[gmx-users] simulation of a protein including calcium ion

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 18 13:27:11 CEST 2010

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 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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