Dear gromacs users, I am planning run a DNA/RNA simulation in presence of an organic ligand molecule. I would like to use amber-ff or charmm parameters for the ligand and parmbsc1 forcefield for the nucleic acid. How can I tackle the forcefield.itp file and the combination rule etc.? In case I want model two molecules in my simulation system with two different forcefields, how do I choose comb-rule, fudgeLJ, fudgeQ parameters etc.? Also the non-bonded parameters in different forcefields are generated according to different combination rule. If I need to use two molecules with two different forcefield parameters, how do I account for the non-bonded parameters? Any help will be much appreciated, thank you
You cannot mix and match force fields; the physical model will be unreliable. If you are using bsc1 for the nucleic acid, use GAFF for the ligand.
Dear Dr. Lemkul, thank you for the explanation, I will plan the simulation accordingly.