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Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS.

ABSTRACT: We provide general AMBER force field (GAFF) parameters for 160 organic molecules including drugs, natural products, and steroids, which can be employed without further processing in molecular dynamics (MD) simulations using GROMACS. We determined these parameters based on quantum mechanical (QM) calculations involving geometry optimization at the HF6-31G* level of theory. For each molecule we provide a coordinate file of the three-dimensional molecular structure, the topology and the parameter file. The applicability of these parameters was demonstrated by MD simulations of these molecules bound to the active site of the main protease of the coronavirus SARS-CoV-2, 3CL^pro, which is a main player during viral replication causing COVID-19.

SUBMITTER: Loschwitz J

PROVIDER: S-EPMC8027721 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS.

Loschwitz Jennifer J Jäckering Anna A Keutmann Monika M Olagunju Maryam M Olubiyi Olujide O OO Strodel Birgit B

Data in brief 20210315

We provide general AMBER force field (GAFF) parameters for 160 organic molecules including drugs, natural products, and steroids, which can be employed without further processing in molecular dynamics (MD) simulations using GROMACS. We determined these parameters based on quantum mechanical (QM) calculations involving geometry optimization at the HF6-31G* level of theory. For each molecule we provide a coordinate file of the three-dimensional molecular structure, the topology and the parameter f ...[more]

PMID: 33855133

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