AMBER Archive (2004)

Subject: AMBER: some bugfixes

From: David A. Case (
Date: Mon May 03 2004 - 13:10:47 CDT

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


================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to