Journal Article

FZJ-2021-01374

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS

Loschwitz, J.FZJ* ; Jäckering, A.FZJ* ; Keutmann, M.FZJ* ; Olagunju, M.FZJ* ; Olubiyi, O. (Corresponding author)FZJ* ; Strodel, B. (Corresponding author)FZJ*

2021
Elsevier Amsterdam [u.a.]

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Please use a persistent id in citations: http://hdl.handle.net/2128/29709  doi:10.1016/j.dib.2021.106948

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, 3CLpro, which is a main player during viral replication causing COVID-19.

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Contributing Institute(s):

1. Strukturbiochemie (IBI-7)

Research Program(s):

1. 5244 - Information Processing in Neuronal Networks (POF4-524) (POF4-524)

Appears in the scientific report 2021

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Database coverage:
; ; ; ; Article Processing Charges ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; DOAJ Seal ; Emerging Sources Citation Index ; Fees ; PubMed Central ; SCOPUS ; Web of Science Core Collection

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