[gmx-users] protein and ligand is not forming complex after completing simulation

[Swagata Patra]

so when the program ask to select a group, what should i select? system or
protein for the first command?

What should I select for the second command? they are asking for selecting
2 groups.

On Wed, Jul 27, 2016 at 8:45 PM, Marlon Sidore <marlon.sidore at gmail.com>
wrote:

> Sorry I just realized I copypasted the -o without noticing it was a pdb.
> You'll want use the output of each command (a .xtc) as input for each
> following command. You also probably don't need the index file with -n.
>
> trjconv_d -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o trj0.xtc -pbc nojump
>
> trjconv_d -s md_0_1.tpr -f trj0.xtc -n index.ndx -o trj1.xtc -center [[Here
> center on your protein for example]]
>
> trjconv_d -s md_0_1.tpr -f trj1.xtc -n index.ndx -o trj2.xtc -pbc mol
>
> Marlon Sidore
>
>
> PhD Student
> Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
> CNRS - UMR7255
> 31, Chemin Joseph Aiguier
> 13402 cedex 20 Marseille
> France
>
>
> 2016-07-27 16:46 GMT+02:00 Swagata Patra <swagataliza at gmail.com>:
>
> > Hi Marlon.
> > The commands that you gave
> > trjconv_d -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o trj0.pdb -pbc
> nojump
> >
> > trjconv_d -s md_0_1.tpr -f trj0.xtc -n index.ndx -o trj1.pdb -center
> [[Here
> > center on your protein for example]]
> >
> > trjconv_d -s md_0_1.tpr -f trj1.xtc -n index.ndx -o trj2.pdb -pbc mol
> >
> > From where will get trj0.xtc file?
> >
> > On Wed, Jul 27, 2016 at 7:30 PM, Swagata Patra <swagataliza at gmail.com>
> > wrote:
> >
> > > Thank you Marlon for your suggestion. It really helped a lot.
> > >
> > > On Wed, Jul 27, 2016 at 7:28 PM, Swagata Patra <swagataliza at gmail.com>
> > > wrote:
> > >
> > >> thank you James and Felipe for your suggestion. It really helped me a
> > >> lot to understand the situation.
> > >> I am trying to resolve the problem.
> > >>
> > >> On Wed, Jul 27, 2016 at 6:00 PM, Felipe Merino <
> > >> felipe.merino at mpi-dortmund.mpg.de> wrote:
> > >>
> > >>> Hey,
> > >>>
> > >>> Of course you can always use VMD, for example, to check several
> > adjacent
> > >>> copies of the simulation cell in order to see if your problem is PBC
> > or not.
> > >>>
> > >>> Felipe
> > >>>
> > >>>
> > >>> On 27/07/16 14:21, Justin Lemkul wrote:
> > >>>
> > >>>>
> > >>>>
> > >>>> On 7/27/16 8:18 AM, Swagata Patra wrote:
> > >>>>
> > >>>>> For trjconv i used the following command:
> > >>>>>
> > >>>>> trjconv_d -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o trj.pdb -pbc
> > mol
> > >>>>> -ur
> > >>>>> compact -dt 30000
> > >>>>>
> > >>>>>
> > >>>> The PBC fitting routines sometimes struggle with large -dt. You're
> > >>>> basically just trying to dump out the final frame, which is
> redundant
> > with
> > >>>> what you're doing below.  If you want to obtain a PBC-corrected
> > trajectory,
> > >>>> follow the link I provided.
> > >>>>
> > >>>> For editconf I simply used : editconf_d -f md_0_1.gro -o md_0_1.pdb
> > >>>>>
> > >>>>> I have analyzed the H-bonds between protein and ligand, there
> showing
> > >>>>> formation of H-bonds.
> > >>>>>
> > >>>>> if ligand is dissociating, what could be the reason?
> > >>>>>
> > >>>>>
> > >>>> Bad topology, incorrect run settings, etc.  But from the simple
> matter
> > >>>> of disagreement above, I doubt there's actually a problem. Nearly
> > always,
> > >>>> "dissociation" is just a PBC issue that needs to be handled
> carefully.
> > >>>>
> > >>>> -Justin
> > >>>>
> > >>>>
> > >>>>> On Wed, Jul 27, 2016 at 5:40 PM, <jkrieger at mrc-lmb.cam.ac.uk>
> wrote:
> > >>>>>
> > >>>>> Hi Swagata,
> > >>>>>>
> > >>>>>> Perhaps your ligand is dissociating during the simulation. What
> > >>>>>> frames are
> > >>>>>> you looking at with trjconv and editconf? If these are different
> you
> > >>>>>> may
> > >>>>>> be seeing bound and unbound snapshots.
> > >>>>>>
> > >>>>>> Best wishes
> > >>>>>> James
> > >>>>>>
> > >>>>>> hi everyone,
> > >>>>>>>
> > >>>>>>> I  simulated protein-ligand complex for 30ns and then visualize
> the
> > >>>>>>> complex
> > >>>>>>> after simulation in pymol.
> > >>>>>>>
> > >>>>>>> I got the .pdb file using two commands from final simulated file.
> > >>>>>>> One is using trjconv, from .xtc to .pdb. When I am visualizing
> this
> > >>>>>>> .pdb
> > >>>>>>> file, protein and ligand has not formed any complex.
> > >>>>>>> Another one is using editconf, from .gro to .pdb. When I am
> > >>>>>>> visualizing
> > >>>>>>> this .pdb file, protein and ligand  formed  complex.
> > >>>>>>>
> > >>>>>>> Why is this happening? Can anyone explain it?
> > >>>>>>>
> > >>>>>>> Thanks in advance.
> > >>>>>>>
> > >>>>>>> --
> > >>>>>>> Swagata Patra
> > >>>>>>> M.Tech (Biotech)
> > >>>>>>> JRF
> > >>>>>>> IIT Guwahati
> > >>>>>>> --
> > >>>>>>> Gromacs Users mailing list
> > >>>>>>>
> > >>>>>>> * Please search the archive at
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> before
> > >>>>>>> posting!
> > >>>>>>>
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> > >>>>>>>
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> > >>>>>>> or
> > >>>>>>>
> > >>>>>> send
> > >>>>>>
> > >>>>>>> a mail to gmx-users-request at gromacs.org.
> > >>>>>>>
> > >>>>>>>
> > >>>>>>
> > >>>>>> --
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> > >>>>>>
> > >>>>>>
> > >>>>>
> > >>>>>
> > >>>>>
> > >>>>
> > >>> --
> > >>> Felipe Merino
> > >>> Max Planck Institute for Molecular Physiology
> > >>> Department of Structural Biochemistry
> > >>> Otto-Hahn-Str. 11
> > >>> 44227 Dortmund
> > >>> Phone: +49 231 133 2315
> > >>>
> > >>>
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> > >>>
> > >>
> > >>
> > >>
> > >> --
> > >> Swagata Patra
> > >> M.Tech (Biotech)
> > >> JRF
> > >> IIT Guwahati
> > >>
> > >
> > >
> > >
> > > --
> > > Swagata Patra
> > > M.Tech (Biotech)
> > > JRF
> > > IIT Guwahati
> > >
> >
> >
> >
> > --
> > Swagata Patra
> > M.Tech (Biotech)
> > JRF
> > IIT Guwahati
> > --
> > Gromacs Users mailing list
> >
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-- 
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati