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Publication

The ACPYPE web server for small-molecule MD topology generation

Journal Contribution - Journal Article

Motivation: The generation of parameter files for molecular dynamics (MD) simulations of small molecules that are suitable for force fields commonly applied to proteins and nucleic acids is often challenging. The ACPYPE software and website aid the generation of such parameter files. Results: ACPYPE uses OpenBabel and ANTECHAMBER to generate MD input files in Gromacs, AMBER, CHARMM, and CNS formats. It can now take a SMILES string as input, in addition to the original PDB or mol2 coordinate files, with GAFF2 support and GLYCAM force field conversion added. It can be installed locally via Anaconda, PyPI, and Docker distributions, while the web server at https://bio2byte.be/acpype/ was updated with an API, and provides visualization of results for uploaded molecules as well as a pre-generated set of 3738 drug molecules.

Journal: Bioinformatics
ISSN: 1367-4803
Issue: 6
Volume: 39
Publication year:2023
Keywords:Software, Computers, Proteins/metabolism, Nucleic Acids, Molecular Dynamics Simulation
Accessibility:Open