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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 2024 Reference Manual in Chapter 2, Section 4, or just go to your amber22_src directory and type

./update_amber --help

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

Version 24 (April, 2024)

  • update.1: Add missing file for AMD GPUs
  • update.2: Pin python from Miniconda to version 3.11, since some systems seem to have issues with version 3.12
  • update.3: Adds tests for


    that supports Thermodynamic Integration Atomic Decomposition; partner to update.2 for Amber24.

Version 23 (April, 2023)

  • update.1: Minor update to


    to fix densities.
  • update.2: Fix an OPC3POLBOX water box bug where "gaps" could occur.
  • update.3: Update


    to support python 3.11.
  • update.4: Adds "extra_solvents.lib", needed for some applications of


  • update.5: Support python 3.11 and update mpi4py.
  • update.6: PMMG and PACKMOL bugfixes.

Version 22 (April, 2022)

  • update.1: Allows

    to display graphs
  • update.2: Update checks on compatible GNU and NVIDIA releases; support NVIDIA 11.7
  • update.3: Update the TeraChem (TCPB-cpp) QM/MM interface
  • update.4: Use bash to run the Miniconda installation script
  • update.5: Fix compatibility with parmed version 4.0.0

Version 21 (April, 2021)

  • update.1: Update


    to work with gfortran11.
  • update.2: Update the way




    are installed.
  • update.3: Update ion parameters in leaprc.water.{opc,tip3p-fb,tip4p-fb}.
  • update.4: Fix v/v concentrations for solvents in


  • update.5: Update


    to handle blank chain-ID's.
  • update.6: Updates to the ff15ipq-m force field files.
  • update.7: Avoid an installation error message if miniconda pip is not present
  • update.8: Adds mcwat test cases for pmemd and pmemd.cuda
  • update.9: Adds support for 3D-RISM on periodic systems like macromolecular crystals.
  • update.10: Adds missing extra_solvents.lib and fixes the 2LPG packing param in


  • update.11: Adds readline support to


  • update.12: Updates how cmake searches for readline.

Version 20 (April, 2020)

  • update.1: Fix the compiler optimization levels for


  • update.2: Various bugfixes for


  • update.3: Various bugfixes for


  • update.4: Improve error reporting in


  • update.5: Fix Miniconda to allow




    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


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


    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


  • update.3: Fix command-line parsing in


  • 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


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


    ; 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


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


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

    '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


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


    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


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


      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


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


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


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


  • update.12: Updates test cases for mcwat in


  • 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


  • update.2: Fix the way in which


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


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


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


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


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


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


    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


    to account for non-periodic systems.

"How's that for maxed out?"

Last modified: Jun 18, 2024