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

Nikhil Maroli scinikhil at gmail.com
Thu Oct 22 19:23:51 CEST 2015

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
i have topolgy parameters from individual system generated from the server
i hope someone can help out here.
Thanks in advance

Nikhil Maroli

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