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CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

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dc.contributor.authorKognole, Abhishek A.en
dc.contributor.authorLee, Juminen
dc.contributor.authorPark, Sang-Junen
dc.contributor.authorJo, Sunhwanen
dc.contributor.authorChatterjee, Payalen
dc.contributor.authorLemkul, Justin A.en
dc.contributor.authorHuang, Jingen
dc.contributor.authorMacKerell, Alexander D.en
dc.contributor.authorIm, Wonpilen
dc.date.accessioned2022-01-06T03:48:33Zen
dc.date.available2022-01-06T03:48:33Zen
dc.date.issued2021-12-07en
dc.date.updated2022-01-06T03:48:24Zen
dc.description.abstractExplicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM-GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre-equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF-based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. In addition, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. The capabilities and availability of Drude Prepper in CHARMM-GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.en
dc.description.versionAccepted versionen
dc.format.extent17 page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1002/jcc.26795en
dc.identifier.eissn1096-987Xen
dc.identifier.issn0192-8651en
dc.identifier.orcidLemkul, Justin [0000-0001-6661-8653]en
dc.identifier.pmid34874077en
dc.identifier.urihttp://hdl.handle.net/10919/107414en
dc.language.isoenen
dc.publisherWileyen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000727351400001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsIn Copyrighten
dc.rights.urihttp://rightsstatements.org/vocab/InC/1.0/en
dc.subjectcarbohydrateen
dc.subjectdipole momenten
dc.subjectDNAen
dc.subjectmembraneen
dc.subjectproteinen
dc.subjectprotein structure fileen
dc.titleCHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force fielden
dc.title.serialJournal of Computational Chemistryen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherArticleen
dc.type.otherEarly Accessen
dc.type.otherJournalen
dcterms.dateAccepted2021-11-25en
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Biochemistryen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen

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