[gmx-users] Visualize Protein ligand complex

[Sainitin Donakonda]

Hi Tsjerk,

Thanks for information i limited number of frames ..which worked perfectly
:)

Cheers,
Sainitin


On Thu, Jun 27, 2013 at 8:06 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Sainitin,
>
> You can extract only the protein and ligand, using a suitable index file,
> or you can limit the number of frames.
>
> Cheers,
>
> Tsjerk
>
>
> On Thu, Jun 27, 2013 at 5:36 PM, Thales Kronenberger <
> kronenberger7 at gmail.com> wrote:
>
> > Don't you wanna try to use the VMD
> >
> > use vmd xxx.gro yyy.trr and then you could highlight your ligand
> >
> >
> >
> >
> > 2013/6/27 Sainitin Donakonda <saigro16 at gmail.com>
> >
> > > Hi,
> > >
> > > I simulated protein ligand complex for 20 ns  now i want to visualize
> > this
> > > complex after simulation in pymol.To look ligand interactions with
> > protein
> > > binding site
> > >
> > > I tried trjconv to convert .xtc trajectory to .pdb but xtc file is too
> > huge
> > > with solvent molecules so pymol couldnot visualize complex
> > >
> > > Can anybody tell me command how to visualize protein ligand complex
> > > trajectory in pymol
> > >
> > > Thanks,
> > > Sainitin
> > > --
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
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