[gmx-users] Ligand moves out of box during EM steps

[raja]

Dear Tsjerk,
        Thanks for your reply. But I have not gone to the stage of
        dynamics yet. I am still struck at energy minimization. Now
        atleast I could reason out why it happens, but I dont know how
        to stop it. The reason is everytime 
when I convert ligand-enzyme complex using pdb2gmx, I trim off the
ligand and convert the protein part alone, later I 
paste the drug molecule in the resultant file. I suspect that could be
the problem,so I try to fix it by myself. 

With thanks !
B.Nataraj
On Wed, 22 Mar 2006 07:54:05 +0100, "Tsjerk Wassenaar"
<tsjerkw at gmail.com> said:
> Hi Raja,
> 
> Probably PBC. Nothing wrong, just visual. You can try to center your
> system
> on the ligand before starting the simulation, which should keep it "in
> place".
> 
> Tsjerk
> 
> On 3/22/06, raja <raja_28 at fastmail.us> wrote:
> >
> > Dear GMXIONS,
> > I reposting the same query since not getting response for my previous
> > posting. In short
> > I am unable to restraint the ligand at its active site during
> > minimization, though I used position restrints
> > for all of the atom types of my ligand. At the end of simulation, it is
> > jumping out of active site and located
> > itself at the corner of the water box.
> >
> > Kindly provide me the solution to retain the ligand at its original
> > position during minimization step!
> >
> >
> > With thanks !
> > B.Nataraj
> >
> >
> >
> > --
> >   raja
> >   raja_28 at fastmail.us
> >
> > --
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> 
> 
> 
> --
> 
> Tsjerk A. Wassenaar, M.Sc.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
-- 
  raja
  raja_28 at fastmail.us

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