Volltext-Downloads (blau) und Frontdoor-Views (grau)

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.

Export metadata

Additional Services

Search Google Scholar Check availability


Show usage statistics
Document Type:Article
Author:Austen Bernardi, Roland Faller, Dirk Reith, Karl N. Kirschner
Parent Title (English):SoftwareX
Article Number:100241
Date of first publication:2019/06/12
Copyright:©2019 Published by Elsevier B.V.
Funding Information:Partial funding for this project was provided by the Defense Threat Reduction Agency, USA (DTRA, grant HDTRA1-15-1-0054).
Keyword:ACPYPE; Carbohydrate; Force field; Glycam06; Gromacs; Nonbonded scaling factor
Departments, institutes and facilities:Fachbereich Informatik
Fachbereich Ingenieurwissenschaften und Kommunikation
Institut für Technik, Ressourcenschonung und Energieeffizienz (TREE)
Dewey Decimal Classification (DDC):0 Informatik, Informationswissenschaft, allgemeine Werke / 00 Informatik, Wissen, Systeme / 005 Computerprogrammierung, Programme, Daten
Fields of research:Institut für Technik, Ressourcenschonung und Energieeffizienz (TREE) / Arbeitsgruppe Computational Chemistry
Entry in this database:2019/06/19