Hi all, I am doing MD simulation of some carbohydrate-protein complex with this 53a6 force-field.
I noted that in any oligosaccharide, the charge assigned for anomeric carbon is 0.232 while C5 (i.e. in a non-terminal mannopyranose) is 0.376. This is kind of counter-intuitive for me since the anomeric carbon C1 is linked to two oxygen atoms O5 and "O1" while C5 is linked to only one oxygen atom O5, and both C1 and C5 are CH type atom. And in other force filed like GLYCAM06, C1 always has a larger positive partial charge than C5. I understand that GROMOS force fields are derived in quite different ways, but I still wonder if it makes sense to switch the charges on C1 and C5? It seems these carbohydrate parameters did not change in the new 54a7 ff, which was tested against nOe and J-coupling data rather than free enthalpy of hydration and solvation, which really puzzles me. Thank you for any explanation and suggestion. Yun Shi
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