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
Thanks
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