[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
Good day.

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.
Best regards
Abhik Mukhopadhyay

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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