[gmx-users] Tryptophan and tyrosine protonation

Justin Lemkul 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
> 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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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