AmberTools Bug Fixes

Notes: Minor versions are independent with respect to bug fixes. Subsequent versions usually contain new features in addition to previous fixes. If you run into problems with older versions then you should download the latest version.

Version 1.3

1.3	December,  2009 (CVS tag: at_1_3)

• bugfix.all: This patch script contains all bug fixes for AmberTools version 1.3 in a single patch script. You can patch your AmberTools distribution to include all of the current bug fixes by downloading this file and saving it in your $AMBERHOME directory. You should then patch your system by running:

  cd $AMBERHOME
  patch -p0 -N < bugfix.all
  

  This should patch your source files with the latest bugfixes. Any bugfixes that appear to have already been applied will be skipped. Once the patching is finished you need to recompile your copy of AmberTools.

• bugfix.1: Make an scf failure a fatal error for sqm, to minimze wasted computer time on a failed calculation.

• bugfix.2: Allow the pbsa program to handle halogens in the GAFF force field.

Version 1.2

1.2	July,  2008 (CVS tag: at_1_2)

• bugfix.all: This patch script contains all bug fixes for AmberTools version 1.2 in a single patch script. You can patch your AmberTools distribution to include all of the current bug fixes by downloading this file and saving it in your $AMBERHOME directory. You should then patch your system by running:

  cd $AMBERHOME
  patch -p0 -N < bugfix.all
  

  This should patch your source files with the latest bugfixes. Any bugfixes that appear to have already been applied will be skipped. Once the patching is finished you need to recompile your copy of AmberTools.

• bugfix.1: antechamber test charmm ala2 output update for phase changes.

• bugfix.2: NAB failed assertion for some dihedral phases, such as in ff99bsc0.

• bugfix.3: fixes to ptraj related to netcdf, remd and compressed files

• bugfix.4: fixes buffer overrun when writing mol2 files in LEaP

• bugfix.5: remove some duplicate parameters in gaff.dat

• bugfix.6: fixes issues with ptraj failing to identify some CHARMM PSF files.

• bugfix.7: fixes issues with ptraj processing of REMD, netcdf trajectories

• bugfix.8: more fixes related to bugfix.7

• bugfix.9: don't allow dihedral phases that are not zero or pi (as in parmbsc0)

• bugfix.10: patch the loadMol2 command in LEaP so that it won't choke on odd residue numbers

• bugfix.11: fix to am1-bcc bond orders (and hence charges) for SO2 and NO2 groups

• bugfix.12: update leaprc files to recognize atom and residue names in PDB 3 format

Version 1.0

1.0	April, 2008 (CVS tag: at_1_0)

• bugfix.all: This patch script contains all bug fixes for AmberTools version 1.0 in a single patch script. You can patch your AmberTools distribution to include all of the current bug fixes by downloading this file and saving it in your $AMBERHOME directory. You should then patch your system by running:

  cd $AMBERHOME
  patch -p0 -N < bugfix.all
  

  This should patch your source files with the latest bugfixes. Any bugfixes that appear to have already been applied will be skipped. Once the patching is finished you need to recompile your copy of AmberTools.

• bugfix.1: nblist.c in NAB won't compile with MPI turned on

• bugfix.2: The readparm() routine will throw an error when MPI is turned on

• bugfix.3: sleap will not read a leaprc file from an arbitrary path

• bugfix.4: sleap does not recognize the closeness parameter in solvateBox

• bugfix.5: sleap cleanups required for Mac OSX

• bugfix.6: sleap fixes to addIons to work with solvated systems

• bugfix.7: Fix to possible segfaults when doing clustering in ptraj