[gmx-users] Tryptophan and tyrosine protonation
jalemkul at vt.edu
Mon May 6 14:05:07 CEST 2013
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On 5/6/13 7:58 AM, Sathish Kumar wrote:
> I want to do simulation of protein at pH 12 so i have to deprotanate
> tyrosine,tryphtophan.Can you please tell me how i can do with pdb2gmx
The answer is the same as with cysteine - either the force field will have
parameters for such species or it won't. If it doesn't, you have to implement
suitable parameters; there is no magic that pdb2gmx can do for you. Anionic
tyrosine is more likely to have parameters available somewhere. I have never
heard of the tryptophan side chain being deprotonated under any conditions.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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