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

Tue Jul 26 16:53:46 CEST 2016

Thank you very much Justin for clearing my doubt. So is it acceptable if I
use the interaction pattern from md_0_1.pdb using pymol.

On Tue, Jul 26, 2016 at 8:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
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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
>
> ==================================================
> --
> Gromacs Users mailing list
>
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-- 
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati