Useful links:

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 compile_with_hip.sh 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

  pmemd.decomp

  that supports
• update.4: Fixes search path for

  pdb2pqr

  .
• update.5: Pins numpy at version 1.26.4; replace miniconda with miniforge3
• update.6: Updates nlopt to version 2.8; uses installed libraries if found

Version 23 (April, 2023)

• update.1: Minor update to

  pbsa.cuda

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

  pytraj

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

  packmol-memgen

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

Version 22 (April, 2022)

• update.1: Allows

  mdout_analyzer.py

  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

  sander

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

  pytraj

  and

  pdb4amber

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

  packmol-memgen

  .
• update.5: Update

  pdb4amber

  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

  packmol-memgen

  .
• update.11: Adds readline support to

  cpptraj

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

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.