[gmx-users] Ligand is not in the same position as in PDB file

[neha bharti]

Hello All

I am trying to perform MD for protein-ligand complex in popc lipid with
charmm36 force field and also follow Justin A. Lemkul tutorial.
I downloaded the pdb structure of protein and ligand complex and the
separate the protein and ligand file and prepare the system.

Finally I perform the MD run for 100 ns, I found that the ligand is not in
the same place as present in PDB file of protein ligand complex.

Is it necessary that the protein should be in the same position as present
in protein ligand complex PDB file ??

Is there something wrong in my work.

Please Help.

Thanks and regards

Neha Bharty