[gmx-users] Ligand moves out of box during EM steps

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Mar 23 09:45:46 CET 2006 

Raja,

Try:

pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh
>>pasting the ligand in<<
make_ndx -f protein.conf
editconf -f protein.conf -o protein.box -d 0.9
editconf -f protein.box -o protein.solv -c -n
... and select first the group corresponding to the ligand (for centering)
and next the system (for output)
genbox -cp protein.conf -cs -o protien.solv -p protein

Tsjerk

On 3/23/06, raja <raja_28 at fastmail.us> wrote:
>
> Thanks for all your suggestions, But according to David mobley, I tried
> but no effect, the ligand still
> found at the corner with its atoms are in distorted condition.
> I use these commands :
>
> >pdb2gmx -f protein.pdb -o protein.gro -p protein.top -ignh
> Where protein with its ligand cut off.
>
> later I pasted the separate gro file for ligand as produced from PRODRG
> server into the  protien.gro output from earlier command.
>
> >editconf -f protein.conf -o protein.solv -d 0.9
>
> >genbox -cp protein.conf -cs -o protien.solv -p protein
>
> Now if I visulazie the output protein.solv.gro, the ligand is separated
> and located at corner.
>
> Though  Alberto Malvezzi  suggested to use SPDBV is good idea, but I
> want to accomplish this thing using
> GROMACS commands as suggested by David mobley,since it helps me to learn
> in depth what exactly gromacs editconf and genbox doing with protein.
>
> And more the  reson why I do cut and paste the ligand in between pdb2gmx
> commands is the lack of RTP entry for my ligand is not updated in
> ffoplsa.rtp file. Simulatenusly I also work on building the proper RTP
> entry for the ligand of my interst. Right now I managed to produced ITP
> file for the ligand by PRODRG. Help is sorted from any of you as a
> script which make RTP format for ligand from its ITP file.
>
> With thanks !
> B.Nataraj
>
>
>
> On Wed, 22 Mar 2006 07:57:29 -0800, "David Mobley" <dmobley at gmail.com>
> said:
> > If I remember correctly, the place where the coordinates of the
> > protein get changed is the step involving genbox (or editconf), where
> > it is translated to the center of the box. So an alternative approach
> > to Alberto's suggestion is to combine the protein and the ligand
> > *before* using editconf/genbox (but after doing pdb2gmx); I think then
> > the ligand will still be placed correctly relative to the protein. I
> > was using this approach at one point, with the additional benefit that
> > you don't have to edit the coordinates using some other program.
> >
> > David
> >
> >
> > On 3/22/06, Alberto Malvezzi <malvezzi at iq.usp.br> wrote:
> > > Hi Nataraj,
> > > this happened to me also.
> > > When you make an energy minimization, gromacs alters the coordinates
> of
> > > your protein. When you place the ligand back to the gro file, it will
> be
> > > placed far from its site. To solve this problem I take the original
> > > complex and fit it to the minimized protein (using DeepView or any
> other
> > > program like Whatif, for example), then save only the ligand of the
> > > complex and use these new coordinates to feed the gro file of the
> > > minimized protein.
> > > Hope I understood your problem.
> > > All the best
> > > Alberto
> > >
> > > raja wrote:
> > >
> > > >Dear Tsjerk,
> > > >          Thanks for your prompt replies, But please bit elaborate
> your
> > > >          answer. Yea I do use editconf
> > > >for the purpose of  renumbering ligand after pasted in original
> protein
> > > >gro file produed by pdb2gmx step (as per my previous mail). But where
> > > >come the option of -s in ediconf as you mentioned in your earlier
> mail
> > > >".... If you place your ligand (-s first atom)".
> > > >
> > > >Please mention the exact command to position the ligand in its
> original
> > > >place using editconf. More I would like to add more observation ,
> during
> > > >the process of these preparation of protein-enzyme complex, upto
> grompp
> > > >for em file, the added ligand atoms are appears to be distorted but
> at
> > > >the end of the energy minimization, the original molecules of ligand
> is
> > > >restored.(may be this is not my concern rightnow,so please give me
> > > >elaborate command to position the ligand in its active site)
> > > >
> > > >With thanks !
> > > >B.Nataraj
> > > >
> > > >
> > > >On Wed, 22 Mar 2006 14:31:42 +0100, "Tsjerk Wassenaar"
> > > ><tsjerkw at gmail.com> said:
> > > >
> > > >
> > > >>Hi Raja,
> > > >>
> > > >>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.
> > > >>
> > > >>Cheers,
> > > >>
> > > >>Tsjerk
> > > >>
> > > >>On 3/22/06, raja <raja_28 at fastmail.us> wrote:
> > > >>
> > > >>
> > > >>>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"
> > > >>><tsjerkw at gmail.com> 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 <raja_28 at fastmail.us> 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
> > > >>>>>  raja_28 at fastmail.us
> > > >>>>>
> > > >>>>>--
> > > >>>>>http://www.fastmail.fm - Email service worth paying for. Try it
> for
> > > >>>>>
> > > >>>>>
> > > >>>free
> > > >>>
> > > >>>
> > > >>>>>_______________________________________________
> > > >>>>>gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> > > >>>>>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
> > > >>>  raja_28 at fastmail.us
> > > >>>
> > > >>>--
> > > >>>http://www.fastmail.fm - Email service worth paying for. Try it for
> free
> > > >>>
> > > >>>_______________________________________________
> > > >>>gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> > > >>>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
> > > >>
> > > >>
> > > _______________________________________________
> > > gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > >
> > _______________________________________________
> > gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> --
>   raja
>   raja_28 at fastmail.us
>
> --
> http://www.fastmail.fm - I mean, what is it about a decent email service?
>
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060323/01d54f93/attachment.html>

More information about the gromacs.org_gmx-users mailing list