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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
command
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
--
========================================
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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