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

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 24 13:14:37 CET 2010

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:


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:



> Please Help
> Regards
> --
> Sonali Dhindwal
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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