Various force fields, in both gromacs and Amber format. Chromophore force fields are included in amber03-star, amber03w and amber03ws For CHARMM force fields, please see Alex Mackerell's website: http://mackerell.umaryland.edu/charmm_ff.shtml Some details: AMBER: **Installation** `amber_format/dat/leap`... basically this stuff needs to go into the corresponding dat/leap folder of your amber installation. e.g. for Amber 14, do a git pull and then do something like `cp -r amber_format/dat/leap TARGET_DIR/amber14/dat`. The force fields are: - ff03x: amber ff03* ([Best, Hummer, JPCB 2009](http://pubs.acs.org/doi/abs/10.1021/jp901540t)) - ff99SBx: amber ff99SB* ([Best, Hummer, JPCB 2009](http://pubs.acs.org/doi/abs/10.1021/jp901540t)) - ff99SBxildn: amber ff99SB*-ILDN ([Best, Hummer, JPCB 2009](http://pubs.acs.org/doi/abs/10.1021/jp901540t) and Lindorff-Larsen et al, Proteins, 2011 for ILDN part) - ff03w: amber ff03w ([Best, Mittal, JPCB, 2010](https://www.ncbi.nlm.nih.gov/pubmed/20536262)) - ff03ws: amber ff03ws ([Best, Zheng, Mittal, JCTC 2014](https://www.ncbi.nlm.nih.gov/pubmed/25400522)) **Note** that for most, one just does a "source leaprc.ff03x" in leap, e.g., to use ff03*. To use ff03ws requires a two-step setup described in the README for the amber force fields. GROMACS: - amber03-star: amber ff03* ([Best, Hummer, JPCB 2009](http://pubs.acs.org/doi/abs/10.1021/jp901540t)) - amber99sb-star: amber ff99SB* ([Best, Hummer, JPCB 2009](http://pubs.acs.org/doi/abs/10.1021/jp901540t)) - amber99sb-star-ildn: amber ff99SB*-ILDN ([Best, Hummer, JPCB 2009](http://pubs.acs.org/doi/abs/10.1021/jp901540t) and Lindorff-Larsen et al, Proteins, 2011 for ILDN part) - amber99sb-star-ildn-q: amber ff99SB*-ILDN-q (same as above, but with backbone charge mods as described in [Best, De Sancho, Mittal, Biophys. J. 2012](https://doi.org/10.1016/j.bpj.2012.02.024) ⋅⋅ - amber03w: amber ff03w ([Best, Mittal, 2010](https://www.ncbi.nlm.nih.gov/pubmed/20536262)) - amber03ws: amber ff03ws ([Best, Zheng, Mittal, 2014](https://www.ncbi.nlm.nih.gov/pubmed/25400522)) - amber99sbw: amber ff99SBw (ref?) - amber99sbws: amber ff99SBws ([Best, Zheng, Mittal, 2014](https://www.ncbi.nlm.nih.gov/pubmed/25400522) -- see the SI) ⋅⋅ - denaturants-amber03ws: urea and guanidium chloride (gdmcl) force fields ([Zheng, Best, JCTC, 2015](http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00778))