Molecular Modeling Team

Software Bugfixes/Updates

General instructions
Select the update to download from the list below. Use
tar -xzvf downloaded_file
to extract the files. Copy the files to their corresponding Brimm subdirectories in your original software installation.

If you download the tarfile to the parent directory of Brimm, the tar command above will automatically overwrite and update the old file(s).

Note: The bug fixes are not cumulative. The full download always incorporates all bug fixes.
Available bugfixes/updates
ProgramDateDescriptionDownload
sietraj2013-05-03Fixes a bug in mutating Ala to Ser. Warns if either target or ligand has zero partial charges on all atoms. Get the full download for this update.
sietraj2012-03-20Virtual alanine mutations are now possible with a simple command line option. A full download is needed for this update.
sietraj2012-02-02Fixes a bug in the Aug 2011 release that altered the radii definitions for two atom types. The bug made calculated results inconsistent with previous versions. This release restores the original atom radii definitions.sietraj_bugfix4.tar.gz
sietraj2011-08-05Modified to work with multiple versions of Tcl. Fixed some memory leaks. A full download is needed for this update.
sietraj2011-03-21Includes a 64-bit version of the program. A full download is needed for this update.
sietraj2011-01-07Incorporated a work-around for a memory bug that occasionally crashed the program. A full download is needed for this update.
sietraj2008-09-10Fixed bug in reading mdcrd files with coordinates that fill up the entire I8 field (e.g., -103.457).

Replaces:
Brimm/scripts/amber_util.tcl
sietraj_bugfix3.tar.gz
sietraj2008-09-02Fixed occasional array out-of-bounds problem in reading in the prmtop file.

Replaces:
Brimm/scripts/Britcl_startup.tcl
Brimm/lib/versions/Britcl-v2.1e.so
sietraj_bugfix2.tar.gz
sietraj2008-04-161) Fixed bug in assignment of LJ coefficients of H-bonding pairs.
2) Added Na atom type and radii definitions for Na+ and K+.

Files affected:
Brimm/scripts/amb2syb.tcl
Brimm/scripts/amber_util.tcl
sietraj_bugfix1.tar.gz