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

[Swagata Patra]

So you mean to say that simulation is correct. But the problem is after
that?

On Wed, Jul 27, 2016 at 5:51 PM, Justin Lemkul <jalemkul at vt.edu> 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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>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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-- 
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati