Rabab Toubar wrote:
So is there a way we can make His neutral before running the simulations as in
case of NAMD?
You can manually set any protonation state you want with pdb2gmx -his.
-Justin
Rabab Toubar
--- On Wed, 6/16/10, Justin A. Lemkul <jalem...@vt.edu> wrote:
From: Justin A. Lemkul <jalem...@vt.edu>
Subject: [gmx-users] Re: His protonation
To: "sagar barage" <sagarbar...@gmail.com>, "Gromacs Users' List"
<gmx-users@gromacs.org>
Date: Wednesday, June 16, 2010, 11:59 PM
Please keep all Gromacs-related correspondence on the
gmx-users list. I am not a private tutor.
sagar barage wrote:
Dear sir,
when i was done the MD of crystal
structure the both nitrogen of immadazol ring of histidine
is protonated
which are not protonated in crystal structure.
There are no protons in crystal structures.
all histidine in
structure contain single protonation but some Histidine is
double protonated at both nitrogen
why this happens in gromacs?
Please read the manual information (or pdb2gmx -h) about
how pdb2gmx attempts to add hydrogens to the input
structure.
-Justingm
-- Sagar H. Barage
sagarbar...@gmail.com
<mailto:sagarbar...@gmail.com>
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use
the www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
