RE: AMBER: Applying bugfixes in Amber

From: Ross Walker <>
Date: Thu, 4 Oct 2007 14:53:31 -0700

Hi Lili,
The standalone bugfixes don't contain path information so you need to place
them in the directory of the files to be patched or alternatively provide
the path to each file. See the last section of the bugfix comment:
apply the following patch to amber9/src/antechamber/prep.c *and* to
so place the bugfix file in $AMBERHOME/src/antechamber/ and then run the
patch command.
Note however that you should probably not worry about the individual
bugfixes and instead just apply bugfix.all from the amber website. Place
this in $AMBERHOME and then
patch -p0 -N -r patch_rejects <bugfix.all
Good luck...

|\oss Walker

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From: [] On Behalf Of
Lili Peng
Sent: Thursday, October 04, 2007 14:28
Subject: AMBER: Applying bugfixes in Amber

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 - 06:07:35 PDT
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