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

[Swagata Patra]

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?



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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
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>>
>>
>>
>> --
>> Swagata Patra
>> M.Tech (Biotech)
>> JRF
>> IIT Guwahati
>>
>
>
>
> --
> Swagata Patra
> M.Tech (Biotech)
> JRF
> IIT Guwahati
>



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