[gmx-users] [Fwd: Problem in running energy minimization in gromacs]
David van der Spoel
spoel at xray.bmc.uu.se
Mon Oct 27 22:22:34 CET 2008
-------- Original Message --------
Subject: Problem in running energy minimization in gromacs
Date: Mon, 27 Oct 2008 15:16:23 +0000
From: abhik mukhopadhyay <abhik at dq.fct.unl.pt>
To: spoel at xray.bmc.uu.se
Dear Dr. Spoel
I am a beginner in Gromacs and having some problem in running energy
minimization. I am working with an enzyme that has a Zn bound to four
residues (3 cys and 1 his). I am trying to run a md simulation. But
after the minimization I always found the Zinc coming out of the enzyme.
I ran the minimization both with generating counter ions and without
generating. The result is same. Do I need to take any special care to
work with metalloenzyme ?
> Yes. You need restraints.
Any suggestion from you will be highly useful for me.
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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