Installing Amber and AmberTools on a
Macbook Pro with 64-bit 2.4 Ghz Intel Core 2 Duo, running OS 10.6.3 (snowleopard)

(1) make the latest OS upgrades
(2) get the latest version of X-tools (3.2.2)
(3) get the latest compilers (4.5). You need gcc  and gfortran. 
    The package vgcc-snwleo-intel-bin.tar.gz from http://HPC.sf.net is working.
(4) This package unpacks as a usr/local directory wherever you unpacked it
(5) sudo copy the contents of the individual subdirectories in to your "real"
    usr/local subdirectories 
(6) Make sure the executables are found by your PATH --  
    (a) add /usr/local/bin to your PATH in 
     IN .cshrc like 
     setenv PATH ${PATH}:/usr/local/bin
     BE CAREFUL!:  this should be one long line.
     IN .bash_profile as
     PATH="/usr/local/bin:${PATH}"
    (b) make sure there are NO compilers in /usr/bin -- they will take precedence over the ones just installed 
(7) check the compilers: 
which gcc
/usr/local/bin/gcc
gcc -v

Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin10/4.5.0/lto-wrapper
Target: x86_64-apple-darwin10
Configured with: ../gcc-4.5-20100107/configure --enable-languages=fortran --host=x86_64-apple-darwin10 --build=x86_64-apple-darwin10 : (reconfigured) ../gcc-4.5-20100107/configure --enable-languages=fortran,c++ --host=x86_64-apple-darwin10 --build=x86_64-apple-darwin10
Thread model: posix
gcc version 4.5.0 20100107 (experimental) (GCC)

which gfortran
/usr/local/bin/gfortran
gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin10/4.5.0/lto-wrapper
Target: x86_64-apple-darwin10
Configured with: ../gcc-4.5-20100107/configure --enable-languages=fortran --host=x86_64-apple-darwin10 --build=x86_64-apple-darwin10 : (reconfigured) ../gcc-4.5-20100107/configure --enable-languages=fortran,c++ --host=x86_64-apple-darwin10 --build=x86_64-apple-darwin10
Thread model: posix
gcc version 4.5.0 20100107 (experimental) (GCC) 
 

(8) create a home directory for AMBER. DONOT CREATE IT IN /usr/local AS SUGGESTED IN THE MANUAL -- THIS WILL CAUSE HOURS OF
     MISERY.  I put it in my home directory: /Users/erikzuiderweg/AMBER_DIR
(9) put both Amber downloads there, and unpack them with tar xvfj xxxxxxx.tar.bz2
(10) in .cshrc set:
   setenv PATH ${PATH}:/usr/local/bin:/Applications/Sparky.app/Contents/MacOS:$AMBERHOME
   setenv AMBERHOME /Users/erikzuiderweg/AMBER_DIR/amber11
   in .bash_profile set:
   export AMBERHOME=/Users/erikzuiderweg/AMBER_DIR/amber11
(11) cd /Users/erikzuiderweg/AMBER_DIR/amber11/AmberTools/src
(12) ./configure -macAccelerate gnu (takes 30 seconds) 
(13) make (takes 20 minutes) 
(14) cd /Users/erikzuiderweg/AMBER_DIR/amber11/AmberTools/test
(15) make test (takes 45 minutes)
(16) cd  /Users/erikzuiderweg/AMBER_DIR/amber11/src
(17) make sure it contains a config.h file (generated by AmberTools)
(18) make serial  (takes 5 minutes)
(19) cd  /Users/erikzuiderweg/AMBER_DIR/amber11/test
(20) make test (takes 45 minutes)