[gmx-users] How to check protein-ligand interaction pattern after completing simulaation.

[Swagata Patra]

Hello Everyone,

I am a very new Gromacs user. I have completed the protein-ligand
simulation. I want to get the protein-ligand interaction using PyMol. I
used editconf to convert the final .gro file to .pdb file. But when I am
checking that .pdb file in pymol it is showing different interaction
pattern from the interaction pattern that i got from docking study.

So my question is, is it the right way to get the protein-ligand
interaction pattern. If yes, then why  I am getting different interaction
pattern in docking and simulation.

Looking forward for your reply

-- 
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati