dc.subjectForce values
dc.subjectLaplacian bond order
dc.subjectMolecular dynamics
dc.subjectHessian
dc.subject.anzsrc0304 Medicinal and Biomolecular Chemistry
dc.subject.anzsrc0306 Physical Chemistry (incl. Structural)
dc.subject.anzsrc0307 Theoretical and Computational Chemistry
dc.titleForceGen: Atomic covalent bond value derivation for Gromacs
dc.typeJournal article
pubs.notesNot known
pubs.organisational-group/Massey University
pubs.organisational-group/Massey University/College of Sciences
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