[gmx-users] Visualize Protein ligand complex

[Swagata Patra]

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