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

[ms]

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.
>
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