Fw: [gmx-users] AMINOACIDS

[fatemeh ramezani]

 Dear Justin

I usepropka site for pKa calculation but I want to know if pKa is smaller than my desired pH , I must consider this amino acid  deprotonate? 
and if pKa of  aminoacids is bigger thanmy desired pH, I must protonate this amino acid?


Thank you

Fatemeh Ramezani





----- Forwarded Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: fatemeh ramezani <fr_750 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, 15 July 2013, 17:00
Subject: Re: [gmx-users] AMINOACIDS
 



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

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