[gmx-users] Visualize Protein ligand complex

Thales Kronenberger kronenberger7 at gmail.com
Thu Jun 27 17:36:38 CEST 2013

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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