[gmx-users] Visualize Protein ligand complex

[shrikant kaushik]

Which version you are using right now. Based on that you just try this
command: eg.

$ gmx-5.1.2 trjconv -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o 1ns.pdb
-dump 1000

and select your protein-ligand complex option(22).

or

Just  you can check your complex.gro, by converting it into complex.pdb and
visualize .pdb in pymol or any visualization tools.
following command can be use:
$ gmx-5.1.2 editconf -f complex.gro -o complex.pdb

With Regards
Shri kant
M Tech (Computational Biology)
Centre for Biotechnology
Anna University, Chennai
600025

On Wed, Jul 27, 2016 at 11:33 AM, Swagata Patra <swagataliza at gmail.com>
wrote:

> Hello everyone,
>
> I simulated protein-ligand complex for 30ns and then visualize the complex
> after simulation in pymol. I used trjconv to convert .xtc file to .pb file.
> Below is the command
> trjconv_d -f md_0_1.xtc -s md_0_1.tpr -o traj.pdb -pbc mol -ur compact -dt
> 500 (select 0 system)
>
> The problem is, when I am visualizing this protein-ligand complex in pymol,
> then protein and ligand is not complexed? Why is this happening.
>
> Looking forward for your reply.
>
> --
> Swagata Patra
> M.Tech (Biotech)
> JRF
> IIT Guwahati
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