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

raja raja_28 at fastmail.us
Thu Mar 23 06:32:02 CET 2006 

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
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> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>
> > >>>>--
> > >>>>
> > >>>>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
> > >>>
> > >>>_______________________________________________
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> > >>>
> > >>>
> > >>>
> > >>
> > >>--
> > >>
> > >>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
> > >>
> > >>
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-- 
  raja
  raja_28 at fastmail.us

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