AMBER: Applying bugfixes in Amber

From: Lili Peng <>
Date: Thu, 4 Oct 2007 14:28:29 -0700

Hi all,

I'm trying to apply bugfix.12 ( in using antechamber. I'm
not used to Linux commands, and I'm not sure what to enter when I reach
"File to patch". Below is a list of my commands:

which setenv
setenv AMBERHOME /usr/local/apps/amber9
patch -p0 -N -r patch_rejects < bugfix.12

After I get this output below, the prompt "File to patch" comes up, and I
just don't know what to do so I pressed enter. I guess that was a dumb move
to do, since it didn't really do anything. Can someone please advise me in
what steps I should take?


"********>Bugfix 12:

Author: Scott Brozell
Date: 08/17/06

Programs: Antechamber

Description: Files of type prepi or prepc with a length greater than 139
             lines cause antechamber programs to fail. The -o output
             file contains garbage. The standard output usually contains:
Info: the atom number exceeds the MAXATOM, reallocate memory automatically
 Unrecognized atomic name , exit

Fix: apply the following patch to amber9/src/antechamber/prep.c *and* to

*** prep.c 3 Apr 2006 23:34:26 -0000 9.0
--- prep.c 18 Aug 2006 05:02:19 -0000
File to patch:

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Received on Sun Oct 07 2007 - 06:07:34 PDT
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