[gmx-users] protein and ligand is not forming complex after completing simulation

[jkrieger at mrc-lmb.cam.ac.uk]

Your editconf command presumably looks at the final frame of the
simulation, which were stored into the .gro at the end of the run.

Your trjconv command would give you a set of frames in the pdb, which
you'd see in pymol as states. Why did you pick 30000? I'd pick a smaller
number and look at more frames. You could also do this with -skip rather
than -dt so you don't have to think in picoseconds.

If you have h-bonds throughout the simulation then they aren't
dissociating. It was just something to think about as complexes aren't
stable in real life so there's a chance they could dissociate in
simulations too. This chance is of course quite small unless you have a
very high k-off that comes into the same timescale as MD.

> For trjconv i used the following command:
>
> trjconv_d -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o trj.pdb -pbc mol -ur
> compact -dt 30000
>
> For editconf I simply used : editconf_d -f md_0_1.gro -o md_0_1.pdb
>
> I have analyzed the H-bonds between protein and ligand, there showing
> formation of H-bonds.
>
> if ligand is dissociating, what could be the reason?
>
>
> On Wed, Jul 27, 2016 at 5:40 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:
>
>> Hi Swagata,
>>
>> Perhaps your ligand is dissociating during the simulation. What frames
>> are
>> you looking at with trjconv and editconf? If these are different you may
>> be seeing bound and unbound snapshots.
>>
>> Best wishes
>> James
>>
>> > hi everyone,
>> >
>> > I  simulated protein-ligand complex for 30ns and then visualize the
>> > complex
>> > after simulation in pymol.
>> >
>> > I got the .pdb file using two commands from final simulated file.
>> > One is using trjconv, from .xtc to .pdb. When I am visualizing this
>> .pdb
>> > file, protein and ligand has not formed any complex.
>> > Another one is using editconf, from .gro to .pdb. When I am
>> visualizing
>> > this .pdb file, protein and ligand  formed  complex.
>> >
>> > Why is this happening? Can anyone explain it?
>> >
>> > Thanks in advance.
>> >
>> > --
>> > Swagata Patra
>> > M.Tech (Biotech)
>> > JRF
>> > IIT Guwahati
>> > --
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>
>
>
> --
> Swagata Patra
> M.Tech (Biotech)
> JRF
> IIT Guwahati
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
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