Jed Goldstone

I think this issue is original to Vina. I noticed that Vina scores differed when identical side chain positions were either flexible or fixed. I had an email exchange with either Oleg Trott about this, but I was never satisfied by the explanation. Whether or not a chain is defined as flexible should not logically affect the binding energy - it's artificial that any side chain is fixed in any case. I think it's an artifact of dividing by the degrees of system freedom, encoded in the original software...