[droe@TheDoctor amber11-Release]$ tar -jxf ../AmberTools-1.5.tar.bz2
[droe@TheDoctor amber11-Release]$ cd amber11/
[droe@TheDoctor amber11]$ pwd
/home/droe/Amber/amber11-Release/amber11
[droe@TheDoctor amber11]$ export AMBERHOME=`pwd`
[droe@TheDoctor amber11]$ patch -p0 -N < ~/Amber/GIT/web_amber/bugfixes/AmberTools/1.5/bugfix.all 
patching file AmberTools/src/cpptraj/src/FrameList.cpp
patching file AmberTools/src/cpptraj/src/FrameList.h
...
patching file AmberTools/test/nab/rism3d.snglpnt.out.check
patching file AmberTools/test/rism1d/check1d
[droe@TheDoctor amber11]$ cd ..
[droe@TheDoctor amber11-Release]$ tar -jxf Amber11.tar.bz2
[droe@TheDoctor amber11-Release]$ cd amber11/
[droe@TheDoctor amber11]$ ../apply_bugfix.x /home/droe/Amber/GIT/web_amber/bugfixes/11.0/bugfix.1to17.tar.bz2
Applying all bugfixes in /home/droe/Amber/GIT/web_amber/bugfixes/11.0/bugfix.1to17.tar.bz2
Patching AMBER installation in /home/droe/Amber/amber11-Release/amber11
...
Applied patches 1 to 16. Now applying bugfix.17
Applied patch 17. CUDA upgrade complete.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!                                                     !!!
!!!  IMPORTANT IMPORTANT IMPORTANT IMPORTANT IMPORTANT  !!!
!!!                                                     !!!
!!!  BE SURE TO APPLY ALL BUG FIXES FOR AMBERTOOLS 1.5  !!!
!!!  BEFORE ATTEMPTING TO BUILD PMEMD.CUDA. YOU MUST    !!!
!!!  HAVE AT LEAST UP TO BUGFIX.13 IN ORDER TO BUILD    !!!
!!!  THE UPDATED PMEMD.CUDA SUCCESSFULLY                !!!
!!!                                                     !!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
[droe@TheDoctor amber11]$ cd AmberTools/src/
[droe@TheDoctor src]$ ./configure gnu

Obtaining the gnu suite version:
...
The configuration file, config.h, was successfully created.
 
The next step is to type 'make serial'
 

 NOTE: after installing AmberTools, if you want to compile
       Amber11 using AmberTools 1.5, you must run the 
       AT15_Amber11.py script first, e.g.:
       cd /home/droe/Amber/amber11-Release/amber11; ./AT15_Amber11.py; cd src; make serial
       (See the Amber11 Users' Manual for full instructions,
       and be sure to have a backup, since the AT15_Amber11.py
       script will modify your Amber11 files.)
[droe@TheDoctor src]$ make serial > compile.log 2>compile.err