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

[neha bharti]

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