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

[Marlon Sidore]

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
> >>>>>>>
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> >>>>>>> posting!
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> >>>>>>>
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> >>>>>>>
> >>>>>>>
> >>>>>>
> >>>>>> --
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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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