Hi Raja,<br><br>I meant your "ligand" or "ligands first atom". Sorry for the confusion there.<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 3/22/06, <b class="gmail_sendername">Alberto Malvezzi
</b> <<a href="mailto:malvezzi@iq.usp.br">malvezzi@iq.usp.br</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;">Hi Nataraj,
<br>this happened to me also.<br>When you make an energy minimization, gromacs alters the coordinates of<br>your protein. When you place the ligand back to the gro file, it will be<br>placed far from its site. To solve this problem I take the original
<br>complex and fit it to the minimized protein (using DeepView or any other<br>program like Whatif, for example), then save only the ligand of the<br>complex and use these new coordinates to feed the gro file of the<br>minimized protein.
<br>Hope I understood your problem.<br>All the best<br>Alberto<br><br>raja wrote:<br><br>>Dear Tsjerk,<br>> Thanks for your prompt replies, But please bit elaborate your<br>> answer. Yea I do use editconf
<br>>for the purpose of renumbering ligand after pasted in original protein<br>>gro file produed by pdb2gmx step (as per my previous mail). But where<br>>come the option of -s in ediconf as you mentioned in your earlier mail
<br>>".... If you place your ligand (-s first atom)".<br>><br>>Please mention the exact command to position the ligand in its original<br>>place using editconf. More I would like to add more observation , during
<br>>the process of these preparation of protein-enzyme complex, upto grompp<br>>for em file, the added ligand atoms are appears to be distorted but at<br>>the end of the energy minimization, the original molecules of ligand is
<br>>restored.(may be this is not my concern rightnow,so please give me<br>>elaborate command to position the ligand in its active site)<br>><br>>With thanks !<br>>B.Nataraj<br>><br>><br>>On Wed, 22 Mar 2006 14:31:42 +0100, "Tsjerk Wassenaar"
<br>><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> said:<br>><br>><br>>>Hi Raja,<br>>><br>>>When you generate a .tpr file (for whatever purpose) all molecules will<br>>>be
<br>>>mapped to a rectangular box as good as possible. For this, the first atom<br>>>of<br>>>the molecule is used. So when a molecule happens to be sticking out of<br>>>the<br>>>rectangular box, or when it is just pushed over the border during EM/PR,
<br>>>it<br>>>will be mapped to the other side and it will appear to have jumped. If<br>>>you<br>>>place your ligand (-s first atom) in the center of the rectangular box<br>>>(editconf -c), it will stay there during EM/PR.
<br>>><br>>>Cheers,<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>>><br>>>>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>>>><br>>>><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>>>>><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
<br>>>>>><br>>>>>><br>>>>is<br>>>><br>>>><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
<br>>>>>><br>>>>>><br>>>>free<br>>>><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>>>>><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
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</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>>><br>_______________________________________________<br>gmx-users mailing list
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</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>