[gmx-users] Updated CHARMM36 force field files

[Justin Lemkul]

Hi All,

An updated set of CHARMM36 force field files for GROMACS is available from our 
website:

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

There are several notable changes in this release that may be of interest to you.

1. The protein parameter set has been updated to include the CHARMM36m 
modifications to better model intrinsically disordered peptides.  The 
corrections dramatically reduce the incorrect alpha-L sampling that was observed 
with C36.  See Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de 
Groot, B.L., Grubmuller, H., and MacKerell, Jr., A.D. CHARMM36m: an improved 
force field for folded and intrinsically disordered proteins, Nature Methods, 
2016, DOI: 10.1038/nmeth.4067

2. A set of modified RNA nucleotides has been added, see Xu, Y., Vanommeslaeghe, 
K., Aleksandrov, A., MacKerell, Jr., A.D., and
Nilsson, L. Additive CHARMM Force Field for Naturally Occurring Modified
Ribonucleotides, Journal of Computational Chemistry, 2016, 37: 896-912.

3. An improved description of halogen bonding has recently been implemented in 
the CGenFF force field for small drug-like molecules.  The approach includes a 
positively charged lone pair along the C-X axis to more accurately represent 
halogen bonding, as described in Gutierrez, I.S., Lin, F.-Y., Vanommeslaeghe, 
K., Lemkul, J.A., Armacost, K.A., Brooks III, C.L., and MacKerell, Jr., A.D. 
Parametrization of halogen bonds in the CHARMM general force field: Improved 
treatment of ligand-protein interactions, Bioorganic & Medicinal Chemistry, 
2016, 24: 4812-4825.

4. Per user requests on this list, I have included the topologies and parameters 
for all D-amino acids.

5. There are several other fixes and tweaks, including neutral N-terminal 
glycine and other missing parameters that have been brought to my attention over 
time.

Otherwise, the contents are the same as previous releases of the force field 
(carbohydrates, lipids, etc).

If there are any questions or problems, please contact me.  I have run the files 
through my stress test of amino acids, DNA, RNA, lipids, and carbohydrates and 
everything looks correct, but we rely on feedback to make sure everything is 
working smoothly.

The complete contents and pertinent references are given in the forcefield.doc file.

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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