<br>
Hi Raja,<br>
<br>
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".<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 3/22/06, <b class="gmail_sendername">raja</b> <<a href="mailto:raja_28@fastmail.us">raja_28@fastmail.us</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear GMXIONS,<br>I reposting the same query since not getting response for my previous<br>posting. In short<br>I am unable to restraint the ligand at its active site during<br>minimization, though I used position restrints
<br>for all of the atom types of my ligand. At the end of simulation, it is<br>jumping out of active site and located<br>itself at the corner of the water box.<br><br>Kindly provide me the solution to retain the ligand at its original
<br>position during minimization step!<br><br><br>With thanks !<br>B.Nataraj<br><br><br><br>--<br> raja<br> <a href="mailto:raja_28@fastmail.us">raja_28@fastmail.us</a><br><br>--<br><a href="http://www.fastmail.fm">http://www.fastmail.fm
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Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>