Amber10 Bug Fixes
10.0 April, 2008 (CVS tag: v_10)
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:
chmod 700 apply_bugfix_all.x
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.
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.
elsize.cc may fail to compile with some compilers.
QMMM Simulations that use the auto diagonalization selection feature can
cause a segfault. This includes QMMM test case 1NLN_auto.
The trajene (imin=5) option does not work as described in the manual.
script always assumes that the argument of the
--with-netcdf-prefix option is a
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
Fix for REMD runs when NMR constraints are being used.
Fix a possible memory allocation error in pmemd.
Configuration files to allow pmemd to be compiled using Intel's
Fix MPI communication problem for PIMD and NEB runs.
Fix for softcore calculations where only one of the two endpoints
contains softcore atoms. E.g. disappearing of softcore atoms.
Update to softcore.f modifications made by bugfix.11. Some compilers
may fail to compile softcore.f.
Update format statements in divcon that gfortran doesn't like.
Fix possible allocation failures during sander QMMM startup.
More patches to make REMD calculations work with netcdf files.
Small fixes to the sander/PUPIL interface
Patches to mm-pbsa for "hybrid model" systems
Don't allow extra points with igb>0
Improve element identification accuracy in QMMM runs.
Pseudoatomic distance corrections were not being used in makeDIST_RST
Eliminate bogus buried atom failure in molsurf module of mm_pbsa
Enforce checking of unsupported CHARMM prmtop files.
Small tweaks to the pbsa program
Fix PMEMD possible incorrect -PMEMD Terminated Abnormally- message.
Constant pH with closely interacting residues can misbehave due to an incorrectly formed tpair array.
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. This also adds support for ig=-1,
setting of the random number seed to the wallclock in microseconds, to PMEMD 10.0.
Update to bugfix.19 - adds support for the element Zinc which was inadvertantly left out of the
Multiple updates and bugfixes for NMR restraints.
Fix to the ECAVITY term in mm-pbsa calculations using PB
Updates to allow sander to work with PUPIL, version 1.3
The pmemd program may run out of lone-pair space for some
Thermodynamic integration calculations in sander will fail when
the dvdl_norest parameter is set.
Workaround for Intel 11.1 compiler bug.
pme_setup.f90(415): error 6404: This name does not have a type, and must have an explicit type. [NATOM]
Fix issues caused by bugfix.31 being originally generated against a code base that was not up to date. Also fix
an issue whereby GB runs on IA64 architectures will ignore the value set for cut and run as if there was no
Fix possible imaging issues for QMMM calculations using very small boxes.