All of Amber (except for pmemd and the X-windows parts) will compile and run on Windows using the Cygwin development tools: see http://www.cygwin.com. The cygwin package provides a way to make Microsoft Windows machines resemble a Linux/Unix environment; if you are unfamiliar with the Linux/Unix environment, you will need to learn at least the basics of that in order to use Amber on Windows.
Note that Cygwin provides a POSIX-compatible environment for Windows. Effective use of this environment requires a basic familiarity with the principles of Linux or Unix operating systems. Building the Windows version is thus somewhat more complex (not simpler) than building under other operating systems. The Windows version has primarily been used in serial (single-cpu) mode; it will work with the LAM libraries supplied with Amber10, or with MPICH2 libraries. For long-running jobs, Windows can have an annoying habit of giving lots (or all) of the CPU time to an interactive process, so that background processes suffer.
The bottom line is that the Windows version is functional, but the primary development and target operating system is Unix or Linux.
Choose the following programs to install:
gcc4, gcc4-fortran, make, m4, flex, diffutils, tcsh, util-linux
then press "next" at the bottom to complete the installation.
tar xvfj AmberTools-1.3.tar.bz2
This will extract the files from the tar file. If you type "ls" (equivalent to the dos "dir" command), you should see two files: the AmberTools file, and a new directory called "amber11". You can explore now, for example with commands like the following:
cd amber11 (moves you "into" the amber11 directory)
ls (lists the files and directories)
cd src (moves you down further into the src directory).
./configure -cygwin -noX11 gnu
[Aside: you can type "./configure --help" to see more options.] Assuming(!) that this works, then type:
export AMBERHOME=/home/name/amber11 (where name is your name!)
make -f Makefile_at
At this point the screen will fill up with compilation messages, for several minutes. The end you should see the message:
"Completed installation of AmberTools ver. 1.3"
cd ../test
make -f Makefile_at test
This will run a series of tests, most of which should say PASS.
Note 1: it looks like sleap is not running correctly on Windows; we'll post a bug-fix if/when we can track this down.
Note 2: Cygwin has just undergone a major change (as of 12/23/09); right now the xleap installation is not working, hence the "-noX11" flag in the instructions above. Since all this used to work with the older cygwin, we will try to post updated instructions here soon.