AMBER Archive (2002)

Subject: follow-up post on missing gaff terms

From: Matthew Randolph Lee, Ph.D. (mrlee_at_sd.lionbioscience.com)
Date: Tue Aug 20 2002 - 12:21:50 CDT

> I came across a couple of missing gaff parameters and would
> like some feedback on copying existing ones.
>
> Specifically, what's missing are two angle terms for the 'nh'
> atom type, an amine nitrogen connected to one or more aromatic rings.
>
> These are the two angle terms missing (as a quote out of
> leap):
>
> Could not find angle parameter: h1 - c3 - nh
> Could not find angle parameter: c3 - c3 - nh

        Dr. Case pointed out, as does the amber7 manual, that I needed to
run parmchk to create the frcmod file, which uses "rules" and "defaults"
to estimate parameters, such as those above, that are missing from
gaff.dat.

--Matt Lee

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Matthew Randolph Lee, Ph.D.

Computational Scientist phone: (858)410-6534
Lion Bioscience Inc. fax: (858)410-6665
9880 Campus Point Drive e-mail: matthew.lee_at_lionbioscience.com
San Diego, CA 92121
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