Well, the charges should obviously be zero for free oxygen (whereas the oxygen in the heme stream file does have a dipole moment), but I'm not sure whether the L-J, which appears to be transfered from the protein force field's carbonyl oxygen, is valid for a free oxygen molecule; same for the O-O bond parameter from heme. Free oxygen is a triplet state and might exhibit some anomalies. I'm not saying it will necessarily be terrible, but just taking heme oxygen, zeroing the charges and setting it free without prior validation does not sound very prudent, unless the heme oxygen would turn out to be parameterized towards free oxygen in the first place, which I doubt but cannot verify.
The papers you're talking about - which heme model did they use? Could you please provide some reference?
Last edited by Kenno; 09/01/10 09:55 PM. Reason: Found out that toppar_heme was parameterized by A. MacKerell and A. Macias