Justin A. Lemkul wrote:
<snip>
were harmonically restrained to their initial positions of pdb, How
can I do this for my fe4s4 cluster. What keywords should I use for
that and in which step I can do?
That's what position restraints are doing.
I should amend this slightly. I assumed your Fe4S4 cluster was simply part of
your protein, which is restrained with posre.itp, generated by pdb2gmx. If this
is not the case, you will have to use genrestr to generate a position restraint
file for the Fe4S4 cluster, if it is indeed a separate molecule type.
I doubt that restraining the Fe4S4 cluster will fix anything. Please see my
last message - there are clashes in your system or inappropriate parameters at
play. If you restrain the atoms, you may be just delaying the inevitable crash.
-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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