Windows Cygwin

You need to download and install Cygwin. When you go through the install process, you need to make sure that you select all of the packages that Amber requires to run.

Packages to install

This section assumes that the Default choice is given for all downloads. Therefore, I will just list the additional packages that I think you should install. You may not need each one for Amber, but the ones listed below will be enough for Amber.

I will break up the packages that you need by section heading (e.g., Accessibility, Admin, Archive, etc.)


  • libzzip-devel


  • autobuild
  • autoconf
  • autoconf2.1
  • automake
  • automake1.11
  • doxygen (Optional — used to create developer documentation for cpptraj,, and
  • flex
  • gcc4
  • gcc4-core
  • gcc4-g++
  • gcc4-fortran
  • gdb (Optional — this is for debugging)
  • libtool
  • make
  • makedepend
  • patchutils
  • readline
  • zlib-devel


Nothing in here is crucial, but you can pick your Linux-style editors that you like here. For example, I install vim (and gvim, since I love that version).


Again, nothing is required here, but I have some suggestions

  • gd
  • gnuplot
  • jpeg
  • libnetpbm-devel (This is the movie-making program that VMD uses, but may not be necessary for Windows)
  • libpng
  • libtiff-devel


  • perl
  • python
  • tcl
  • tcl-tk


  • netcdf
  • libnetcdf-devel


  • openssh


  • python-tkinter


  • bash-completion (Optional, but I highly recommend it!)
  • tcsh
  • xterm


  • bc (Optional — command-line calculator ideal for bash-scripting)
  • patch
  • util-linux


  • wget (Optional, but several workflows published for Amber use it to download files from the command-line)


  • libXt-devel
  • libXtst-devel
  • xinit
  • xorg-scripts
  • xorg-server-devel
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