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
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raja
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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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