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

[Swagata Patra]

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