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

[Tsjerk Wassenaar]

Hi Raja,

When you generate a .tpr file (for whatever purpose) all molecules will be
mapped to a rectangular box as good as possible. For this, the first atom of
the molecule is used. So when a molecule happens to be sticking out of the
rectangular box, or when it is just pushed over the border during EM/PR, it
will be mapped to the other side and it will appear to have jumped. If you
place your ligand (-s first atom) in the center of the rectangular box
(editconf -c), it will stay there during EM/PR.

Cheers,

Tsjerk

On 3/22/06, raja <raja_28 at fastmail.us> wrote:
>
> 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
> > >
> > > --
> > > http://www.fastmail.fm - Email service worth paying for. Try it for
> free
> > >
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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
>
> --
> http://www.fastmail.fm - Email service worth paying for. Try it for free
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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
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