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

[Marlon Sidore]

I had success in the past by first unwrapping the trajectory, then
centering on a portion of interest and then putting back everything in the
pbc, with something like this (based on your example commands):

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

I also had success with this protocol even with a cut down trajectory
(using trjconv -skip 1000). I also had a great number of fails when trying
to use trjconv only once, instead of 3 times like this.

Hope this helps

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 14:26 GMT+02:00 Swagata Patra <swagataliza at gmail.com>:

> So you mean to say that simulation is correct. But the problem is after
> that?
>
> On Wed, Jul 27, 2016 at 5:51 PM, Justin Lemkul <jalemkul at vt.edu> 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
> >>>> --
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> >>
> >>
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
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>
>
> --
> Swagata Patra
> M.Tech (Biotech)
> JRF
> IIT Guwahati
> --
> Gromacs Users mailing list
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