[gmx-users] parametrization of protein-ligand covalent bond

[Leandro Bortot]

Dear users,

     I need to simulate an inhibitor covalently bound to a protein. What is
the best approach to get the parameters for adequately modeling the
protein-ligand bond and the new residue partial charges?

     I was thinking about doing a standard parametrization using the ligand
attached to the residue as my chemical entity. By doing this, I should have
the parameters for the bond and the new partial charges.

Thank you for your attention,
Leandro.