follow-up post on missing gaff terms

From: Matthew Randolph Lee, Ph.D. <>
Date: Tue 20 Aug 2002 10:21:50 -0700

> 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

--Matt Lee

Matthew Randolph Lee, Ph.D.

Computational Scientist phone: (858)410-6534
Lion Bioscience Inc. fax: (858)410-6665
9880 Campus Point Drive e-mail:
San Diego, CA 92121
Received on Tue Aug 20 2002 - 10:21:50 PDT
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