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

[Mark Abraham]

Hi,

Probably you are seeing normal behaviour in the presence of
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions.
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.

Mark

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

> 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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