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 to...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2019-07-01
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| Series: | SoftwareX |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352711018300736 |
| _version_ | 1818130634581737472 |
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| author | Austen Bernardi Roland Faller Dirk Reith Karl N. Kirschner |
| author_facet | Austen Bernardi Roland Faller Dirk Reith Karl N. Kirschner |
| author_sort | Austen Bernardi |
| collection | DOAJ |
| description | 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. Keywords: ACPYPE, Glycam06, Force field, Nonbonded scaling factor, Carbohydrate, Gromacs |
| first_indexed | 2024-12-11T08:08:10Z |
| format | Article |
| id | doaj.art-08ac9dfa052549e9b2cb209d1e03bd8f |
| institution | Directory Open Access Journal |
| issn | 2352-7110 |
| language | English |
| last_indexed | 2024-12-11T08:08:10Z |
| publishDate | 2019-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | SoftwareX |
| spelling | doaj.art-08ac9dfa052549e9b2cb209d1e03bd8f2022-12-22T01:14:57ZengElsevierSoftwareX2352-71102019-07-0110ACPYPE update for nonuniform 1–4 scale factors: Conversion of the GLYCAM06 force field from AMBER to GROMACSAusten Bernardi0Roland Faller1Dirk Reith2Karl N. Kirschner3UC Davis, Department of Chemical Engineering, Davis, 95616, CA, USAUC Davis, Department of Chemical Engineering, Davis, 95616, CA, USABonn-Rhein-Sieg University of Applied Sciences, Department of Electrical Engineering, Mechanical Engineering and Technical Journalism, Grantham-Allee 20, 53757 Sankt Augustin, GermanyBonn-Rhein-Sieg University of Applied Sciences, Department of Electrical Engineering, Mechanical Engineering and Technical Journalism, Grantham-Allee 20, 53757 Sankt Augustin, Germany; Bonn-Rhein-Sieg University of Applied Sciences, Department of Computer Science, Grantham-Allee 20, 53757 Sankt Augustin, Germany; Corresponding author at: Bonn-Rhein-Sieg University of Applied Sciences, Department of Electrical Engineering, Mechanical Engineering and Technical Journalism, Grantham-Allee 20, 53757 Sankt Augustin, Germany.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. Keywords: ACPYPE, Glycam06, Force field, Nonbonded scaling factor, Carbohydrate, Gromacshttp://www.sciencedirect.com/science/article/pii/S2352711018300736 |
| spellingShingle | Austen Bernardi Roland Faller Dirk Reith Karl N. Kirschner ACPYPE update for nonuniform 1–4 scale factors: Conversion of the GLYCAM06 force field from AMBER to GROMACS SoftwareX |
| title | ACPYPE update for nonuniform 1–4 scale factors: Conversion of the GLYCAM06 force field from AMBER to GROMACS |
| title_full | ACPYPE update for nonuniform 1–4 scale factors: Conversion of the GLYCAM06 force field from AMBER to GROMACS |
| title_fullStr | ACPYPE update for nonuniform 1–4 scale factors: Conversion of the GLYCAM06 force field from AMBER to GROMACS |
| title_full_unstemmed | ACPYPE update for nonuniform 1–4 scale factors: Conversion of the GLYCAM06 force field from AMBER to GROMACS |
| title_short | ACPYPE update for nonuniform 1–4 scale factors: Conversion of the GLYCAM06 force field from AMBER to GROMACS |
| title_sort | acpype update for nonuniform 1 4 scale factors conversion of the glycam06 force field from amber to gromacs |
| url | http://www.sciencedirect.com/science/article/pii/S2352711018300736 |
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