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

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

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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