[gmx-users] How to check protein-ligand interaction pattern after completing simulaation.

[Justin Lemkul]

On 7/26/16 10:46 AM, Swagata Patra wrote:
> Ok.
>
> I have one more doubt. I used editconf to converge the md_0_1.gro file to
> md_0_1.pdb file. So when I am looking into the .pdb file, the
> protein-ligand complex reached below the solvated box. Why did this happen?
>
>

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

>
> On Tue, Jul 26, 2016 at 8:15 PM, Swagata Patra <swagataliza at gmail.com>
> wrote:
>
>> Ok.
>>
>> I have one more doubt. I used editconf to converge the md_0_1.gro file to
>> md_0_1.pdb file. So when I am looking into the .pdb file, the
>> protein-ligand complex reached below the solvated box. Why did this happen?
>>
>> I am also attaching the md_0_1.pdb file file.
>>
>> On Tue, Jul 26, 2016 at 8:05 PM, Swagata Patra <swagataliza at gmail.com>
>> wrote:
>>
>>> Ok.
>>>
>>> I have one more doubt. I used editconf to converge the md_0_1.gro file to
>>> md_0_1.pdb file. So when I am looking into the .pdb file, the
>>> protein-ligand complex reached below the solvated box. Why did this happen?
>>>
>>> I am also attaching the md_0_1.pdb file and em.pdb file.
>>>
>>> On Tue, Jul 26, 2016 at 7:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>>
>>>>
>>>> On 7/26/16 10:24 AM, Swagata Patra wrote:
>>>>
>>>>> Thank you Justin for your reply. I already analysed RMSD, RMSF, gyration
>>>>> and no of H bonds using your tutorial.
>>>>>
>>>>> Actually I had gone through some paper where they mention this thing
>>>>> (same
>>>>> interaction pattern between docking result and simulation). That's why I
>>>>> wanted to know.
>>>>>
>>>>> So, are RMSD, RMSF, gyration and No. of H bonds enough to describe the
>>>>> protein-ligand simulation.
>>>>>
>>>>>
>>>> The analysis section of my tutorial is intended to give the reader a
>>>> feel for the generic syntax of GROMACS analysis commands (as is the purpose
>>>> of the tutorial).  It is not intended to be necessarily useful or valid for
>>>> approaching scientific questions.
>>>>
>>>> RMSD, in general, tells you little.  RMSF is only meaningful if you're
>>>> looking at whether or not the ligand modulates the flexibility of parts of
>>>> your protein.  Radius of gyration is useless for a folded protein.
>>>> Hydrogen bonds are useful if that type of interaction is present and
>>>> functionally meaningful in your simulation; if the ligand is hydrophobic it
>>>> may not be appropriate.
>>>>
>>>> There is no recipe for analysis.  You should have decided on what you
>>>> wanted to examine long before you even started the simulation, because only
>>>> with those questions in mind will you be able to determine if the
>>>> simulation is converged, if you are appropriately addressing your
>>>> underlying goal(s), etc.
>>>>
>>>> -Justin
>>>>
>>>>
>>>> On Tue, Jul 26, 2016 at 7:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>
>>>>>
>>>>>>
>>>>>> On 7/26/16 10:04 AM, Swagata Patra wrote:
>>>>>>
>>>>>> Hello Everyone,
>>>>>>>
>>>>>>> I am a very new Gromacs user. I have completed the protein-ligand
>>>>>>> simulation. I want to get the protein-ligand interaction using PyMol.
>>>>>>> I
>>>>>>> used editconf to convert the final .gro file to .pdb file. But when I
>>>>>>> am
>>>>>>> checking that .pdb file in pymol it is showing different interaction
>>>>>>> pattern from the interaction pattern that i got from docking study.
>>>>>>>
>>>>>>> So my question is, is it the right way to get the protein-ligand
>>>>>>> interaction pattern. If yes, then why  I am getting different
>>>>>>> interaction
>>>>>>> pattern in docking and simulation.
>>>>>>>
>>>>>>>
>>>>>>> I would not expect a docking and MD result to be the same; MD includes
>>>>>> solvation effects and dynamics whereas docking is in vacuo and largely
>>>>>> rigid.
>>>>>>
>>>>>> Moreover, simply looking at the final snapshot of the MD is not enough;
>>>>>> you've got a whole trajectory worth of information and that's the whole
>>>>>> point of MD. The final snapshot may not even be representative of what
>>>>>> occurred during the MD.
>>>>>>
>>>>>> Use the large suite of tools that GROMACS provides to get insight as to
>>>>>> what happened during the MD and how it can help you answer whatever
>>>>>> scientific question(s) you have.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>> --
>>>>>> ==================================================
>>>>>>
>>>>>> 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
>>>>>>
>>>>>> ==================================================
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
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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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>>>> Gromacs Users mailing list
>>>>
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>>>
>>>
>>>
>>> --
>>> Swagata Patra
>>> M.Tech (Biotech)
>>> JRF
>>> IIT Guwahati
>>>
>>
>>
>>
>> --
>> Swagata Patra
>> M.Tech (Biotech)
>> JRF
>> IIT Guwahati
>>
>
>
>

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

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

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