Fw: [gmx-users] AMINOACIDS

[Justin Lemkul]

On 7/15/13 8:54 AM, fatemeh ramezani wrote:
>
>
>   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?
>

Please consult any basic biochemistry text and/or website describing the 
Henderson-Hasselbalch equation.

-Justin

>
> 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
>
> -- ==================================================
>
> 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
>
> ==================================================
>

-- 
==================================================

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

==================================================