[gmx-users] Visualize Protein ligand complex

[shrikant kaushik]

How far away your ligand from protein binding pocket?
For how many ns dump (.pdb ) you checked. just try for different intervals
of time dump command ( like for 2ns, 5,ns 8ns and 10ns and so on)

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

On Wed, Jul 27, 2016 at 12:31 PM, Swagata Patra <swagataliza at gmail.com>
wrote:

> Hi shrikant,
>
> When I am using trjconv, in that .pdb file protein-ligand is not complexed.
> They are separated from each other.
>
> But when I am using editonf, in that .pdb file protein-ligand is complexed.
>
> why is this happening?
>
> On Wed, Jul 27, 2016 at 12:12 PM, Swagata Patra <swagataliza at gmail.com>
> wrote:
>
> > 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
> >
>
>
>
> --
> Swagata Patra
> M.Tech (Biotech)
> JRF
> IIT Guwahati
> --
> Gromacs Users mailing list
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