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 > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > > 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] -- http://www.fastmail.fm - Email service worth paying for. Try it for free _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php