AMBER Archive (2008)

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

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Nov 19 2008 - 08:35:45 CST

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
problems.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu