Amber10 Bug Fixes

10.0	April, 2008 (CVS tag: v_10)

• bugfix.all: This patch script contains all of the bug fixes detailed below in a single patch script. You can patch your Amber10 distribution to include all of the current bug fixes by downloading this file and saving it in your $AMBERHOME directory. You should also download the following script that will apply the bugfixes for you and save it in your $AMBERHOME directory. (apply_bugfix_all.x) You should then patch your system by running:

  cd $AMBERHOME
  chmod 700 apply_bugfix_all.x
  ./apply_bugfix_all.x 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 Amber10.

• bugfix.1: The umbrella forces are not accumulated correctly if the atoms involved in the reaction coordinate do not reside on the master node of a sander job.

• bugfix.2: elsize.cc may fail to compile with some compilers.

• bugfix.3: QMMM Simulations that use the auto diagonalization selection feature can cause a segfault. This includes QMMM test case 1NLN_auto.

• bugfix.4: The trajene (imin=5) option does not work as described in the manual.

• bugfix.5: The src/ncsu-umbrella-slice/configure script always assumes that the argument of the --with-netcdf-prefix option is a relative path.

• bugfix.6: There is a small possibility that QMMM calculations run in parallel where the diagonalization routine is set to automatically select the fastest routine can either hang due to a MPI race condition or quit with a MPI message synchronization error.

• bugfix.7: Fix for REMD runs when NMR constraints are being used.

• bugfix.8: Fix a possible memory allocation error in pmemd.

• bugfix.9: Configuration files to allow pmemd to be compiled using Intel's MPI.

• bugfix.10: Fix MPI communication problem for PIMD and NEB runs.

• bugfix.11: Fix for softcore calculations where only one of the two endpoints contains softcore atoms. E.g. disappearing of softcore atoms.

• bugfix.12: Update to softcore.f modifications made by bugfix.11. Some compilers may fail to compile softcore.f.

• bugfix.13: Update format statements in divcon that gfortran doesn't like.

• bugfix.14: Fix possible allocation failures during sander QMMM startup.

• bugfix.15: More patches to make REMD calculations work with netcdf files.

• bugfix.16: Small fixes to the sander/PUPIL interface

• bugfix.17: Patches to mm-pbsa for "hybrid model" systems

• bugfix.18: Don't allow extra points with igb>0

• bugfix.19: Improve element identification accuracy in QMMM runs.

• bugfix.20: Pseudoatomic distance corrections were not being used in makeDIST_RST

• bugfix.21: Eliminate bogus buried atom failure in molsurf module of mm_pbsa

• bugfix.22: Enforce checking of unsupported CHARMM prmtop files.

• bugfix.23: Small tweaks to the pbsa program

• bugfix.24: Fix PMEMD possible incorrect -PMEMD Terminated Abnormally- message.

• bugfix.25: Constant pH with closely interacting residues can misbehave due to an incorrectly formed tpair array.

• bugfix.26: Add support for CHARMM force field prmtop files (chamber, AMBERTools 1.3) to PMEMD 10.0. Fix various minor bugs in pmemd including possible array out of bounds and unitialized variables. Support prmtop files containing variable 1-4 scaling information in PMEMD 10.0.

• bugfix.27: Update to bugfix.19 - adds support for the element Zinc which was inadvertantly left out of the previous bugfix.

• bugfix.28: Multiple updates and bugfixes for NMR restraints.

• bugfix.29: Fix to the ECAVITY term in mm-pbsa calculations using PB

• bugfix.30: Updates to allow sander to work with PUPIL, version 1.3