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

[andrea]

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