[gmx-users] Visualize Protein ligand complex

[Swagata Patra]

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