[gmx-users] Visualize Protein ligand complex

[Swagata Patra]

Thank you so much shrikant. I am trying to do this. If I face any problem I
ll let you know.

On Wed, Jul 27, 2016 at 12:03 PM, shrikant kaushik <
shrikant92pharmacy at gmail.com> wrote:

> 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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-- 
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati