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

[Justin A. Lemkul]

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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-- 
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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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