[gmx-users] ligand falling out of active site during EM

Diane Fournier diane.fournier at crchul.ulaval.ca
Mon May 8 17:26:14 CEST 2006

Still on the same problem, I made a pr run on the complex, and had the same result (ligand is out of the active site at time = 0.000 ps. Then I ran the same pr run, but with dt = 0.001 ps with all coordinates output for my trajectory. It turns out the ligand starts out of the active site, even if my input coordinates have the ligand inside. What is happening ??

-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Diane Fournier
Sent: Fri 5/5/2006 3:05 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] ligand falling out of active site during EM
Hello !

I'm trying to run a molecular dynamics on a drug-enzyme complex. I did John Kerrigan's tutorial and everything worked fine. Now I'm trying with my system but I get a problem : the ligand keeps falling out of the active site during EM. I thought maybe it was a pbc problem and used comm-grps = protein in my .mdp file, but I get the same result. I transformed the .gro input file to .pdb to view it in pymol and the ligand is in the active site before simulation. So it seems this happens during steepest descents EM. 

The ligand is a hybrid inhibitor containing a steroid moiety (estradiol) linked to an adenosine-like moiety with a 13-methylene alkyl chain.

Is there a way to keep/force the ligand in the active site during EM (maybe using PR) ?

Is this reflecting some physical phenomenon, ie the ligand has low affinity ?

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