AMBER Archive (2008)

Subject: AMBER: problem with Mg2+ during MD

From: Zhenwei Lu (
Date: Thu Apr 03 2008 - 11:48:13 CDT

Dear amber user:

    I am working on a homo-dimer protein with two substrates and mg2+ ions,
each subunit containing one active site. the Mg2+ ion coordination is built
according to inhibitor complex structure. I first minimize the built
complex, then put it in a water box and running minimization with weak
constraint on protein and ligand. temperature increase slowly to 300K
through several steps with total time 1ns and the force constraint reduces
slowly to very small value (1kcal/mol/A). then for the production MD
running. everything is OK until 1.7ns in the production. before that, Mg2+
is coordinated with three Carboxyl oxygen(D/E), two oxygen from ligand and
one from water in both monomer. what happens is in one subunit one carboxyl
group rotates in and forms bifurcated bonds with Mg and breaks bond between
ligand and Mg2+. For the other subunit, the Mg2+ coordination is stable.

   I have two question.
   first, Is this normal for MD simulation. If not, how to fix the problem?

   Second, If this is not unusual for MD, since the interaction between Mg2+
and substrate is important, I want to restraint the interaction during MD
simulation. please give me some suggestion on the suitable way to setup
restraint for my situation. Thanks a lot.

Zhenwei Lu
Graduate Student
Biochemistry & Molecular Biology
313 Biochemistry building
Tel: 517-353-8786

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