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

[Felipe Merino]

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