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charmm力场的使用

已有 12390 次阅读 2018-12-4 19:41 |个人分类:分子模拟|系统分类:科研笔记| charmm, charmm

三大力场顺序应该是Amber, Charmm, OPLS-AA.

 

Charmm力场:

能量形式:

多了一项Urey-Bradley,是charmm的特色,反映的是bond-angle vibration between a triplet of atoms.

 

1998年:Charmm22是和charmm package version 22一起发布的。

https://pubs.acs.org/doi/abs/10.1021/jp973084f

提到了当时的力场情形:Recently, Kaminski and Jorgensen have stressed the importance of the correct representation of liquid properties by molecular mechanics force fields. They made comparisons of a new OPLS all-atom force field, AMBER 94, and MMFF. The best agreement for liquid NMA was obtained for the OPLS force field; the calculated values ∆Hvap = 13.61 kcal/mol and a molecular volume of 133.8 Å3 are almost identical to those reported here.

 

gromacs软件包里的是charmm27 with cmap.

2001年:扩展到nucleic acids,称为charmm27

https://onlinelibrary.wiley.com/doi/full/10.1002/1097-0282%282000%2956%3A4%3C257%3A%3AAID-BIP10029%3E3.0.CO%3B2-W

 

2004年:with the CMAP backbone correction

https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.20065

 

对于TRPCA-C,对应CT1-C. bond interactionb0=0.149 ,k_b=209200.0. CA的电荷为0.07,均来自charmm22文章。

 

 

【发展】

CHARMM22*,类似ff99SB*, with newly modified backbone torsion potentials done by DE Shaw.

2009: CHARMM General Force Field (CGenFF): for drug-like molecules

https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.21367

 

2012charmm36:

https://pubs.acs.org/doi/10.1021/ct300400x

 

 

【近期应用】

2013年:https://pubs.acs.org/doi/10.1021/jp401563n

and they say:

“We found that AMBER does not predict any β-sheet structure, whereas GROMOS favors antiparallel β-sheet structures, and OPLS predicts diverse structures. The impact of all-atom force fields on the stability of preformed β-sheet oligomers has also been discussed.”

说明charmm27 and tip3p也是可以的。



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