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.

Table of Contents

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.)

Devel

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

Editors

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).

Graphics

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

Interpreters

perl
python
tcl
tcl-tk

Libs

netcdf
libnetcdf-devel

Net

openssh

Python

python-tkinter

Shells

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

Utils

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

Web

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

X11

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

jswails

Computers, Chemistry, and Misc.