[gmx-users] protein and ligand is not forming complex after completing simulation

[Swagata Patra]

thank you James and Felipe for your suggestion. It really helped me a lot
to understand the situation.
I am trying to resolve the problem.

On Wed, Jul 27, 2016 at 6:00 PM, Felipe Merino <
felipe.merino at mpi-dortmund.mpg.de> wrote:

> Hey,
>
> Of course you can always use VMD, for example, to check several adjacent
> copies of the simulation cell in order to see if your problem is PBC or not.
>
> Felipe
>
>
> On 27/07/16 14:21, Justin Lemkul wrote:
>
>>
>>
>> On 7/27/16 8:18 AM, Swagata Patra wrote:
>>
>>> For trjconv i used the following command:
>>>
>>> trjconv_d -s md_0_1.tpr -f md_0_1.xtc -n index.ndx -o trj.pdb -pbc mol
>>> -ur
>>> compact -dt 30000
>>>
>>>
>> The PBC fitting routines sometimes struggle with large -dt. You're
>> basically just trying to dump out the final frame, which is redundant with
>> what you're doing below.  If you want to obtain a PBC-corrected trajectory,
>> follow the link I provided.
>>
>> For editconf I simply used : editconf_d -f md_0_1.gro -o md_0_1.pdb
>>>
>>> I have analyzed the H-bonds between protein and ligand, there showing
>>> formation of H-bonds.
>>>
>>> if ligand is dissociating, what could be the reason?
>>>
>>>
>> Bad topology, incorrect run settings, etc.  But from the simple matter of
>> disagreement above, I doubt there's actually a problem. Nearly always,
>> "dissociation" is just a PBC issue that needs to be handled carefully.
>>
>> -Justin
>>
>>
>>> On Wed, Jul 27, 2016 at 5:40 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:
>>>
>>> Hi Swagata,
>>>>
>>>> Perhaps your ligand is dissociating during the simulation. What frames
>>>> are
>>>> you looking at with trjconv and editconf? If these are different you may
>>>> be seeing bound and unbound snapshots.
>>>>
>>>> Best wishes
>>>> James
>>>>
>>>> hi everyone,
>>>>>
>>>>> I  simulated protein-ligand complex for 30ns and then visualize the
>>>>> complex
>>>>> after simulation in pymol.
>>>>>
>>>>> I got the .pdb file using two commands from final simulated file.
>>>>> One is using trjconv, from .xtc to .pdb. When I am visualizing this
>>>>> .pdb
>>>>> file, protein and ligand has not formed any complex.
>>>>> Another one is using editconf, from .gro to .pdb. When I am visualizing
>>>>> this .pdb file, protein and ligand  formed  complex.
>>>>>
>>>>> Why is this happening? Can anyone explain it?
>>>>>
>>>>> Thanks in advance.
>>>>>
>>>>> --
>>>>> Swagata Patra
>>>>> M.Tech (Biotech)
>>>>> JRF
>>>>> IIT Guwahati
>>>>> --
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>>>
>>>
>>
> --
> Felipe Merino
> Max Planck Institute for Molecular Physiology
> Department of Structural Biochemistry
> Otto-Hahn-Str. 11
> 44227 Dortmund
> Phone: +49 231 133 2315
>
>
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-- 
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati