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 <[EMAIL PROTECTED]> 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"
<[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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
> > [EMAIL PROTECTED]
> >
> > --
> > 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
[EMAIL PROTECTED]
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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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