[gmx-users] Visualize Protein ligand complex

[Swagata Patra]

trjconv_d -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o trj.pdb -pbc mol -ur
compact -dt 500


Is above command ok? I am using gromacs 4.5.6

is it necessary to use -pbc?


On Wed, Jul 27, 2016 at 12:47 PM, shrikant kaushik <
shrikant92pharmacy at gmail.com> wrote:

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