[gmx-users] Tryptophan and tyrosine protonation

[Justin Lemkul]

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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

-- 
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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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