AMBER Archive (2007)

Subject: Re: AMBER: missing impropers for nitros?

From: David Mobley (dmobley_at_gmail.com)
Date: Mon May 14 2007 - 08:28:34 CDT


Hi,

> I think you already know this, but just in case: these are just informational
> messages. There is no requirement that every possible improper be included.

Right. Formerly it was the case that ANTECHAMBER would issue these
warnings a lot. Now, this seems not to be the case (i.e., when I run
it on 504 different small molecules, the ONLY cases where it issues
these warnings are the two cases I mentioned), which makes me
suspicious.

> That said, Junmei can probably comment on whether this is intentional or an
> oversight. If the former, we might put a "zeroed" out entry in gaff.dat to
> suppress the warning message.

We thought the nitros were supposed to be planar, which might be why
it's issuing this warning...

I look forward to hearing from Junmei.

Thanks,
David

> ...dac
>
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