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ACPYPE update for nonuniform 1–4 scale factors: Conversion of the GLYCAM06 force field from AMBER to GROMACS

  • Herein we report an update to ACPYPE, a Python3 tool that now properly converts AMBER to GROMACS topologies for force fields that utilize nondefault and nonuniform 1–4 electrostatic and nonbonded scaling factors or negative dihedral force constants. Prior to this work, ACPYPE only converted AMBER topologies that used uniform, default 1–4 scaling factors and positive dihedral force constants. We demonstrate that the updated ACPYPE accurately transfers the GLYCAM06 force field from AMBER to GROMACS topology files, which employs non-uniform 1–4 scaling factors as well as negative dihedral force constants. Validation was performed using β-d-GlcNAc through gas-phase analysis of dihedral energy curves and probability density functions. The updated ACPYPE retains all of its original functionality, but now allows the simulation of complex glycomolecular systems in GROMACS using AMBER-originated force fields. ACPYPE is available for download at https://github.com/alanwilter/acpype.

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Metadaten
Document Type:Article
Language:English
Author:Austen Bernardi, Roland Faller, Dirk Reith, Karl N. Kirschner
Parent Title (English):SoftwareX
Volume:10
First Page:100241
ISSN:2352-7110
DOI:https://doi.org/10.1016/j.softx.2019.100241
Publisher:Elsevier
Date of first publication:2019/06/12
Tag:ACPYPE; Carbohydrate; Force field; Glycam06; Gromacs; Nonbonded scaling factor
Departments, institutes and facilities:Fachbereich Informatik
Fachbereich Elektrotechnik, Maschinenbau, Technikjournalismus
Institut für Technik, Ressourcenschonung und Energieeffizienz (TREE)
Dewey Decimal Classification (DDC):0 Informatik, Informationswissenschaft, allgemeine Werke / 00 Informatik, Wissen, Systeme / 005 Computerprogrammierung, Programme, Daten
Entry in this database:2019/06/19