[gmx-users] apply protonation state CYS amino acid

[Justin Lemkul]

On 5/4/20 11:46 PM, azadeh kordzadeh wrote:
> Hi
> Thank you very much for your answer to my former question
> I want to select CYSH state but we have this option for this amino acid.
> already I could determine especial state for his,lys,arg,asp by command -his
> but this command doesn't work for CYS

Deprotonated (anionic) Cys is treated as a special residue by all force 
fields, usually something like CYM because it is not normally considered 
a titratable amino acid. Check the force field .rtp file and adjust the 
residue name accordingly.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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