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

Kognole, Abhishek A.; Lee, Jumin; Park, Sang‐Jun; Jo, Sunhwan; Chatterjee, Payal; Lemkul, Justin A.; Huang, Jing; MacKerell, Jr., Alexander D.; Im, Wonpil

doi:10.1002/jcc.26795

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

Journal Article · Tue Dec 07 00:00:00 EST 2021 · Journal of Computational Chemistry

DOI:https://doi.org/10.1002/jcc.26795· OSTI ID:1995504

^[1]; Lee, Jumin ^[2]; Park, Sang‐Jun ^[2]; Jo, Sunhwan ^[3]; Chatterjee, Payal ^[1];

^[4];

^[5];

^[1];

^[2]

Univ. of Maryland, Baltimore, MD (United States)
Lehigh Univ., Bethlehem, PA (United States)
Argonne National Laboratory (ANL), Argonne, IL (United States)
Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)
Westlake Univ., Hangzhou (China)

Explicit 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. Additionally, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. Finally, 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.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH); National Science Foundation (NSF)

Grant/Contract Number:: AC02-06CH11357; GM131710; GM133754; GM138472; ACI-1548562

OSTI ID:: 1995504

Journal Information:: Journal of Computational Chemistry, Vol. 43, Issue 5; ISSN 0192-8651

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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