Re: AMBER: some bugfixes

From: Sébastien Osborne <>
Date: Mon, 03 May 2004 14:14:33 -0400

Another bug to tell you... Gibbs does not read CUTCAP, XCAP, YCAP and
ZCAP from the topology file, which causes gibbs simulation with solvent
cap to crash because the center of the cap is set at 0.0 with a 0
radius. Found that out the hard way ;)

Sebastien Osborne
University of Ottawa

David A. Case wrote:

>There are a couple of new bugfixes at the amber web site that should be
>1. If you try to use a "restraintmask" or "bellymask" string that has a
> distance constraint in sander, it will fail; (reported by Oliver Hucke).
> Fixed with bugfix.7.
>2. Problems with antechamber when mol2 files are used as input, and particular
> problems with pyridine rings; (also reported by Oliver Hucke,
> Fixed with bugfix.6. [At least, we hope it is fixed; it will of interest
> to see if this patch fixes the original poster's problem.]
>Also, for users of Amber 7: Junmei Wang has prepared some sample ""
>files for the mopac508mn (and similar programs) and for mopac7 and mopac8.
>Go to the Amber web site (, the follow the links
>to "antechamber", then to "What's New".
>Thanks to Oliver Hucke for the error reports, and to Viktor Hornak and Junmei
>Wang for the fixes.
>...dave case

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Mon May 03 2004 - 19:53:01 PDT
Custom Search