[gmx-users] Visualize Protein ligand complex

[shrikant kaushik]

You have done for 30ns. do you have single .xtc or trr; so use following
command:

trjconv_d -s npt.tpr -f md_30ns.xtc -n index.ndx -o trj.pdb -pbc mol -ur
compact -dt 500
or
if you have extended different simulation file (in parts)first concatenate
it:
$gmx-4.5.6 trjcat -f md_0_1.xtc md_0_5.xtc md_0_10.xtc ... -o final.xtc

It is not necessary, but it (-pbc) prevents your complex to go away or out
of from your virtual box. So just try with it or as you wish !

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

On Wed, Jul 27, 2016 at 12:52 PM, Swagata Patra <swagataliza at gmail.com>
wrote:

> 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
> > > >> > --
> > > >> > Gromacs Users mailing list
> > > >> >
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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
> --
> Gromacs Users mailing list
>
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