leila karami wrote:
Dear Justin
Is there any way for this problem?
Please keep Tsjerk's comments
(http://lists.gromacs.org/pipermail/gmx-users/2010-October/054938.html) in mind.
If the calcium coordination complex plays only a minor structural role, you
can probably justify using distance restraints (added to the topology after
pdb2gmx). If it has some other functionally-significant role, then you have
harder decisions to make.
In either case, you should turn to the literature to understand how others
typically address metal coordination complexes and make an educated choice that
suits your needs best. Posting to the mailing list and getting a few tips
should not take place of doing your homework thoroughly.
-Justin
--
========================================
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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