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

[Swagata Patra]

Thank you Marlon for your suggestion. It really helped a lot.

On Wed, Jul 27, 2016 at 7:28 PM, Swagata Patra <swagataliza at gmail.com>
wrote:

> 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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>>>>>
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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
>



-- 
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati