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Oxygen Gas Force Field Parameter
#25068 08/08/10 11:55 PM
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Does anyone have oxygen force field parameters ?

Re: Oxygen Gas Force Field Parameter
Raviprasad #25254 08/31/10 05:28 PM
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Doesn't look like it. frown

Re: Oxygen Gas Force Field Parameter
Kenno #25255 08/31/10 05:39 PM
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What about the O2 molecule in the distributed 'heme' stream file?


Rick Venable
computational chemist

Re: Oxygen Gas Force Field Parameter
rmv #25257 08/31/10 06:15 PM
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I looked at that but it looks like something that can only be valid in the context of a heme group. One could of course zero the charges and cross one's fingers, but I won't hold my breath.

I don't know anything about the origins of that heme stream file - it doesn't contain any attribution nor reference to any publication. My best guess is that it has been put together in our lab long before I joined. I believe Alex told me a couple of years ago not to pull anything from it into CGenFF because it may be poorly transferable. Whatever be its source, he's probably right - the heme group is a very special chemical environment and parameters that describe it well aren't necessarily valid in other environments.

Re: Oxygen Gas Force Field Parameter
Kenno #25258 08/31/10 06:21 PM
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Well, there is not much you can do about the charges in a two-point model of O2. The old papers on oxygen diffusion in myoglobin may contain some information; at least they worked quite well in a protein context - resulting in quite important publications which gave physical insight into one of the problems raised by the first protein crystal structures.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Oxygen Gas Force Field Parameter
lennart #25263 08/31/10 07:05 PM
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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

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