AMBER Archive (2006)

Subject: Re: AMBER: antechamber failure on FMN

From: David A. Case (
Date: Tue Aug 15 2006 - 18:14:41 CDT

On Tue, Aug 15, 2006, David Mobley wrote:
> OK, I have a little more on that. FMNH is supposed to be a neutral
> radical, so one of the carbons has only three bonds. This is probably
> the origin of the problem, which leads me to two further questions:
> (1) Is there any way to deal with this in antechamber and any gaff
> atom type for it? If not,

I don't think that gaff has any parameters that represent a carbon
radical site.

> (2) If I do a Hartree-Fock 6-31G* calculation to calculate charges for
> FMNH in its radical form, will antechamber be able to handle RESP
> fitting?

It seems worth a try....RESP fitting, per se, should not depend on having a
closed-shell molecule. But the parsing of the Gaussian output file might
be fragile enough that it would fail. I would think you should give it a try.

...good luck...dac

[p.s.: I'm assuming that you now understand the origin of this earlier problem:

> >(2) Running antechamber on FMNH.mol2 gives an error about an odd
> >number of electrons,

If not, please re-ask.]
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