Most software developed in the Molecular Simulation group can be found on our
group Github page (still somewhat under construction).
SCRIPTS
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Python script for modifying methyl rotation barriers in the CHARMM36/CHARMM36m protein force fields (GROMACS topology .itp or .top files), as described in F. Hoffmann et al., Predicting NMR Relaxation of Proteins from Molecular Dynamics Simulations with Accurate Methyl Rotation Barriers. J. Chem. Phys., 2020, 152, 084102. DOI: 10.1063/1.5135379
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Python script for modifying methyl rotation barriers in AMBER99SB (and related) protein force fields (GROMACS topology .itp or .top files), as described in F. Hoffmann et al., Accurate Methyl Group Dynamics in Protein Simulations with AMBER Force Fields. J. Phys. Chem. B, 2018, 122 (19), 5038-5048. DOI: 10.1021/acs.jpcb.8b02769. Please note that by default, the modified C-gamma parameters of Kümmerer et al. are used, see DOI: 10.1021/acs.jctc.3c00174.
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Python script for modifying methyl rotation barriers in the AMBER ff15ipq protein force field (GROMACS topology .itp or .top files), as described in F. Hoffmann et al., Predicting NMR Relaxation of Proteins from Molecular Dynamics Simulations with Accurate Methyl Rotation Barriers. J. Chem. Phys., 2020, 152, 084102. DOI: 10.1063/1.5135379