There is one combined Amber and AmberTools reference manual:
Amber 2025 Reference Manual as an
Acrobat (PDF) file. (Last updated on 30 April 2025.)
Update, April 2024:Istvan Kolossvary has recently converted
an updated version of the lmod examples to work with sander. You can download these here:
lmod-sander-examples.tar.bz2.
These include an example of the new co-vibrational analysis.