Unknown@Unknown-PC /cygdrive/c/AMBER
$ ./configure -cygwin gnu
Checking for updates...
AmberTools12 has 20 unapplied patches: 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33

There are patches available. Do you want to apply them now? [y/n] (Recommended Y)
n
NOT updating your tree and continuing anyway.
Could not find the X11 libraries; you may need to edit config.h
   to set the XHOME and XLIBS variables.
Searching for python2... Python 2.7.3
Only found /cygdrive/c/Python27-32Bit/python. Version  is not supported.
Python programs will not work unless you install a version
of Python2 version Python 2.4 to 2.7.

Obtaining the gnu suite version:
      gcc -v
The version is 4.5.3
Testing the gfortran compiler:
     gfortran  -O0 -o testp.exe testp.f
OK

Testing mixed C/Fortran compilation:
     gcc  -DCYGWIN  -c -o testp.c.o testp.c
     gfortran  -O0 -c -o testp.f.o testp.f
     gcc  -DCYGWIN -o testp.exe testp.c.o testp.f.o -lgfortran -w
OK

Testing pointer size:
     gcc  -DCYGWIN  -o test_pointer_size.exe test_pointer_size.c
Detected 32 bit operating system.

Testing flex: OK

Configuring NetCDF (may be time-consuming)...

    NetCDF configure succeeded.

Checking for zlib: OK

Checking for libbz2: OK
Configuring fftw-3.3 (may be time-consuming)...

    fftw-3.3 configure succeeded.

The configuration file, config.h, was successfully created.

The next step is to type 'make install'

Cleaning the src directories. This may take a few moments.
Configure complete.

Unknown@Unknown-PC /cygdrive/c/AMBER
$ make install
cd AmberTools/src && make install
make[1]: Entering directory `/cygdrive/c/AMBER/AmberTools/src'
Makefile:80: *** target pattern contains no `%'.  Stop.
make[1]: Leaving directory `/cygdrive/c/AMBER/AmberTools/src'
Makefile:7: recipe for target `install' failed
make: *** [install] Error 2
Unknown@Unknown-PC /cygdrive/c/AMBER
$