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an improved force field for folded and disordered protein

已有 839 次阅读 2017-8-20 15:32 |个人分类:科研笔记|系统分类:科研笔记

CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins. Nature Methods, 2017 Jan; 14(1): 71–73. doi:  10.1038/nmeth.4067


Disordered protein is a challenge for molecular dynamic simulations, especially considering the lack of a proper force field. In a recent benchmark study on the structural ensembles of a disordered arginine/serine (RS) peptide obtained with different force fields, the old CHARMM36 (C36) protein FF was found to generate a high population of left-handed α-helix (αL), inconsistent with nuclear magnetic resonance (NMR) and small-angle X-ray scattering (SAXS) experimental measurements. Recently, Alexander D MacKerell's group has  an improved C36 FF (Charmm36m) based on a refined backbone CMAP potential derived from reweighting calculation (Online Methods) and a better description of specific salt bridge interactions .    


SAXS profiles of the RS peptide. Ensemble-averaged scattering curves from the C36 simulation (blue) and the C36m simulation (red) are plotted, with the experimental curve shown with error in gray. The nonweighted error function χ2 as defined in Ref.  was 0.63 using C36, and 0.12 using C36m. The error bars represent the standard deviation computed by dividing the conformational ensembles in two, and computing the average SAXS profile for each half separately. For the C36m ensemble, the error bars are smaller than the line width.


Dowload latest Charmm36m FF for Gromacs here

CHARMM36 force field in GROMACS format, including CGenFF version 4.0 and the CHARMM36m protein force field revision. Updated July 2017. Changes since November 2016 include addition of more lipid residues and parameters, NAD and polyphosphates, metals, silicates, and the ability of the user to choose between C36 and C36m for protein simulations via the GROMACS "define" mechanism:

define = -DUSE_OLD_C36

The C36m parameter set is recommended for all protein simulations, but the ability to toggle between old and new parameter sets may be useful in the case of force field comparisons.

charmm36-jul2017.ff.tgz

A Python program to convert ParamChem CGenFF toppar stream file from CHARMM to GROMACS format. The comments section in the beginning of the program provides usage information.

cgenff_charmm2gmx.py




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