Build of Ambertools dependend on availability of https://ambermd.org/

[laraPPr]

At the moment https://ambermd.org/ is down so builds of AmberTools on our system are failing during the patching step.

The following command needs to be run

easybuild-easyblocks/easybuild/easyblocks/a/amber.py

Line 104 in 2c400f0

cmd = "%s ./update_amber --update" % python_cmd

and it will fail if https://ambermd.org/ is not available.

Because of this it might be interesting to explore if we could not depend the build of Ambertools on their website being available or not.

[branfosj]

I did a manual test by running the following - to update AmberTools to patch level 2 and Amber to patch level 1. I then checked the diff (diff.txt):

$ python3 update_amber --update-to AmberTools/2
$ python3 update_amber --update-to Amber/1
$ diff -rauN amber24_src.orig amber24_src

Based on this, it has:

• applied https://ambermd.org/bugfixes/AmberTools/24.0/update.1
• applied https://ambermd.org/bugfixes/AmberTools/24.0/update.2
• applied https://ambermd.org/bugfixes/24.0/update.1
• put a copy of the first and second in .patches/AmberTools24_Applied_Patches and the third in .patches/Amber24_Applied_Patches

Also, based on https://ambermd.org/AmberPatches.php we'd need to make a change at some point for the new update_pmemd script that looks to have replaced (/be replacing) update_amber.