[gmx-users] Updated CHARMM36 force field files available

[Justin Lemkul]

All,

I upload a new version of the GROMACS port for the CHARMM36 force field today. 
You can find the files at:

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

We have steadily been adding to these files since the last release in March. 
Most fixes are trivial nomenclature adjustments and changes related to a few 
bugs that were propagated in files found in charmm27.ff that were subsequently 
fixed.  All were things that would have been obvious because they would have 
triggered fatal errors when running pdb2gmx.

New in this version of the force field are:

1. Changed nucleic acid nomenclature (H5' and H5'') for ease of interfacing with 
CHARMM-GUI
2. New atom type for Mg2+ to use parameters from dx.doi.org/10.1021/ct3000734, 
see MG entry in ions.itp for the "define" keyword
3. Addition of phosphorylated amino acids (mono- and dianionic forms of Ser, 
Thr, and Tyr)
4. Addition of bacterial lipids
5. Addition of S-adenosyl methionine

Happy simulating!

-Justin

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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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