Hi Mark and Justin, I think I should be more specific here. So i.e., I want to study the interaction between a protein receptor and a carbohydrate ligand with MD simulation, and I plan to use ff99sb for protein while glycam06 for carbohydrate.
Since the two force fields are parameterized using different scaling factors, I should use different fudge values, although these values will not DIRECTLY affect inter-molecular interactions. So how to set this up, if it is possible, within .top file and .itp files? Thanks, Yun
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