[gmx-users] MD simulations of covalent bound protein-ligand complex by gromacs

[mircial at sjtu.edu.cn]

Dear All:

I am simulating a complex of protein and ligand, however, the ligand is covalent bound to the protein. I have calculated the charges of the ligand and the non-standard residue by QM method and trying to use the bond parameters in the GROMOS force field. However, I don't know how to made the topology file of the complex, do I need to change the topology file manually to add the necessary things?

Thanks in advance!

R.X.G.