1. First, extract the files in some location (we use /home/myname as an example here):
tar xvfj AmberTools-1.4.tar.bz2
After this, check for bugfixes at http://ambermd.org/bugfixesat.html;
follow the instruc-
tions there to install any needed updates.
2. Next, set your AMBERHOME environment variable:
setenv AMBERHOME /home/myname/amber11
# (for bash, zsh, ksh, etc.)
# (for csh, tcsh)
Be sure to change the “/home/myname” above to whatever directory is appropriate for
your machine. You should also add $AMBERHOME/bin to your PATH.
3. Now, in the src directory, you should run the configure script:
will show you the options. Choose the compiler and flags you want; for most systems,
the following should work:
Don’t choose any parallel options at this point. (You may need to edit the resulting con-
fig.h file to change any variables that don’t match your compilers and OS. The comments
in the config.h file should help.)
will compile the codes. If the make fails, it is possible that some of the entries in “con-
fig.h” are not correct.
5. This can be followed by
which will run tests and will report successes or failures.