[gmx-users] Query regarding toplogy of Manganese ion in protein

[sonali dhindwal]

Thanks for your help
I hope it will work.
Regards

--
Sonali Dhindwal

--- On Wed, 24/3/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:

From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] Query regarding toplogy of Manganese ion in protein
To: "Discussion list for GROMACS users" <gmx-users at 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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