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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--
========================================
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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