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 /<[email protected]>/* wrote:
From: Justin A. Lemkul <[email protected]>
Subject: Re: [gmx-users] Query regarding toplogy of Manganese ion in
protein
To: "Discussion list for GROMACS users" <[email protected]>
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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