[gmx-users] How to do Energy minimization and MD of protein-new ligand complex

priyabrata panigrahi priyabrata0 at gmail.com
Sat Aug 21 12:06:55 CEST 2010

I am new to Gromacs. I have a protein where ligand  is bound to it. I got
this complex after carrying out docking of ligand to protein.The ligand is
new. So no topology and parameter files are available. At first i want to
carryout energy minimization of this complex and then I want to find out how
ligand interacts with the protein active site residue by carrying a MD
simulation. So can anyone guide me how to proceed. It would be a great help

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