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

[Justin Lemkul]

On 7/27/16 8:26 AM, Swagata Patra wrote:
> So you mean to say that simulation is correct. But the problem is after
> that?
>

You need to prove that yourself by properly using trjconv to account for the 
periodicity effects so you know that what you are seeing is the real physical 
behavior.

-Justin

> 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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>
>
>

-- 
==================================================

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

==================================================