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

Mark Abraham mark.j.abraham at gmail.com
Tue Nov 11 10:11:22 CET 2014


Probably you are seeing normal behaviour in the presence of
If you want to visualize the protein and ligand as a complex, you need to
post-process the output accordingly. mdrun doesn't know that you plan to
treat them as special.


On Tue, Nov 11, 2014 at 9:50 AM, neha bharti <nehabharty123 at gmail.com>

> 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
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