[gmx-users] Visualize Protein ligand complex

[Tsjerk Wassenaar]

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.