[gmx-users] force feield paremeters for magnesium

[Justin A. Lemkul]

Mahnam wrote:
> 
> hello GMX users
> I want to do simulation for a protein that has magnesium, how can I find 
> force feield paremeters for magnesium and carboxyle oxygen ?.
>  

Ions are described in ions.itp, and carboxylate groups are a part of the 
description of the corresponding amino acid(s) found in the .rtp entry.

You might be interested in reading Project, et al. (2008) JCC 29.  It describes 
inconsistencies in force field parameters for carboxylate-Ca2+ and 
carboxylate-Mg2+ interactions, as well as some potential modifications to the 
nonbonded parameters.

-Justin

> In God We Trust
> Hello Dear
> Â 
> Many thanks in advance for your help and your reply.
> Yours truly
> Karim Mahnam
> Institute of  Biochemistry  and  Biophysics (IBB)
> Tehran University
> P.O.box 13145-1384
> Tehran
> Iran
> http://www.ibb.ut.ac.ir/
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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