[gmx-users] Protein Ligand Interaction or Docking using Gromacs

[bipin singh]

A reference:

http://pubs.acs.org/doi/abs/10.1021/jz301635h


On Wed, Apr 23, 2014 at 1:54 PM, andrea <andrea.spitaleri at iit.it> wrote:

> Brute force is one solution (long simulation).
> You can have look to "accelerated MD" or "rare event MD" in pubmed. You
> will find that docking a ligand onto the receptor by MD is feasible using
> new strategies based (i.e. metadynamics with plumed plugin in gromacs)
>
> cheers
>
> and
>
>
> On 23/04/2014 10:14, ms wrote:
>
>> On 4/23/14 9:55 AM, neha_bharty wrote:
>>
>>> Hello
>>>
>>> I want to find the protein ligand interaction using gromacs.
>>> Is it possible to perform protein-ligand docking with the help of
>>> gromacs or
>>> I have to dock the protein and ligand with some tools like autodock and
>>> then
>>> only I can view its interaction using gromacs??
>>>
>> In theory it is possible to put the ligand in solution and wait for it to
>> attach to the protein, in a molecular dynamics simulation. However in
>> practice this is almost impossible unless you are going to do very, *very*
>> huge simulations. The group of David Shaw did that with his custom Anton
>> hardware (and Desmond, not Gromacs): http://www.pnas.org/content/
>> 108/32/13118.long
>>
>> So, the *practical* answer would be: yes, usually you need to dock the
>> ligand first in some reasonable binding pose. You can use "classical"
>> Autodock, VINA/Idock or even better HADDOCK to do that.
>>
>>
>>> Is there any tutorial to perform Protein - ligand interaction or docking
>>> using gromacs??
>>>
>> Google is your friend. http://www.bevanlab.biochem.
>> vt.edu/Pages/Personal/justin/gmx-tutorials/complex/
>>
>>  which force field or time steps are require for this study?
>>>
>> A force field compatible with the way you parametrized your ligand, I
>> would say.  The tutorial linked above covers this issue.
>>
>> Massimo
>>
>>  Thanks.
>>>
>>> --
>>> View this message in context: http://gromacs.5086.x6.nabble.
>>> com/Re-Protein-Ligand-Interaction-or-Docking-using-
>>> Gromacs-tp5016011.html
>>> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>>>
>>
>>
> --
> -------------------------------------------------------
> Andrea Spitaleri PhD
> D3 - Drug Discovery & Development
> Istituto Italiano di Tecnologia
> Via Morego, 30 16163 Genova
> cell: +39 3485188790
> http://www.iit.it/en/d3-people/andrea-spitaleri.html
> ORCID: http://orcid.org/0000-0003-3012-3557
>
>
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-- 

===========================
Thanks and Regards,
Bipin Singh
Ph.D. Student in Bioinformatics
CCNSB, IIIT-Hyderabad

bipin.singh at research.iiit.ac.in
http://researchweb.iiit.ac.in/~bipin.singh
===========================