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

raja raja_28 at fastmail.us
Fri Mar 24 05:07:10 CET 2006


Dear Tsjerk ,
Thanks for your reply. Now I could retain the ligand in active site upto
the stage of solvating it in the water box. Now to add counter ions, I
run grompp and later added 10 Na+ counter ion to neutralize system using
genion. At the output of genion, the ligand moved out to the corner, not
only moved out , its atoms are distorted, If I tried to minimize at the
same state , the whole system got minimized and ligand also restored to
its original state(which mean bonds are all formed between the atoms). 

Now tell me whether those newly added counter ion will make a effect of
this behaviour of shifting ligand to corner. 
And more is it right to neutralize the system without inclusion of
ligand charge( Since ligand was not the part of the system while I was
computing the charge of the system in pdb2gmx step). 

With thanks !
B.Natatraj 

On Thu, 23 Mar 2006 22:57:07 +0100, "Tsjerk Wassenaar"
<tsjerkw at gmail.com> said:
> Hi Raja,
> 
> 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.
> 
> Hope it helps,
> 
> Tsjerk
> 
> On 3/23/06, raja <raja_28 at fastmail.us> wrote:
> >
> > 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
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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
> > > > > > >>>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
> > > > > > >>
> > > > > > >>
> > > > > > _______________________________________________
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> > > > --
> > > >   raja
> > > >   raja_28 at fastmail.us
> > > >
> > > > --
> > > > http://www.fastmail.fm - I mean, what is it about a decent email
> > service?
> > > >
> > > > _______________________________________________
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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 - Same, same, but different&#65533;
> >
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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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