Re: [AMBER] Parameters

From: FyD <>
Date: Mon, 30 Jan 2017 09:25:08 +0100

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. for that and
define MOD_GAUSSIAN_JOB = Complex is the System.config file.

regards, Francois

           F.-Y. Dupradeau

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Received on Mon Jan 30 2017 - 00:30:02 PST
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