Dear Dr Case, dear Anna,
>> Amber force field has the parameters of the diatomic O2 molecule? Which
>> atom type use to define it?
>
> O2 is not a standard unit in any Amber libraries. See tutorial B4 for
> general instructions on creating such units. O2 is so simple, you could also
> do it my hand (if you were familiar with the file formats), but I'd recommend
> antechamber anyway.
O=O or .O-O. is so simple, that it might be an big head ache to get
something representative ;-)
The formal charge of O2 = 0 and the 2 oxygen atoms are supposed to be
chemically equivalent thus bearing a partial charge = 0 each; so no
need to run a charge fit. However I bet a ugly RRMS and r2 values are
obtained (like for H2)...
To avoid this problem and if O2 is a ligand of a molecule, I would
vote to compute the partial charges of O2 + its counterpart together...
I would use PyRED at RED-Server Dev.
http://q4md-forcefieldtools.org/REDServer-Development/ for that and
define MOD_GAUSSIAN_JOB = Complex is the System.config file.
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-4-demo21.pdf
regards, Francois
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Mon Jan 30 2017 - 00:30:02 PST
