[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.

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



    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


              It will be appreciable, if
              you could help me regarding the same, how to deprotonate
              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

| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
| Tel: +61 3 9902 9376
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| E-mail: Itamar.Kass at monash.edu

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