Quoting FyD <fyd.q4md-forcefieldtools.org>:
>
>>> 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
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
... breaking chemical equivalencing for O=O...
regards, Francois
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Mon Jan 30 2017 - 01:30:03 PST
