Hi Raja,<br>
<br>
The "protein.conf" I took from your mail.., so that is whatever you did
to get "protein.conf"! I think in your mail that was the structure
obtained from pdb2gmx combined with the ligand. And what do you mean
with the solvent box has shifted? I hoped the ligand would have
shifted. If you use the same definition for the simulation cell, it
couldn't have shifted, as it is defined from the origin, using the
orthogonal components of the box vectors (first three numbers in the
last line of the .gro file). If you meant that your ligand is now in
the center of the box, nicely surrounded by the water and your protein
is sticking out, that's ok. That was what I intended for you to obtain.
That way, your ligand won't jump when you start to run your
simulations. <br>
<br>
Hope it helps,<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;">
Dear Tsjerk Wassenaar,<br> Thanks for your reply, Following your commands I could center<br> ligand up in original position but the solvent box is shifted<br> from its center... Please recheck the command you provided for
<br> me..since you have given as "make_ndx -f protein.conf" but where<br> comes the file protein.conf in previous step.<br><br>With thanks !<br>B.Nataraj<br><br><br>On Thu, 23 Mar 2006 09:45:46 +0100, "Tsjerk Wassenaar"
<br><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> said:<br>> 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<br>> centering)
<br>> and next the system (for output)<br>> genbox -cp protein.conf -cs -o protien.solv -p protein<br>><br>> Tsjerk<br>><br>> On 3/23/06, raja <<a href="mailto:raja_28@fastmail.us">raja_28@fastmail.us
</a>> wrote:<br>> ><br>> > 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<br>> > of<br>> > > > your protein. When you place the ligand back to the gro file, it will<br>> > 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<br>> > 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<br>> > your<br>> > > > > answer. Yea I do use editconf<br>> > > > >for the purpose of renumbering ligand after pasted in original
<br>> > 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<br>> > mail
<br>> > > > >".... If you place your ligand (-s first atom)".<br>> > > > ><br>> > > > >Please mention the exact command to position the ligand in its<br>> > original
<br>> > > > >place using editconf. More I would like to add more observation ,<br>> > during<br>> > > > >the process of these preparation of protein-enzyme complex, upto<br>> > grompp
<br>> > > > >for em file, the added ligand atoms are appears to be distorted but<br>> > at<br>> > > > >the end of the energy minimization, the original molecules of ligand<br>> > 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
<br>> > will<br>> > > > >>be<br>> > > > >>mapped to a rectangular box as good as possible. For this, the first<br>> > atom<br>> > > > >>of<br>> > > > >>the molecule is used. So when a molecule happens to be sticking out
<br>> > of<br>> > > > >>the<br>> > > > >>rectangular box, or when it is just pushed over the border during<br>> > EM/PR,<br>> > > > >>it<br>> > > > >>will be mapped to the other side and it will appear to have jumped.
<br>> > If<br>> > > > >>you<br>> > > > >>place your ligand (-s first atom) in the center of the rectangular<br>> > 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<br>> > 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<br>> > 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<br>> > your<br>> > > > >>>>system<br>> > > > >>>>on the ligand before starting the simulation, which should keep it
<br>> > "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
<br>> > 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,<br>> > 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<br>> > 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<br>> > 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<br>> > 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
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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
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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> 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> - Same, same, but different�<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>