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

[Mark Abraham]

Hi,

Did you consult the link I provided? ;-)

Mark

On Tue, Nov 11, 2014 at 11:18 AM, neha bharti <nehabharty123 at gmail.com>
wrote:

> Thank you very much mark for your reply.
> I merge the protein and ligand file before starting the molecular dynamics
> simulation.
> Then I start the MD run.
> I don't how to  post-process the output. can you please tell me how to
> perform it or is there any article or tutorial available for that.
>
> Thanks and regards
> Neha Bharty
>
>
> >Hi,
>
> >Probably you are seeing normal behaviour in the presence of
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> <
> 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 regard
> --
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