wilsonjcarter / force_fields Goto Github PK

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))