Thanks for your help
I hope it will work.
Regards
--
Sonali Dhindwal
--- On Wed, 24/3/10, Justin A. Lemkul <jalem...@vt.edu> wrote:
From: Justin A. Lemkul <jalem...@vt.edu>
Subject: Re: [gmx-users] Query regarding toplogy of Manganese ion in protein
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Date: Wednesday, 24 March, 2010, 5:44 PM
sonali dhindwal wrote:
> Hello,
>
> I have protein in my protein, for which i want to run MD simulation.
> Could you please help me to know how to generate topology file for Manganese
> and which force field to use, as none of the force field in Gromacs supports
> Mn ion.
Parameterization is considered a very advanced task, and generating good
parameters for a transition metal is especially challenging. See here:
http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species
Parameters for Mn are available for the AMBER force fields, which can be
incorporated into Gromacs with the ffamber ports. The reference for Mn can be
found at:
http://www.pharmacy.manchester.ac.uk/bryce/amber#ion
-Justin
> Please Help
> Regards
>
> --
> Sonali Dhindwal
>
>
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-- ========================================
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
========================================
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