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 <jalem...@vt.edu>
To: fatemeh ramezani <fr_...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@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
jalem...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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