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Amber Bug Fixes and Updates

Note: The individual bug fixes are described below in case you want to see what they do, or you don't want to use update_amber for some reason. Most users are encouraged to use the update_amber 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 Amber Reference Manual in Chapter 2, Section 3. See Jason's wiki page for more detailed instructions. Note that update_amber has built-in Proxy support (see the Amber Reference Manual for instructions on setting up your Proxy).

If you wish to apply these updates, run the command

$AMBERHOME/update_amber --update

Alternatively, the Amber configure script automatically checks for and downloads updates so you can just recompile Amber.

Amber16 Updates (April, 2016)

  • update.1: Adds GPU support for including external electric fields.
  • update.2: Completes GPU support for including external electric fields.
  • update.3: Adds support for Intel Xeon and Intel Xeon Phi Optimizations.
  • update.4: New free energy routines in

    pmemd

    ; see nfe.pdf for full documentation.
  • update.5: Support Titan-XP in AMBER 16 pmemd.cuda.
  • update.6: Provides a 10 to 15 percent performance boost to GP102,104 and 107 based gpus, which include GTX-1060,1070,1080, Titan-XP, Quadro P5000 and P6000. Also enables execution on P100 based GPUs.
  • update.7: Updates printouts in the code (re SM60) to match those on the gpu page of the web page.
  • update.8: Fix NetCDF restart writing for

    pmemd

    when internal coordinate axes are flipped.
  • update.9: Fixes and extensions to the "nfe" options in

    pmemd

    .
  • update.10: Fix vulnerability that allowed Lennard-Jones 12-6-4 potentials to be applied with incompatible features in

    pmemd

    .
  • update.11: Fixes overwriting output in gamd.log when continuing a simulation.

    pmemd

    .
  • update.12: Fixes dt and nstep passing in gpu force calculations (primarily used in oscillating electric fields).

    pmemd,sander

    .

Amber14 Updates (April, 2014)

  • update.1: Fixes a bug in

    pmemd.amoeba.MPI

    when running on multiple processors as well as a small fix in the

    pmemd.amoeba

    softcore code.
  • update.2: Fixes a bug in

    pmemd.MPI

    when running with constant pressure ntp = 1, barostat = 1 (default) and a large number of processors. This bug causes a deviation in the pressure calculation. Presence of this bug can be identified when running under constant pressure and block_fft = 1 appears in the output file.
  • update.3: Fixes printout of NMRopt trace variables (distances, angles, torsions, etc.) when using the Monte Carlo barostat in

    pmemd

    . Also prevents illegal values of mcbarint with multiple time-stepping integrators.
  • update.4: Fixes incorrect printing of Ewald Error Estimate for CPU based

    pmemd

    runs.
  • update.5: Adds MIC offload support to

    pmemd

    . This update enables use of Intel Xeon Phi co-processor cards in offload mode where the card acts as an accelerator for the direct space sum.
  • update.6: Updates GPU code to v14.0.1 - add support for CUDA 6.5, fixes issues on > 4 gpus, enables peer to peer support on 8 gpus for systems that support it in hardware and adds checks for NANs in restrt files.
  • update.7: Fixes a bug in that would cause the number of shake constraints removed to be reported incorrectly with softcore TI. Add an additional warning if shake is attempted for bonds that have large differences in equilibirum bond lengths.
  • update.8: Update code to use 80 character line width to fix compile issues with certain compilers.
  • update.9: Enhancements have been made to the MIC offload implementation for improved performance. Please refer to the documentation for more details.
  • update.10: Center of mass distance restraints now supported in the GPU engine. Usage follows the same setup and protocol as in the CPU implemetation. For the GPU implementation all calculations including COM are done on the GPU.
  • update.11: Updates and bug fixes in pmemd.cuda relating to emap, COM restraints and the GB solvent model:
    1. emap: A check has been added to prevent restraints when using emap as they are not yet supported on the GPU.
    2. COM restraints: The number of atoms in a COM grouping has been increased from 200 to 1024. A bug has been fixed that was preventing distance restraints from correctly being detected when the restrain involved atom 1.
    3. GB: Fixes undocumented uninitialized variable in DPFP GB simulations that was causing inconsistent results.
  • update.12: Updates test cases for the new GBneck2 nucleic acid parameters introduced with AmberTools 15. This should make sure that all Amber14 tests pass after upgrading.
  • update.13: Fixes GPU-COM distance restraint bug in pmemd.cuda. Adds error checking code to catch ir6 = 1 when used with GPU-COM distance restraints. Improves the GPU-COM distance restraint test cases.

Amber12 Updates (March, 2012)

  • bugfix.1: Fix issue where restart files from pmemd can be truncated upon abnormal termination of

    pmemd

    .
  • bugfix.2: This updates the version number of all Amber programs (

    sander

    ,

    pmemd

    , and

    addles

    ) to report Amber 12.
  • bugfix.3: This turns EMAP reading errors into fatal errors and fixes restart file printing for pmemd minimizations (completing bugfix.1)
  • bugfix.4: Prevents potential user errors with the QM/MM interface to external QM packages if the QM region has a charge. Also included are missing test files for mechanical embedding.
  • bugfix.5: Fix to prevent compilation and linking errors on

    sander.PUPIL

    program.
  • bugfix.6: Sometimes the temperature was not set from the ASCII restart file when restarting a T-REMD simulation.
  • bugfix.7: Fix bugfix.1 so you don't get errors opening the restart file if you don't use "-O" on the command-line.
  • bugfix.8: Remove an optimization directive that causes sporadic softcore-TI run SHAKE errors with some compilers.
  • bugfix.9.bz2_: Large CUDA upgrade patch. This is a major update to the GPU support in AMBER 12 and also contains minor bug fixes for the CPU version of pmemd.
    1. Support for Kepler K10 and GTX6XX GPUs
    2. New, high-performance, lower-memory footprint hybrid fixed precision model: SPFP
    3. Support for REMD using 1 GPU per replica
    4. Various bugfixes and tweaks for aMD, IPS, GB and NMR restrained simulations
  • bugfix.10: Multiple bugfixes for regular and softcore TI.
  • bugfix.11: Update to bugfix.10, for the net charge removal code.
  • bugfix.12: Fix race condition in pmemd.cuda.MPI that may cause failures in parallel GPU simulations.
  • bugfix.13: Fix the instability problem of H-REMD trajectories (both sander and pmemd) by swapping velocities as well as coordinates. updating test/h_rem and test/cnstph_remd appropriately.
  • bugfix.14: Multiple fixes and updates for GPU code:
    1. Adds support for CUDA Toolkit 5.0
    2. Fixes bugs in the Jarzynski code on GPUs and re-enables it.
    3. Fixes a bug with the use of harmonic restraints when running with NPT.
    4. Enables GBSA simulations in GPU runs.
    5. Updates requested citations.
    6. Fixes uninitialized variables in NMRopt = 1 runs that could cause crashes with some compilers.
    7. Adds check for forgetting to specify gamma_ln with ntb>1 and ntt=3 .or. 4
    8. Updates GPU code to v.12.2
  • bugfix.15: Fixes for QM/MM Ewald:
    1. Add self-plasma term for charged systems
    2. Improve default values for k space vectors
    3. Corresponding updates to tests
  • bugfix.19: Minor updates to

    pmemd.cuda

    :
    1. Adds support for CUDA 5.5. - via accompanying AMBERTools 13 bugfix.16.
    2. Disables NMROPT on multiple GPUs due to unfixed bugs in the MPI version at present.
    3. Enables support for GTX-Titan and GTX780 GPUs and checks that the minimum required driver version of v325.15 is installed.
    4. Fix spurious crash with kNLBuildNeighborListOrthogonal16_kernel for systems containing large vacuum bubbles or very low density.
    5. Updates GPU code citation.
    6. Adds missing test case output for GPU Jarinski Tests.
    7. Updates GPU code to v12.3.1
  • bugfix.20: Allow

    pmemd.cuda

    to run with CUDA driver version 319.60 or older.
  • bugfix.21: EXTERN QM/MM enhancements and bug fixes:
    • For Orca:
      1. Fix bug with forces on MM atoms (update read format for Orca .pcgrad files)
      2. Fix problems with parallel Orca runs
      3. Enable single point trajectory post-processing
      4. Update dipole moment output to Debye
    • For Gaussian:
      1. QM/MM with MP2 and electrostatic embedding now uses MP2 density to compute correct MP2 forces on MM atoms
      2. Allow 256 character route section (avoids truncation)
      3. Fix problems with Gaussian 03
    • For ADF:
      1. Update dipole moment ouput to Debye
    • For all:
      1. Template input files support 256 characters per line (avoids truncation)
      2. Input of charge and spin multiplicity in the namelist of the external
      3. QM program has been deprecated - this needs to be given in the &qmmm namelist (variables qmcharge and spin)
      4. Includes updates to tests

Amber11 Bug Fixes (April, 2010)

  • bugfix.all.tar.bz2 This is the complete package of bug fixes for Amber 11. Apply it in this manner:
    chmod 700 apply_bugfix.x
    ./apply_bugfix.x /path/to/bugfix.all.tar.bz2
    This should patch your source files with the latest bugfixes. Any bugfixes that appear to have already been applied will be skipped. You can then go to the $AMBERHOME/AmberTools/src directory, type ./configure ‐‐help, and continue with the installation.
  • bugfix.1: Fix possible imaging issues for QMMM calculations using very small boxes.
  • bugfix.2: Fix problems when water molecules were included as part of a softcore region. Be sure to apply bugfix.15 as well.
  • bugfix.3: Do not allow es_cutoff /= vdw_cutoff in

    pmemd.CUDA

    .
  • bugfix.4: Fix possible segfault when running with iwrap = 1 in

    pmemd.CUDA

    .
  • bugfix.5: Update bugfix.4 to also support ntb = 2.
  • bugfix.6: Exit gracefully if user asks for GB or PB with PUPIL: this combination is not supported.
  • bugfix.7: Fix mm_pbsa: clean finish, greater 255 threads, space tolerance
  • bugfix.8: Certain versions of the Intel Compiler may not optimize

    pmemd

    correctly at link time, leading to poor performance.
  • bugfix.9: This is a large scale bug and feature patch for the AMBER 11 NVIDIA GPU (CUDA) code developed in close collaboration with NVIDIA. Specifically

    pmemd.cuda

    . The patch addresses a number of outstanding bugs, includes some minor single GPU performance improvements, and most importantly, through funding provided by NSF Grant 1047875 and UC Lab award 09-LR-06-117792-WALR, provides support for MPI runs over multiple GPUs. For updated installation instructions and performance numbers please see: http://ambermd.org/gpus/
  • bugfix.10: The alpha, beta, and gamma OBC parameters were never initialized for hybrid REMD methods. This affects the cases hybridgb = 2 or hybridgb = 5, but hybridgb = 1 works as expected.
  • bugfix.11: CUDA: Segfaults and/or shake failures could occur when running NPT calculations, with truncated octahedron boxes and restraints on molecules identified to be part of the solvent. This bug fix addresses this. It also restricts the selection of FFT grid dimensions for GPU runs to match those that provide optimum performance with NVCC v3.2.
  • bugfix.12: CUDA: Fixes several recently discovered bugs in the CUDA code. This includes problems when using cutoffs or .gt. 8.0 when running with small boxes. Fixes problems with large simulations, such as the cellulose benchmark dying randomly with an allocation failure and also provides a possible workaround for simulation hangs experiences on GTX4XX and GTX5XX series cards.
  • bugfix.13: TI requires identical trajectories between both groups in multisander. If the random seed is different for each group, then the coordinates diverge from one another and the simulation blows up. The same thing happens if the user inputs different seeds. Fix this by broadcasting the worldrank==0's ig value to all other commsander masters in mdread.f.
  • bugfix.14: A bug in keeping running averages accumulates the wrong total Epot on one of the nodes. This only occurs when ntave .ne. 0. The fix also changes the expected output for a softcore test.
  • bugfix.15: This completes bugfix.2 which allows atoms with a negative ic type to be flagged soft core. The fix now checks for that possibility and correctly ignores 10-12 flagged vdW interactions. Previously, this could lead to unallocated values added to the potential. The problem mainly concerns decoupling water molecules. Be sure to apply bugfix.2 first.
  • bugfix.16: For some circumstances with "use_sander=1" in

    MMPBSA.py

    , a bug of

    sander

    would prevent it from finishing all the trajectory frames. This is something to do with imin = 5 option and

    PBSA

    module. This fix introduces the fix from the developer's tree that Irvine team already pushed several months ago.
  • bugfix.17: This bugfix is included in part of the tarball bugfix.all.tar.bz2 and does not exist as a standalone file. It must be applied as described at the top of this page. This updates the

    pmemd.cuda

    GPU support from v2.1 to 2.2. This update effectively doubles PME performance across the board and addresses a number of bugs including issues with running NPT calculations with restraints and running simulations with organic solvents. It additionally adds support for extra points in the GPU code. A complete list of items addressed by this update is available here.
  • bugfix.18: This bugfix is also included in the tarball bugfix.all.tar.bz2, but it can be applied directly using patch -p0 -N < bugfix.18 from AMBERHOME. This patch fixes the calculation of 10-12 non-bonded terms in

    sander

    and

    pmemd

    .
  • bugfix.19: This patch fixes weird many-millions of steps crashes for large (9A and up) nonbond cutoffs. This bugfix is also included in the tarball. bugfix.all.tar.bz2, but it can be applied directly using patch -p0 -N < bugfix.19 from AMBERHOME.
  • bugfix.20: Fix for multiple GPU issues, including NaN results when iwrap=1 and a possible hang at MPI_Win_fence() caused by vacuum bubbles in the solvent. This bugfix is also included in the tarball. bugfix.all.tar.bz2, but it can be applied directly using patch -p0 -N < bugfix.20 from AMBERHOME.
  • bugfix.21: Fix issues with running NPT calculations with Chamber prmtops on GPUs.
  • bugfix.22: Fixes problems with restart files being truncated in

    pmemd

    /

    pmemd.cuda

    on certain linux installations.
  • bugfix.23: Completes bugfix.22 so restart file writing behavior is correct.

Amber10 Bug Fixes (April, 2008)

  • 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. This also adds support for ig = -1, setting of the random number seed to the wallclock in microseconds, to

    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
  • bugfix.31: The

    pmemd

    program may run out of lone-pair space for some

    glycamEP

    runs
  • bugfix.32: Thermodynamic integration calculations in sander will fail when the dvdl_norest parameter is set.
  • bugfix.33: 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]
  • bugfix.34: 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 cut off.
  • bugfix.35: Fix possible imaging issues for QMMM calculations using very small boxes.

Amber9 Bug Fixes (April, 2008)

  • bugfix.all: This patch script contains all of the bug fixes detailed below in a single patch script. You can patch your amber 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 -r patch_rejects < 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 amber.
  • bugfix.1:

    ptraj.c

    may fail to compile with some compilers.
  • bugfix.2: Solvent accessibility calculations using

    pbsa

    may crash on some machines.
  • bugfix.3: Compilation of

    LEaP

    may fail on some versions of MacOSX.
  • bugfix.4:

    Antechamber

    may have memory problems on some machines when analyzing ring systems.
  • bugfix.5: The

    frcmod.ff03

    is corrupted, giving bad backbone torsions.
  • bugfix.6: The "make clean" command in the lmod directories removes too many files.
  • bugfix.7: The

    ambmask

    program has a bad initialization.
  • bugfix.8: The iwrap=1 option in pmemd does not work correctly.
  • bugfix.9: Poisson-Boltzmann calculations on some machines can lead to a divide-by-zero.
  • bugfix.10: The

    top2mol2

    program does not explicitly set a return value.
  • bugfix.11: Minimizations in

    sander

    can trigger a divide-by-zero error.
  • bugfix.12:

    Antechamber

    fails on long input files of type prepi and prepc.
  • bugfix.13:

    bondtype

    may have memory problems for some molecules.
  • bugfix.14: A correction (for some compilers) to bugfix 12 for

    antechamber

    .
  • bugfix.15:

    ptraj's

    actions.h may fail to compile with some compilers.
  • bugfix.16:

    sander

    's lmod.f fails to compile with gfortran.
  • bugfix.17: The "make clean" command in the

    lmod

    directories doesn't remove enough files.
  • bugfix.18:

    sander

    can give a bad information message in some QM/MM calculations.
  • bugfix.19: Removes the requirement that there be a space after "TER" in pdb files.
  • bugfix.20: Fixes quasiharmonic analysis in

    ptraj

    when the eigenvector file has more than 9999 elements.
  • bugfix.21: Workaround for an Intel v9.1 compiler bug that can cause calculations that use

    divcon

    , including

    sander

    calculations that use divcon for the QM/MM part, to segfault.
  • bugfix.22: Statistics on born radii will be incorrect if nrespai is used.
  • bugfix.23: Some benchmarks that were meant only for development purposes were acidentally left in the benchmark makefile.
  • bugfix.24: The

    ff03ua

    force field is missing a parameter needed for HID residues.
  • bugfix.25:

    LEaP's

    setbox command ignores its third argument.
  • bugfix.26: Error messages related to incorrect spin and charge combinations can give fortran formatting errors instead of the actual error message.
  • bugfix.27: Increase

    sander

    's ability to handle complex masks for QM/MM
  • bugfix.28: The (usused) random.F90 file in

    dcqtp

    may fail to compile with some compilers.
  • bugfix.29: Fix for some new C compilers that have trouble compiling

    Xleap

    . Addresses the specific error: conflicting types for XawScrolledTableSetLocation.
  • bugfix.30: Numerous minor bug fixes that may cause problems such as segfaults or file open errors on some systems depending on the compiler being used.
  • bugfix.31: Updates to the iRED analysis facility in

    ptraj

    , to provide more precision and more eigenvalues/eigenvectors.
  • bugfix.32: Fix an error when the rk2a parameter is not set for Jarzynsky runs.
  • bugfix.33: Allow sander to compile when -DHAS_10_12 is specified.
  • bugfix.34: Allow sander to compile on SGI Altix with netcdf support.
  • bugfix.35: Fix problem with final Mulliken charges not being printed in QM/MM simulations. This patch also updates the DFTB test cases to coincide with the changes that were made by bugfix.18.
  • bugfix.36: Fix problem with some gas phase simulations incorrectly switching to a less efficient list building algorithm.
  • bugfix.37: Fix problem whereby some QM/MM simulations could crash if the QM region diffused out of the central box.
  • bugfix.38: This bugfix resolves an issue with the SMD module in which the program would generate and error if the moving distance was large (around 100 Angstroms).
  • bugfix.39: Update

    pmemd

    to provide better GB performance on the IA64 (Itanium) architecture.
  • bugfix.40: The

    ambmask

    program has some obsolete use of integers as characters.
  • bugfix.41: Fix up the first energy when generalized Born is used with nrespa > 1.
  • bugfix.42: Add warning message and stop the calculation when spin > 1 is used in QMMM calculations.
  • bugfix.43: Fix to allow the "-y" switch to work for imin = 5.
  • bugfix.44: Fix to restart behavior in replica exchange runs.
  • bugfix.45: elsize.cc may fail to compile with some compilers.
  • bugfix.46: Fix possible allocation failures during

    sander

    QMMM startup.
  • bugfix.47: Constant pH with closely interacting residues can misbehave due to an incorrectly formed tpair array.

Amber8 Bug Fixes (March, 2004, CVS tag: v8_0)

  • bugfix.all: This patch script contains all of the bug fixes detailed below in a single patch script. You can patch your amber 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 -r patch_rejects <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 amber.
  • bugfix.1:

    LEaP

    may crash when writing a prmtop for a unit with unbonded hydrogens.
  • bugfix.2: The configure option -scali does not produce MPI executables.
  • bugfix.3:

    Antechamber

    will mis-read pdb files that have a non-blank chainID.
  • bugfix.4:

    PBSA

    can fail with a "PB Bomb in epsbnd()" error message.
  • bugfix.5: The configure targets hpf90 and HP-UX do not produce a functional

    xleap

    .
  • bugfix.6: antechamber will generally fail when the input is a mol2 file; plus other smaller antechamber fixups.
  • bugfix.7: Using a restraintmask or a bellymask that invokes distance comparisons will fail.
  • bugfix.8: A follow-on to bugfix.6: needed if you use antechamber with both the -fi mol2 and the -j 5 flags at the same time.
  • bugfix.9: The ioutfm = 1 option in sander is broken.
  • bugfix.10: The

    leaprc.ff03

    file loads old versions of ACE and NME protecting groups.
  • bugfix.11: New format prmtop files with more than 999999 lines are read incorrectly.
  • bugfix.12: Having zero masses for extra points can cause problems on some machines.
  • bugfix.13: Several fixes to sander.QMMM.
  • bugfix.14:

    LEaP

    can print out incorrect warnings about perturbed charges
  • bugfix.15: Improved error reporting in transforming chirality orientations in

    LEaP

    .
  • bugfix.16: Parallel sander might fail on some platforms due to a bad broadcast.
  • bugfix.17: The

    ptraj

    program may give spurious errors about not being able to open a file for output when writing amber restrt files.
  • bugfix.18: Group specifications don't work correctly when igrp(i) < 0.
  • bugfix.19: Charges for neutral lysine (LYN) are incorrect in the ff03 force field.
  • bugfix.20: The

    glycam04EP.dat

    file has some spurious lines that need to be removed.
  • bugfix.21: Remove empty Fortran statements that NEC compilers (and others?) won't accept.
  • bugfix.22: The anal program prints an incorrect error message for insufficient memory.
  • bugfix.23: Constant pH simulations with only a single titrating site may fail.
  • bugfix.24: Use of the grid command in ptraj will sometimes fail.
  • bugfix.25: Langevin dynamics will fail when the target temperature is changed during the run.
  • bugfix.26: MD simulations with

    sander.QMMM

    involving link atoms may fail.
  • bugfix.27:

    Sander

    class="ourapp"> fails to ignore the dielc variable for GB calculations; this can lead to problems with mm_pbsa if the interior dielectric is not unity.
  • bugfix.28: The

    gaff.dat

    parameter file has some duplicate and erroneous entries.
  • bugfix.29: Fixes possible segmentation fault in

    ambpdb

    . Also adds dynamic memory allocation to

    ambpdb

    .
  • bugfix.30: If the Intel C/C++ compilers are used, icpc should be used for the

    bondtype

    program, not icc.
  • bugfix.31: The

    pmemd

    program can write unnecessary information to fort.35 if DUMPAVE is requested.
  • bugfix.32: The mden file can contain a bad value for pressure when the pressure is not being regulated.
  • bugfix.33: The forces for "cap" water are not accompanied by a corresponding energy term. (See also bugfixes 40, 43 and 45, below.)
  • bugfix.34: The OMIT_NAMES option to

    prepgen

    may not work correctly.
  • bugfix.35: The

    pmemd

    program won't compile with the Portland group compiler.
  • bugfix.36: The GROUP commands don't work in nmode.
  • bugfix.37: Some targeted MD tests are not suitable for running in parallel and may make the test procedure fail.
  • bugfix.38: Modifications to pmemd for the pathscale compilers.
  • bugfix.39: The configure targets sparc and SunOS do not produce a functional

    xleap

    .
  • bugfix.40: Same as bugfix.33, but also for

    sander.QMMM

  • bugfix.41: Resetting an atom's pertType in

    tleap

    does not update the PERTURBED flag.
  • bugfix.42: Modify

    leap

    's bond command to use S, D, T, A for single, double, triple and aromatic bonds, instead of -, =, #, :, respectively. The old method might not work on all machines.
  • bugfix.43: Updates the test case results that were changed as a result of bugfix.33.
  • bugfix.44:

    LEaP

    may crash when loading a prep file with LOOP bonds between atoms of type dummy.
  • bugfix.45: Updates another test case result that was changed as a result of bugfix.33.
  • bugfix.46: Protects

    pmemd

    from very rare error involving incorrect fractional coordinates.
  • bugfix.47: Fixes MPI calls in

    sander

    when the noBTREE is set during compilation.
  • bugfix.48: Fix potential error with nmr weight restraints where value1 or value2 = 0.0.
  • bugfix.49: The

    pbsa

    program can output highly fluctuating reaction field energies for neutral systems.
  • bugfix.50: The

    sander

    program can produce erroneous errors related to FFT dimensions for large non-periodic systems.
  • bugfix.51: Use of TIP3PBOX or SPCBOX directly (not via the solvateoct or solvatebox commands) in

    Leap

    can create an inpcrd file with incorrect box angles.
  • bugfix.52: Manual setting of lastrst needs to be allowed for regular Ewald simulations.
  • bugfix.53: Leap: Improper torsions specified in a frcmod file may not trump the same improper torsions defined in the main parmxx.dat file.
  • bugfix.54: The ntt = 2 option in sander can result in average temperatures that are too high.
  • bugfix.55: The

    pmemd

    doesn't properly echo the title of new-style prmtop files.
  • bugfix.56: Update to bugfix.54, which failed to work properly in parallel.
  • bugfix.57: Equivalent to bugfix.11, for

    pmemd

    .
  • bugfix.58: Equivalent to bugfixes 32, 54, and 56, for

    pmemd

    .
  • bugfix.59: Compiling

    sander

    with MMTSB support may fail.
  • bugfix.60: Provide 64-bit support for

    xleap

    .
  • bugfix.61: Solvent accessibility calculations with

    pbsa

    may fail on some machines.
  • bugfix.62: The

    ambpdb

    program doesn't allocate enough space for an internal array.
  • bugfix.63: The iwrap = 1 option in

    pmemd

    does not work correctly.
  • bugfix.64: A workaround to ifort compiler bugs on itanium (ia64) machines
  • Older versions of Amber are no longer supported for bug fixes. If you are using one of these versions, all of the functionality that you might have gotten through the

    sander

    program or auxiliary software are now distributed freely with much never releases of AmberTools.

"Insert clever motto here."

Last modified: Feb 10, 2018