[gmx-users] AMINOACIDS

[Justin Lemkul]

On 7/15/13 7:56 AM, fatemeh ramezani wrote:
>
>
>   Dear Justin
> I don't know how can I detect the protonation state of amino acids in specific pH. Can you help me?
>

There are various methods for pKa calculations, and based on those results you 
can choose the appropriate states with pdb2gmx command-line options.  Again, 
this topic is covered extensively in the archive and you would benefit from some 
of the previous discussions that I will not repeat here.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Associate

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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