<br>Hi Raja,<br><br>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.
<br><br>Cheers,<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 Tsjerk,<br> Thanks for your reply. But I have not gone to the stage of<br> dynamics yet. I am still struck at energy minimization. Now<br> atleast I could reason out why it happens, but I dont know how
<br> to stop it. The reason is everytime<br>when I convert ligand-enzyme complex using pdb2gmx, I trim off the<br>ligand and convert the protein part alone, later I<br>paste the drug molecule in the resultant file. I suspect that could be
<br>the problem,so I try to fix it by myself.<br><br>With thanks !<br>B.Nataraj<br>On Wed, 22 Mar 2006 07:54:05 +0100, "Tsjerk Wassenaar"<br><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> said:
<br>> Hi Raja,<br>><br>> Probably PBC. Nothing wrong, just visual. You can try to center your<br>> system<br>> on the ligand before starting the simulation, which should keep it "in<br>> place".
<br>><br>> Tsjerk<br>><br>> On 3/22/06, raja <<a href="mailto:raja_28@fastmail.us">raja_28@fastmail.us</a>> wrote:<br>> ><br>> > 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</a> - Email service worth paying for. Try it for free<br>> ><br>> > _______________________________________________
<br>> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> > <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users
</a><br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> > Can't post? Read
<a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>> ><br>><br>><br>><br>> --<br>><br>> Tsjerk A. Wassenaar, M.Sc.<br>> 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>--<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</a> - Email service worth paying for. Try it for free<br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote>
</div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>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>