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

[Mark Abraham]

On 24/03/2010 11:37 PM, sonali dhindwal wrote:
> Thanks for your help
> I hope it will work.

Better than just hoping is design a small test case to see if the 
parameters are vaguely suitable for *your* purpose - and read up on how 
they were parameterized and for what purpose... Your problem could 
easily be too large in scope for someone without years of MD experience.

Mark

> --- 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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