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

[Tsjerk Wassenaar]

Hi Raja,

I meant your "ligand"  or "ligands first atom". Sorry for the confusion
there.

Tsjerk

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
> >>>
> >>>
> >>>>>_______________________________________________
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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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>



--

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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