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

neha bharti nehabharty123 at gmail.com
Tue Nov 11 11:18:52 CET 2014

Thank you very much mark for your reply.
I merge the protein and ligand file before starting the molecular dynamics
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


>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
>> 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
>> in protein ligand complex PDB file ??
>> Is there something wrong in my work.
>> Please Help.
>>Thanks and regard

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