[gmx-users] Thiolate cysteine

[Justin Lemkul]

On 5/6/13 7:03 AM, Sathish Kumar wrote:
>   I want to do simulation of protein at pH 12, in this case experimentally
> reported that the disulphide bonds of protein was broken and sulphurs
> become S negative  . Can you please tell me making of disulphide as S-  and
> S- is it correct and how to set force field to this.

Some force fields (like the Amber parameter sets and some others) have the CYM 
residue, which is the thiolate form of cysteine.  Find which force fields have 
this residue, read about their use, and make a choice based on what you find.

-Justin

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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