AMBER Page

AmberTools Bug Fixes and Updates

Note: The individual bug fixes for AmberTools 12 and 13 are described below in case you want to see what they do, or you don't want to use update_amber or patch_amber.py for some reason. For older versions of AmberTools, see the instructions associated with that particular version, although we strongly suggest upgrading to the latest version since they are more actively supported.

Most users are encouraged to use the update_amber (or patch_amber.py) script (which is in $AMBERHOME, and is automatically run during the configure step) to handle patching tasks. This script automatically downloads and applies patches on this site individually and keeps track of every patch that has been applied, making patching and trouble-shooting easier.

Instructions for using update_amber can be found in the AmberTools 13 manual in Chapter 1 Section 5. See Jason's wiki page for more detailed instructions, as well as a work-around in case you are behind a firewall that blocks patch_amber.py from contacting ambermd.org. Note, for update_amber, there is built-in Proxy support (see the AmberTools 13 manual for instructions on setting up your Proxy).

If you wish to apply the listed AmberTools updates, run configure again and make sure to re-compile AmberTools (and Amber if you have it).


AMBERTOOLS 13 CYGWIN USERS: There is currently an issue with Cygwin that prevents the 4th update in AmberTools 13 from being applied due to the implicit carriage return-to-newline conversion that cygwin does on text files. Because there is no way to go 'back' and add this fix before it becomes necessary, you need to fix update_amber on Cygwin with an extra command. This only needs to be done once. To fix update_amber, go to $AMBERHOME and type the following command:

./update_amber --apply http://ambermd.org/bugfixes/AmberTools/13.0/cygwin_fix


Version 13

23	April,  2013

Version 12

12	April,  2012


Gaussian 09 fix

In Gaussian09 rev B.01, the facility to write out the electrostatic potential on a grid of points was inadvertently deleted. This means that antechamber and resp jobs won't work as they should. Fernando Clemente of Gaussian has kindly provided a script to work around the problem. Download the fixreadinesp.sh file, and follow the instructions there. (Note: you will have to make the script executable by typing chmod +x fixreadinesp.sh.)


Version 1.5

1.5	April,  2011 (git tag: at15)


Version 1.4

1.4	April,  2010 (git tag: v_11)


Version 1.3

1.3	December,  2009 (CVS tag: at_1_3)


Version 1.2

1.2	July,  2008 (CVS tag: at_1_2)


Version 1.0

1.0	April, 2008 (CVS tag: at_1_0)