[gmx-users] Visualize Protein ligand complex

[Thales Kronenberger]

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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>