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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