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AmberTools Bug Fixes and Updates

Note: The individual bug fixes for AmberTools are described below in case you want to see what they do, or apply patches by hand. Most users are encouraged to use the update_amber script (which is automatically run during the cmake 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 4, or just go to your amber20_src directory and type

./update_amber --help

If you wish to apply the listed AmberTools updates, run cmake again.

Version 21 (April, 2021)

No updates yet.

Version 20 (April, 2020)

  • update.1: Fix the compiler optimization levels for

    sander

    .
  • update.2: Various bugfixes for

    cpptraj

    .
  • update.3: Various bugfixes for

    packmol-memgen

    .
  • update.4: Improve error reporting in

    LEaP

    .
  • update.5: Fix Miniconda to allow

    pytraj

    and

    pdb4amber

    to install properly.
  • update.6: Support Ampere GPU's and Cuda 11.0.
  • update.7: Update the way Plumed handles truncated octahedral boundary conditions.
  • update.8: Fix test case for RAMD; see bugfix.4 for Amber20.
  • update.9: Update

    sander

    to the latest version of plumed.
  • update.10: Add the ff1ipq-m force field for protein mimetics.
  • update.11: Teach

    cmake

    about .tbd files on OSX
  • update.12: Update some C code to the C99 standard; allows building on OSX 11
  • update.13: Support use of CUDA SDK version 11.1
  • update.14: Updates to the ff15ipq-m force field files
  • update.15: Support Ampere GPUs in the legacy build procedure

Version 19 (April, 2019)

  • update.1: Remove some pmemd.MPI test cases that should not be run.
  • update.2: Avoid using the wrong pdb files in

    packmol-memgen

    .
  • update.3: Fix command-line parsing in

    rism3d.snglpnt

    .
  • update.4: Add molecular reconstruction analysis to 3D-RISM calculations in

    sander, rism1d, rism3d.snglpnt

    .
  • update.5: Have configure download the current Miniconda version (4.6.14) since the earlier version now gives problems for Python 2.
  • update.6: Fix test cases to be more resilient on newer Linux distributions.
  • update.7: Modifies

    rism3d.snglpnt

    command line argument parsing, enabling MMPBSA.py to work with 3D-RISM.
  • update.8: Modifies the way softcore free energy calculations are done in

    sander

    ; more info.
  • update.9: Add files needed to implement the ff19SB protein force field.
  • update.10: Fix the +3 and +4 ion parameters for TIP3P and TIP4P/EW water models.
  • update.11: Add a cluster size check for cluster-particle interactions in the 3D-RISM treecode.
  • update.12: Fix problem with downloading miniconda on Mac OSX

Version 18 (April, 2018)

  • update.1: Fix compilation of

    cpptraj

    with Intel compilers on older systems.
  • update.2: Adds an error message to

    sander

    when users run REMD and the box sizes are not the same across all replicas.
  • update.3: Fixes typo in

    genremdinputs.py

    's help message, and corrects E,pH,T-REMD and pH,T-REMD tests affected by Amber18's update.2.
  • update.4: Fixes test for boost libraries need by

    packmol_memgen

    .
  • update.5: Fixes a memory leak in NAB/libsff programs.
  • update.6: Updates the sample

    rism1d

    mdl files, to reflect up-to-date ion parameters.
  • update.7: Updates the configure script to allow cuda version 9.2 to be used.
  • update.8: This update fixes the following:
    1. Corrects REMD error trap for different box sizes in

      sander

      to account for non-periodic systems.
    2. Bugfix in

      sander

      to properly restart MultiD-REMD simulations with two or more pH, redox potential or temperature dimensions.
    3. Corrects one Amber test affected by the bugfix.
    4. Fixes typos in

      fitpkaeo.py

      and

      genremdinputs.py

      .
  • update.9: Companion patch to the Amber update.4, updating the configure script (which is a part of AmberTools). This patch only affects

    pmemd.cuda

    .
  • update.10: Fix and extend the NFE capabilities in

    sander

    .
  • update.11: Small tweaks to the parallel version of

    rism3d

    .
  • update.12: Updates test cases for mcwat in

    pmemd

    .
  • update.13: Configure script changes to go along with update.12 for Amber18.
  • update.14: Bring rism1d test cases output up to the current code.

Version 17 (April, 2017)

  • update.1: Fix MDL SDF file reading and make other minor improvements in the

    antechamber

    package.
  • update.2: Fix the way in which

    pytleap

    uses gaff2.
  • update.3: Fix file format usage in

    antechamber

    's acdoctor mode and make other minor improvements.
  • update.4: Add option to

    pdb4amber

    to allow reduce to be used for proteins but not for ligands.
  • update.5: Fix uninitialized variable usage in

    pyMSMT

    .
  • update.6: Add missing "cs" atom type to

    parmchk2

    database.
  • update.7: Fix some histidine ring dihedral parameters that were incorrectly interpreted by tleap in the

    ff15ipq

    force field.
  • update.8: Add support for CUDA 9.0 compilation and add support for V100 GPUs.
  • update.9: Adds an error message to

    sander

    when users run REMD and the box sizes are not the same across all replicas.
  • update.10: Corrects REMD error trap for different box sizes in

    sander

    to account for non-periodic systems.

"How's that for maxed out?"

Last modified: May 3, 2021