Hi all,
I want to study the interaction of a carbohydrate ligand with a protein
receptor, and they are of course NOT covalently linked.
It seems people would use glycam for the sugar part and ff99sb for the
protein part while implementing the 'amber' scaling factors for the entire
system. But I wonder if it would be reasonable to apply different set of
scaling factors for the protein part and the sugar part, since amber11
already has this function?
And it seems to me that different set of scaling factors will not affect
inter-molecular interactions.
Thanks,
Yun
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Received on Sat Sep 17 2011 - 16:00:02 PDT
