[gmx-users] Query regarding protonation and deprotonation of some residues
sonali dhindwal
sonali11dhindwal at yahoo.co.in
Mon Sep 27 08:49:36 CEST 2010
Thanks Kass for the help.
I want to specifically protonate one of the lysine near the active site and deprotonate Tyr and Ser. It will be kind if you can please help me to know how to select that specific residue number.
Regards
--
Sonali Dhindwal
--- On Mon, 27/9/10, Itamar Kass <itamar.kass at monash.edu> wrote:
From: Itamar Kass <itamar.kass at monash.edu>
Subject: Re: [gmx-users] Query regarding protonation and deprotonation of some residues
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Monday, 27 September, 2010, 10:07 AM
Hi,
You need to define the protonation sate vie pdb2gmx.
pdb2gmx -tyr -lys
On 27/09/10 2:34 PM, sonali dhindwal wrote:
Hello All,
I came through this research article, in which author has
selectively deprotonated and protonated some of the
residues to
simulate the condition for electrostatic interaction with
the substrate while carrying out molecular dynamics
simulation.
It will be appreciable, if
you could help me regarding the same, how to deprotonate
Tyr
and Ser residue and protonate Lysine residue of the
protein while
preparing the protein topology to be used for molecular
dynamics simulation in Gromacs.
Thanks and Regards.
--
Sonali Dhindwal
--
"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut
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| Itamar Kass, Ph.D.
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| Tel: +61 3 9902 9376
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