I want to dock a carbohydrate molecule as a ligand on a protein. What is the best scoring function/force field that I can use for this type of docking?
Are you using a freeware software or commercial software. If freeware means dock score is best and forcefield is mmf is better as carbohydrates are small molecules. In case of commercial glide score is better.
Thanks Danish and Pritam for your answers. But Pritam I don't get it from your answers. What you want to say about amber? is it good to use or should be carefully used?