Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS
Jennifer Loschwitz,
Anna Jäckering,
Monika Keutmann,
Maryam Olagunju,
Olujide O. Olubiyi,
Birgit Strodel
Affiliations
Jennifer Loschwitz
Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52428, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
Anna Jäckering
Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52428, Germany
Monika Keutmann
Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52428, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
Maryam Olagunju
Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52428, Germany
Olujide O. Olubiyi
Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52428, Germany; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria; Corresponding authors.
Birgit Strodel
Corresponding authors.; Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jülich 52428, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
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.
