[gmx-users] Ligand moves out of box during EM steps
raja
raja_28 at fastmail.us
Thu Mar 23 15:03:34 CET 2006
Dear Tsjerk Wassenaar,
Thanks for your reply, Following your commands I could center
ligand up in original position but the solvent box is shifted
from its center... Please recheck the command you provided for
me..since you have given as "make_ndx -f protein.conf" but where
comes the file protein.conf in previous step.
With thanks !
B.Nataraj
On Thu, 23 Mar 2006 09:45:46 +0100, "Tsjerk Wassenaar"
<tsjerkw at gmail.com> said:
> 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
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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
> > > > >>>
> > > > >>>_______________________________________________
> > > > >>>gmx-users mailing list gmx-users at gromacs.org
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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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> >
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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
--
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