Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)

From: David A. Case <>
Date: Wed, 19 Nov 2008 09:35:45 -0500

On Tue, Nov 18, 2008, John Chodera wrote:
> I just noticed that the copy of gaff.dat (the GAFF parameter
> definition file) appearing in AmberTools 1.2 contains repeated
> entries, but with these entries specifying different parameters. For
> example, in the bond section:
> cd-cd 418.3 1.429 SOURCE1 740 0.0058 0.0069
> cd-cd 504.0 1.371 SOURCE3 523 same as cc-cd

This appears to have been caused by Junmei himself, who did not use CVS
at one point in 2006 in creating an updated gaff.dat file. This lost
corrections made in CVS revisions 8.1 and 8.2.

I have fixed this in CVS, and posted a bugfix to the web site.

Thanks again to John for pointing this out. Please let us know if still find


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Received on Fri Dec 05 2008 - 16:01:17 PST
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