[gmx-users] MD of two structure together-receptor+ligand

sun sun.iba2 at gmail.com
Fri Oct 23 20:09:09 CEST 2015

Follow Justin's tutorial for protein-ligand MD. You might want to view Hbonds between inhibitor and protein, for that Hbond mapping helps. You can also calculate binding energy. If the protein has specific conformation, you can view the frames for any structural change or stability.

Sent from my iPhone

> On 22-Oct-2015, at 10:53 pm, Nikhil Maroli <scinikhil at gmail.com> wrote:
> Dear Gromacs users,
> i wanted to do MD after docking,i done docking and i selected one
> conformation  i have receptor pdb and ligand pdb and i made one pdb with
> both ?
> now i wanted to do MD and see how the interaction goes on and to
> learn/predict inhibition and antagonist behavior of the system.
> so can anyone tell me how should start ?
> should i start with one single pdb if yes how should i add topolgy for
> drugs?
> i have topolgy parameters from individual system generated from the server
> i hope someone can help out here.
> Thanks in advance
> -- 
> Ragards,
> Nikhil Maroli
> -- 
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