[gmx-users] Query regarding protonation and deprotonation of some residues
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.
--- 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:
I came through this research article, in which author has
selectively deprotonated and protonated some of the
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
preparing the protein topology to be used for molecular
dynamics simulation in Gromacs.
Thanks and Regards.
"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
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu
-----Inline Attachment Follows-----
gmx-users mailing list gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users