Raja,<br><br>Try:<br><br>pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh<br>>>pasting the ligand in<<<br>make_ndx -f protein.conf<br>editconf -f protein.conf -o protein.box -d 0.9<br>editconf -f protein.box
-o protein.solv -c -n <br>... and select first the group corresponding to the ligand (for centering) and next the system (for output)<br>genbox -cp protein.conf -cs -o protien.solv -p protein<br><br>Tsjerk<br><br><div><span class="gmail_quote">
On 3/23/06, <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;">
Thanks for all your suggestions, But according to David mobley, I tried<br>but no effect, the ligand still<br>found at the corner with its atoms are in distorted condition.<br>I use these commands :<br><br>>pdb2gmx -f
protein.pdb -o protein.gro -p protein.top -ignh<br>Where protein with its ligand cut off.<br><br>later I pasted the separate gro file for ligand as produced from PRODRG<br>server into the protien.gro output from earlier command.
<br><br>>editconf -f protein.conf -o protein.solv -d 0.9<br><br>>genbox -cp protein.conf -cs -o protien.solv -p protein<br><br>Now if I visulazie the output protein.solv.gro, the ligand is separated<br>and located at corner.
<br><br>Though Alberto Malvezzi suggested to use SPDBV is good idea, but I<br>want to accomplish this thing using<br>GROMACS commands as suggested by David mobley,since it helps me to learn<br>in depth what exactly gromacs editconf and genbox doing with protein.
<br><br>And more the reson why I do cut and paste the ligand in between pdb2gmx<br>commands is the lack of RTP entry for my ligand is not updated in<br>ffoplsa.rtp file. Simulatenusly I also work on building the proper RTP
<br>entry for the ligand of my interst. Right now I managed to produced ITP<br>file for the ligand by PRODRG. Help is sorted from any of you as a<br>script which make RTP format for ligand from its ITP file.<br><br>With thanks !
<br>B.Nataraj<br><br><br><br>On Wed, 22 Mar 2006 07:57:29 -0800, "David Mobley" <<a href="mailto:dmobley@gmail.com">dmobley@gmail.com</a>><br>said:<br>> If I remember correctly, the place where the coordinates of the
<br>> protein get changed is the step involving genbox (or editconf), where<br>> it is translated to the center of the box. So an alternative approach<br>> to Alberto's suggestion is to combine the protein and the ligand
<br>> *before* using editconf/genbox (but after doing pdb2gmx); I think then<br>> the ligand will still be placed correctly relative to the protein. I<br>> was using this approach at one point, with the additional benefit that
<br>> you don't have to edit the coordinates using some other program.<br>><br>> David<br>><br>><br>> On 3/22/06, Alberto Malvezzi <<a href="mailto:malvezzi@iq.usp.br">malvezzi@iq.usp.br</a>> wrote:
<br>> > 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
<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>> > 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>> 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> 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> - I mean, what is it about a decent email service?<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>