AMBER Page

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 you don't want to use update_amber for some reason. For versions of AmberTools older than version 12, see the instructions associated with that particular version, although we strongly suggest upgrading to the latest version since numerous bugs have been fixed and they are actively supported.

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 the listed AmberTools updates, run configure again and make sure to re-compile Amber/AmberTools.

Version 18

April, 2018

update.1: Fix compilation of cpptraj with Intel compilers on older systems.

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.

Version 16

April, 2016

update.1: LEaP, fixes typo in leaprc.water.tip4pew.
update.2: RISM, fixes bug in RISM excess charge for solvents containing ions; bug in volume for non-orthorhomic cells; re-labels some output to be more like previous versions.
update.3: cpinutil.py, fixes bug when trying to write a radii-adjusted prmtop file when generating a cpin file for CpHMD simulations in explicit solvent.
update.4: fixes apparent failure in the BSC1 DNA force field test. Code is/was always OK, but tests were using out-dated comparison files.
update.5: adds AmberTools components for Intel Xeon & Xeon Phi (KNL) pmemd support
update.6: adds support for CUDA 8.0 and Pascal (GTX-1080) hardware.
update.7: adds a leaprc.water.spceb file, especially for use with ff15ipq
update.8: improve reading of ccif files in antechamber
update.9: New free energy routines in sander; see nfe.pdf for full documentation.
update.10: Very minor tweaks to allow compilation with gcc6
update.11: Support Titan-XP.
update.12 Update cpptraj to version 16.12. Fixes the following:
1. Correctly handle Amber restart files with no EOL.
2. Fix potential compilation issue with stringstreams and bleeding-edge compilers.
3. Fix reading of force information when velocity information is not present.
4. Fix 'stfcdiffusion' command: initial coordinates are now properly set up when atom mask selecttion does not start at the first atom, and distance calculations are now properly image when a second mask is specified.
5. Fix 'stat' analysis command: torsion values between 0.0 and 30.0 are now correctly assigned as 'c'.
6. Fix potential memory issue when inverting atom masks.
update.13: Add some missing hybridizations and non-bonded parameters to gaff2 files.
update.14 Update cpptraj to version 16.14. Fixes the following:
1. Fix bug in 'crdaction' for actions that modify topology (e.g. strip, closest, etc).
2. Fix reading extended format for CHARMM COR files.
3. Fix potential segfault in 'rotdif' command when 'corrout' file can not be opened.
4. Fix potential segfault when reading CIF files.
5. PDB: Atom names with 2 character element names are now correctly aligned on column 13 instead of 14.
6. PDB: Fix conversion of nucleic acid residue names for 'pdbres'.
7. PDB: Water residue name now changed to HOH for 'pdbres' to be consistent with PDB V3 standard.
8. PDB: Residue numbers > 9999 and atom numbers > 99999 now wrap to 0 instead of 1 to make atom/residue counting easier.
9. PDB: Make sure when 'terbyres' is specified that TER cards are printed when going from solvent to solute as well as vice versa.

update.15 Update ParmEd to version 2.6.1. Numerous updates and improvements. For a full list, see https://github.com/ParmEd/ParmEd/releases/tag/2.6.0 for more information.

update.16 Update cpptraj to version 16.16. Fixes the following:
1. Fix compilation with OpenMPI 2.
2. Fix handling of shape matrix information in CHARMM trajectories.
3. Fix detection of rhombic dodecahedron unit cells.
4. In the 'drmsd' command correctly set reference mask from reference expression.
5. PDB: For 'terbyres' option do not put TER cards between ions (same behavior as solvent).
6. PDB: Actually make PDB atom/residue numbers wrap to 0 after 99999/9999.
7. PDB: For 'terbyres' option correctly output nonstandard residues as HETATM.
8. Removes an unnecessary file from the cpptraj test directory.

update.17 Fix 3D-RSIM codes to correct for double counting of the solute-solvent potential energy.

update.18 Fix pbsa for uniform dielectric; update options when frcopt=0.

update.19 Fix addles to treat larger molecules, allow multiple conformations in the solvent

update.20: Changes to the configure script to accommodate update.6 for Amber16.

update.21: Changes to the atom names and charges of the OHE residue, for use with 5' terminal phosphates in RNA

update.22: Forces update_amber to use Python 2, since the upgrade process in this case requires that.

Version 15

May, 2015

update.1: ParmEd, MMPBSA.py, and cpptraj:
Three main fixes:
1. Fixes Python 2.4 and 2.5 support for MMPBSA.py and ParmEd
2. Fixes the MMPBSA.py Python API
3. Fixes charge scaling in cpptraj's LIE action when non-unity dielectric constant is specified

update.2: Adds support for CUDA 7 and fixes an erroneous error message regarding Python modules when building only OpenMP, CUDA, or CUDA-MPI versions of Amber.

update.3: Bugfix for LMOD docking where there are fixed atoms in the receptor

update.4: Update to the Lipid14 force field to add cholesterol parameters. See Madej et al, J. Phys. Chem. B. 2015.

update.5: Fix Python 2.6 compatibility with ParmEd

update.6: Adds support for CUDA 7.5. Optional support given to CUDA 7.0 due to performance regressions and GPU selection errors.

Version 14

April, 2014

update.1: charmmlipid2amber.py:
1. charmmlipid2amber.py is a script to prepare lipid PDB format files to be read with LEaP for the Lipid14 force field.
2. The script takes PDB files in the CHARMM lipid format (i.e. from the CHARMM-GUI web site) and converts them into a format that LEaP can read with the Lipid14 force field.
3. More generally, this script can rename atoms in residues, reorder atoms in residues, and add TER cards to residues in PDB format files.
4. charmmlipid2amber.py replaces charmmlipid2amber.x (deprecated).
update.2: A handful of small fixes for cpptraj, ParmEd, makeANG_RST, tleap, and the ff14ipq force field. Specifically,
1. Cpptraj:
  - Fix OpenMP compilation with certain PGI compilers.
  - Fix bug where topology was not properly modified in 'crdaction' command.
  - Fix bug where incorrect exclusion list could be written after a 'parmstrip' command.
  - Fix 'lifetime' analysis 'max' and 'avg' file output when file is not in current directory.
  - Fix potential segfaults that could occur when processing malformed mask expressions.
  - Fix bug in 'lifetime' analysis of solvent hydrogen bonds (*[solventhb] data sets).
  - Fix 'nmwiz' output for 'diagmatrix' analysis command; additional mask can now be specified with 'nmwizmask' so that nmwiz output can match eigenvector output.
2. ParmEd:
3. tleap:
4. makeANG_RST:
5. ff14ipq:
6. reduce:
7. Updated cpptraj functionality:
update.3: Improve error handling and small fixes for tiMerge in ParmEd
1. Fixed error handling for the tiMerge command. Added additional checks to make sure molecules to be merged are adjacent in the input topology file. Increased the default tolerance to 0.01 to prevent issues with merging larger molecules with small coordinate differences.
update.4: Fix a number of small bugs in ParmEd, tleap, and MMPBSA.py:
1. Improve 10-12 potential detection in ParmEd when printing warnings that these topology files are not supported by frcmod file writing
2. Fix identification of angle-with-hydrogen torsions in rare cases where hydrogens are connected to both heavy and dummy atoms
3. Fix subtle bug in alanine scanning in MMPBSA.py that occasionally results in bad mutations.
4. Fix determination of dihedral parameter equality in ParmEd, eliminating duplicate (but reordered) dihedral parameters in frcmods printed from topology files.
5. Dramatically improve performance of tleap when it has to split many residues (like with CHARMM-converted lipid PDBs)

update.5: Fix a number of small bugs in PBSA that were patched in previous releases but were missing in the latest release:
1. Memory allocation for torsional parameters was too small in locmem.
2. Potential printing was in the internal unit.
3. PBSA failed to stop when radii and charges are missing from prmtop.
4. Misc updates in warning and error messages.

update.6: Fixes for cpptraj: update to version 14.05.
1. Fix segfault in 'atomiccorr' action.
2. Fixes for DSSP algorithm; SS priority is better taken into account, which fixes odd SS patterns that could occasionally pop up. Add bend SS output. Add 'totalout ' which writes total SS over all residues vs time, and 'assignout ' which prints overall SS assignment based on averages in a format similar to PDB. Also fix potential segfault when using 'ptrajformat' output.
3. Fix bug in projection of dihedral covariance that led to incorrect results/memory errors.
4. Fix potential segfault when trying to use stripped reference structure.
5. Fix potential segfault caused by not enough frames in rmsavgcorr calc.
6. Fix problem where loading multiple trajectories into a TRAJ Coords DataSet would fail.
7. Fix potential topology-related bug when ensemble processing with a single thread.
8. Fix segfault in 'statistics' torsion/pucker analysis from invalid values like NaN.
9. Fix 2 character element name recognition in PDB files.
10. Fix incorrect detection of dihedrals between separate molecules in 'multidihedral'.
11. Fix potential issues when compiling OpenMP with certain compilers.
12. Fix bug in 'pairwise' that precented delta Es from being calculated.

update.7: Fixes for paramfit and chamber:
1. Paramfit:
2. Chamber:

update.8: Xeon Phi support for pmemd:
1. Adds MIC offload support to pmemd.
2. Modifies configure and test suite to support use of Intel Xeon Phi card as an accelerator for the direct space sum.

update.9: Fixes for cpptraj: update to version 14.09.
1. 'projection' action will attempt to read modes data from file if no data set is present; restores backwards compatibility with older scripts.

update.10: Fixes for netcdf:
1. Small fix to defines in netcdf.

update.11: Fixes for chamber:
1. Allow chamber to process longer atom types.
2. Fixing bug where parameters could be assigned incorrectly.
3. Allows greater compatibility with CGenFF.

update.12: Support CUDA 6.5:
1. Update GPU code to support NVCC CUDA v6.5.

update.13: Fixes for pbsa
1. Fixed incorrect scaling of volumetric potential maps when output from pbsa using dx format

update.14: Adds missing force field XML files for MTK++ and MTK++-derived programs (like MCPB)

update.15: Fixes a bug in ParmEd in which incorrect 12-6-4 parameters may be assigned to atoms if the addLJType command is run before add12_6_4.

update.16: Provisional support for SM5.0 GPUs - AKA NVIDIA-Maxwell - GTX980/970:
1. Update GPU code to support NVIDIA Maxwell GPUs - currently GTX980/970. This is provisional support. At present the code has not been optimized for Maxwell cards. As such GTX980 performance is approximately the same as GTX780. Future updates will improve GTX980 performance substantially.

update.17: Fixes for cpptraj: update to version 14.17.
1. Fix gist calculation so 4 closest waters are correctly compared instead of only the closest water.
2. Fix detection of solute residues for systems where solvent molecules are not the last molecules in the system (affects secstruct, dihedralscan, jcoupling, multidihedral, nastruct, rmsd perres, surf
3. Fix centroid calculation for symmetric RMSD and DME cluster metrics.
4. Allow TRAJ data sets (from loadtraj) to be used in clustering.
5. Fix support for RXSGLD trajectories.
6. In pairwise command, energies now correctly printed w.r.t. cutoffs and when not comparing to reference structure energies.
7. Fix potential problems with element recognition for PDBs with truncated ATOM records.
8. Allow box coordinates to be written to PDB in CRYST1 record if present (unless nobox specified). Also add readbox command to PDB parm read to enable read of unit cell info from CRYST1 record.
9. Fix formatting and potential round-off errors when writing XPLOR density files.
10. Fix off-by-one issue with '-ms' command line flag output.
11. Fix and improve reading of MDOUT files.
12. Reference coordinates are now properly modified when topologies are.
13. Many small non-critical bugfixes for various actions including: dihedralscan, surf, cluster, multihist, strip
14. Improve various output, error, and warning messages to make them more informative.

update.18: Adds support for multiple active zones in sander.PUPIL

update.19: Improve handling of insertion codes by pdb4amber

update.20: Fixes a bug in sander.MPI that could cause issues in running vacuum softcore simulations with ntt = 3, the langevin thermostat.

update.21: Fixes a compilation problem with sander when using GCC 4.9 or higher.

update.22: Fixes for cpptraj: update to version 14.22.
1. Fix bugs in density command.
2. Add silenceactions command to silence action init/setup messages.
3. Fix potential segfault when reading multiple trajectories with and without replica indices.
4. Add usevelascoords option to Amber restart.
5. Fix counting of bonds in temperature command (only affects ntc > 1).
6. Read unit cell params from PDB/CIF trajin.
7. Write out CRYST1 record for PDB files beyond the first when multi specified.
8. Fix bug in matrix command that caused incorrect output when multiple topologies processed in the same run.

update.23: Enhancements have been made to the MIC offload implementation for improved performance. The execution command for pmemd.mic_offload.MPI has been simplified from version 1. Please refer to the documentation for more details.

update.24: Fix for pbsa: reset igb flag in addition to ipb so pbsa cannot be turned on in sander when no charge or radius is read in.

update.25: Fixes for cpptraj: update to version 14.25.
1. Fix autoimage centering to box center for general triclinic cells.
2. Make selection of reference structure by name/tag more robust.
3. Fix bug where reference structure was always being centered in 2drms 'nofit' calc.
4. Fix OpenMP-related segfaults with TRAJ data sets and in the checkstructure action.

update.26: Fix for sander: update test case sander_pbsa_decres.

Version 13

April, 2013

AMBERTOOLS 13 CYGWIN USERS: There is an issue with Cygwin that prevents the 4^th update in AmberTools 13 from being applied due to the implicit carriage return-to-newline conversion that cygwin does on text files. Because there is no way to go 'back' and add this fix before it becomes necessary, you need to fix update_amber on Cygwin with an extra command. This only needs to be done once. To fix update_amber, go to $AMBERHOME and type the following command:

./update_amber --apply http://ambermd.org/bugfixes/AmberTools/13.0/cygwin_fix

update.1: Multiple Cpptraj fixes:
1. Fix dimensions of VolMap grid when centering on a mask
2. Fix handling of box coordinates when a DCD file has big-endian bit ordering
3. Fix clustering of data sets
4. Remove vestigial variable
5. Update version
update.2: Prevents MMPBSA.py from ignoring changes to _MMPBSA_info that it deems may be permitted. Also fixes the checkValidity action in ParmEd.
update.3: Multiple fixes to cpptraj, ParmEd, and calcpka:
1. (cpptraj) Expanded error messages for topologies broken by tleap
2. (cpptraj) Enable noheader option for gnuplot
3. (cpptraj) Recognize rms keyword in clustering
4. (cpptraj) Fix possible segfault in hist when giving same data name twice
5. (cpptraj) Improve identificatino of string data sets in standard data files
6. (ParmEd) Add to the setMolecules option to fix prmtop files broken by tleap when non-adjacent molecules are cross-linked by bonds
7. (ParmEd) Add the ability to read and write Amber NetCDF Restart files.
8. (calcpka) Fix the horrible formatting of the populations.dat file
update.4: Fix the nonpolar energy and timing report in PBSA:
- Add timer stopper before early return from pb_exmol
- Modify a condition in pb_read so that (inp=1,radiopt=0) and (inp=2,radiopt=1) are consistent with AT 1.5.
- Change the default value of radiopt to 0 in pbsa and mmpbsa.
- Update MMPBSA.py test cases accordingly.
update.5: Fixes LCPO surface area calculation in MMPBSA.py when a water is present in either the receptor or ligand. Also fixes a number of small issues in cpptraj and one in ParmEd including:
1. Makes the cluster analysis in cpptraj more consistent with ptraj
2. Fixes minor indexing issue in the cpptraj 2-D Matrix code
3. Adds the missing Karplus.txt file for computing J-couplings
4. Provide the 'none' keyword option to the cpptraj 'solvent' command
5. Fixes cluster sorting in cpptraj
6. Fixes the parmout and outparm actions in ParmEd (also fixing ante-MMPBSA.py as a result)
update.6: Updates the configure script to support newer GPUs for Amber 12 GPU patch update 18 (bzip2-compressed).
update.7: Fixes update_amber so it does not show an error when an online patch is compressed.
update.8: Fixes a potential issue with the configure script on certain platforms (like Ubuntu) when trying to do a CUDA build.
update.9: Fixes MMPBSA.py calculations when the igb==8 model is used with the NAB program mmpbsa_py_energy
update.10: Update CPPTRAJ to version 13.10:
1. Add the 'mindist' action.
2. Fix normalization of RDF integral for 'radial intrdf'.
3. cluster: Add timing data to clustering; add option 'sievetoframe' to DBSCAN; fix potential bugs in average cluster distance output when number of cluster frames is large.
4. Fix multidihedral so that all nucleic acid chi (chin) correctly recognized.
5. jcoupling no longer fails when an atom is not found for a residue/dihedral combination, it continues to the next dihedral.
6. Add 'printatomnum' option to hbond for printing atom numbers in hbond output.
7. Fix potential segfault in crdfluct analysis when COORDS are empty.
8. Prevent tests that depend on NetCDF from running when compiled with '-nobintraj'.
9. Fix various typos.
update.11: Fixes some ugly formatting in the CSV-formatted decomposition output file.
update.12: Update CPPTRAJ to version 13.12:
1. Cpptraj will no longer automatically fail when reading/generating topology files with molecules containing non-sequential atoms; instead it will proceed without molecule/solvent information; only actions that depend on such information will not work.
2. PDBs generated by the 'mask' action no longer contain molecule information (such information can be added if desired and if the PDB is valid by re-reading the PDB into cpptraj); update the Test_Mask output to reflect this.
3. Fix the 'parmbox' command so that explicitly specifying the parm index immediately after the command is no longer required (it can be placed anywhere or omitted to use the default topology).
4. Fix potential error in autoimage when using multiple topologies in a single run.
5. Fix writing of PDB files when molecule information not present in Topology.
6. When processing command line flags do not process input files until after all other flags processed.
7. Fix up residue numbers in NAstruct data set legend strings.
8. Add 'center2' and 'nointramol' options to radial for using center of atoms in mask 2 (similar to center1) and ignoring intramolecular distances; center1, center2, and nointramol are mutually exclusive.
9. Fix error compiling with old GNU compilers: "DihedralSearch.cpp:53: error: unknown escape sequence '\*'"
update.13: Fix ParmEd's NetCDF restart file writing so that netCDF4-Python will create restart files that Amber programs can read.
update.14: This update fixes several small bugs and issues:
1. Fix MMPBSA.py alanine scanning when mutant residue is either the C- or N-terminus.
2. Fix issue when MMPBSA.py would sometimes fail to print PB decomposition energies.
3. Fix ParmEd so the atomic number is identified from the ATOMIC_NUMBER section of the topology file when present or based on the mass of each atom at read time when not present. Changing mass now no longer changes the assigned element in addAtomicNumber.
4. Fix parsing of imin=5 output files in MdoutAnalyzer.py
5. Fix possible NetCDF-related build issues when a NetCDF installation is already present in the main system locations.
6. Rebuild Amber's NetCDF library when necessary and avoid configuring it when unnecessary.
7. Fix ambpdb residue naming for nucleic acids to match PDB v.3
update.15: Update CPPTRAJ to version 13.15:
1. Add 'fixatomorder' command which can repair topologies/trajectories where atom numbering in molecules is non-consecutive.
2. Support 'checkoverlap' for 'check' and 'closestwaters' for 'closest' to maintain backwards compatibility with ptraj commands.
3. In 'atommap', provide better warning messages when chirality of reference and target seem not to match.
4. In interactive mode, enable autocompletion for commands as well as file names.
5. Add citation to output on clean exit.
6. Fix bug where 'rms2d reftraj' output would be incorrect when # input frames != # reference frames.
7. Detect when number of histogram bins overflows.
8. In 'autoimage', properly reset lists when multiple topologies are used in a single run.
9. Fix segfault when calculating correlation function for periodic (i.e. angle) data sets.
10. In 'cluster summaryhalf', fix normalization of frac1 and frac2 columns.
11. Fix potential segfaults in 'crdaction' and 'crdout' commands when strange arguments are given to 'crdframes' keyword.
update.16: Update pmemd.cuda to support CUDA 5.5.
1. Adds support for CUDA 5.5 to GPU code.
update.17: Update CPPTRAJ to version 13.17:
1. Enable 'nointramol' keyword in 'hbond' for ignoring intra-molecular hydrogen bonds.
2. In 'hbond' prevent automatic addition of solvent donors/acceptors when not asked for.
3. Enable writing of velocity information to Netcdf trajectory files via the 'velocity' keyword.
4. Fix problem where number of extra points was not being written to Amber topology files.
5. When using an LES topology, print warnings that CPPTRAJ does not yet support splitting LES trajectories.
6. Fix problem where CPPTRAJ could not properly read compressed Amber restart files.
7. In 'createcrd' action, warn if number of atoms in current topology does not match the one the action was set up for.
8. Recognize PDB TER cards that are only 3 characters long (as opposed to 6 characters with 3 trailing spaces).
update.18: Fix parsing of chamber topology files with ParmEd and MMPBSA.py
update.19: Fix MdoutAnalyzer.py on some systems that may have negative values for screen coordinates. Also fix MMPBSA.py for QM/MM-GBSA calculations in which a QM region has a non-zero net charge.
update.20: Fix MMPBSA.py input file creation for mmpbsa_py_energy.
update.21: Fixes defaults for pbsa and mmpbsa when using inp=1 option
update.22: Update CPPTRAJ to version 13.22:
1. Keep velocity information (if present) in strip, closest, and fixatomorder commands.
2. Fix potential segfault in radial when duplicate data set name used.
3. No longer truncate data set legends in standard data output; update test output to match.
4. Fix segfault when using parmstrip on a topology that needs to be used to read in a trajectory file.
5. Fix Hbond ordering so it is always consistent (first by frames, then by average distance).
6. Fix problem where actions that require sorting would give erroneous results with PGI compilers.
7. Remove extraneous debug statements.
8. Enable 'rms2d' as an alias for '2drms' in PTRAJ.
update.23: Fix for QM-MM/GBSA calculations using certain Hamiltonians.
update.24: Update CPPTRAJ to version 13.24:
1. Fix small error in calculation of number of hbonds between base pairs on first frame when residue range is not continuous.
2. Fix bug that was causing # of frames in Gzip Amber trajectory files larger than 4 GB to not be detected properly.
update.25: Fix PBSA memory allocation error in locmem.
update.26: Explicitly add -lstdc++ to the pmemd.cuda linker line to solve occasional pmemd.cuda compilation errors with some systems.

Version 12

April, 2012

bugfix.1: Fixes Python mask parser (used by ParmEd, xParmEd, and MMPBSA.py) so it properly recognizes wildcards for multiple atom name/type selection. Also add a "deleteDihedral" function to ParmEd for topology file modification.
bugfix.2: (1) Cpptraj: Fix reading of Charmm PSF files, fix frame and atom #s in 'closestout' output of closest command, update version string to 12.1. (2) Ptraj: Update version string to 12.0.
bugfix.3: Fixes a regular expression in patch_amber.py so it will match file names and directories with a period and + in them.
bugfix.4: Fixes a number of bugs, mostly improving error messages. (1) RATTLE errors are now fatal in NAB (2) Fix a name clash in rism1d that prevented successful compiling with GNU 4.7 compilers (3) Fix CHAMBER real()-type declarations to be consistent, avoiding errors on some platforms (notably Mac OS X 10.7 with Xcode 4.3.2). (4) Correct MMPBSA.py error reporting when necessary programs are not present or AMBERHOME is not set. Also fix PBSA/decomp/stability input file.
bugfix.5: Makes cpptraj 'closest' action behavior match ptraj (solute is always kept intact).
bugfix.6: Fixes a number of small bugs for rism1d that were primarily seen on 32-bit operating systems. Also improves configure argument suggestions on Mac OS X.
bugfix.7: Fixes Intel 12 compiler problem for FFTW 3.3.
bugfix.8: Fix unresolved symbols compiling cuda code on some versions of Ubuntu and possibly other Linux flavors. Also attempt to work around missing mpi.h when compiling the MPI version of cuda the code using system installed MPI instances.
bugfix.9: Cpptraj: -Fix how number of outputted frames is determined -Adds 'nastruct' keywords 'hbcut' to set cutoff for determining H-bond cutoff in base pairing (Angstrom), 'origincut' to set the base reference axes cutoff for determining base pairing (Angstrom), and 'ref' to use a reference structure for base pair identification -Fix issue where large PDB files can overflow atom number columns
MMPBSA.py: Adjust to cpptraj fix above -- this fixes MMPBSA calculations with only 1 frame in the input trajectory
ante-MMPBSA.py: Allow users to specify a new PBRadii set that is appropriate to the solvent model they want to use
bugfix.10: Cpptraj: Correct how cpptraj handles DCD box information so that imaging is performed correctly. Also solves a possible situation in which cpptraj hangs indefinitely when trying to image a DCD file with an orthorhombic box.
bugfix.11: Same as bugfix.8 but includes the GNU compiler which was inadvertently missed in the first version of this bugfix.
bugfix.12: PBSA: Fix a bug in water-related energy decomposition; Eliminate round-off errors in the level set function.
bugfix.13: There's a chance that configure may not apply all bug fixes if authorized to do so. This bugfix addresses that.
bugfix.14: Fixes the changeLJSingleType command in ParmEd (both parmed.py and xparmed.py)
bugfix.15: Fixes DELTA G binding calculations when nmode entropy is included in cases where fewer frames are included in the normal mode calculations than the implicit solvent calculations.
bugfix.16: Add new action to cpptraj, autoimage. Performs automatic imaging of a system with little to no additional input from user.
bugfix.17: Fixed bug missing newline bug when writing DX format files. Fixes units of potential maps written in DX format. Will now be properly scaled to kcal/mol-e rather than the unscaled array values.
bugfix.18: Fix potential segfault in autoimage when preceded by a strip command that removes all solvent. Also add the charmm keyword back to trajout.
bugfix.19: Fix d orbital bug in semiempirical code: a) Use d orbitals with MNDO/d also for Br and I, b) Fix Slater-Condon parameter calculations for d orbitals with principal quantum number n>4
bugfix.20: Remove pol12 force field files that are not yet ready for release.
bugfix.21: Cpptraj: Fix bug where reading restart files with velocity info after an initial restart with no velocity info would result in corruption of box coordinates.
bugfix.22: patch_amber.py: Fixes support for compressed patches necessary for the large Amber 12 CUDA patch.
bugfix.23: configure, MMPBSA.py tests: Updates the configure script to work with the large CUDA upgrade in Amber 12 (bugfix.9). Also updates the MMPBSA.py tests to reflect the tweak to the igb=5 parameters in sander and pmemd.
bugfix.24: MMPBSA.py: Recover error messages printed by PBSA to stdout. This doesn't fix PBSA errors, but it will now print error messages to the screen during MMPBSA.py calculations to aid in debugging.
bugfix.25: MMPBSA.py: fix alanine scanning when mutant_only=1
bugfix.26: Cpptraj: Fix reading of Charmm PSF files when atom type is not an integer. Also add detection of DCD # frames by file size to avoid spurious errors in the case where # of frames reported by DCD file does not match actual # of frames.
bugfix.27: NAB and MMPBSA.py: Fix reporting of EDISPER in NAB programs (including mmpbsa_py_energy) when inp is 2.
bugfix.28: Fix comments in leaprc.ff12SB to more correctly describe what files are used.
bugfix.29: Fix bug with two-electron integrals in sqm for atoms separated by more than 10 Angstrom.
bugfix.30: Fixes error with QM/MM switching function in presence of link atoms (affects AMBER sander simulations that use sqmlib)
bugfix.31: Cpptraj: Fix infinite loops in orthorhombic dist calc/imaging when box lengths == 0.0 (bug 209); fix hbond autosearch when either only donor or only acceptor mask specified; fix parsing of input files with DOS-style lines; fix memory leak in DCD box read.
bugfix.32: MMPBSA.py: Fixes defaults for APBS calculations, fixes calculations using sander that require inp=1, and improves error messages for incompatible topology files used with alanine scanning.
bugfix.33: MMPBSA.py: Expand the list of allowable QM models to match SQM when running QM/MMGBSA calculations.
bugfix.34: ParmEd (xparmed.py, parmed.py): Fix stripping atoms from the middle of a topology file when the coordinates from a restart file are present.
bugfix.35: SQMLIB: QM/MM Ewald bug fixes (affects AMBER sander simulations that use sqmlib, see also AMBER bugfix.15; has no effect on sqm)
1. add self-plasma term for charged systems
2. improve default values for k space vectors
bugfix.36: MMPBSA.py: Fix to allow chamber topology files to work with MMPBSA.py
bugfix.37: patch_amber.py and update_amber: A re-write of the automatic updating/patch applying script with many performance and stability improvements.
bugfix.38: fixes default values for pbsa and mmpbsa when using inp=1 option

Gaussian 09 fix

In Gaussian09 rev B.01, the facility to write out the electrostatic potential on a grid of points was inadvertently deleted. This means that antechamber and resp jobs won't work as they should. Fernando Clemente of Gaussian has kindly provided a script to work around the problem. Download the fixreadinesp.sh file, and follow the instructions there. (Note: you will have to make the script executable by typing chmod +x fixreadinesp.sh.)

Version 1.5

1.5 April, 2011 (git tag: at15)

bugfix.all: This patch script contains all bug fixes for AmberTools version 1.5 in a single patch script. You can patch your AmberTools 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 < 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 AmberTools.
bugfix.1: Enhancements and fixes for cpptraj. From version 1.0.5 to 1.0.8.
Enhancements: (1) Added "average" keyword to "reference" command; allows one to average the coordinates of an input trajectory and use as a reference struct. (2) Added "precision" keyword to "datafile" command; users can specify an output width and precision for data sets in a data file. (3) Added "maxmin" keyword to "outtraj" command; users can direct outtraj to only print frames that are between a specified max and min based on specified data set.
Bug fixes: (1) Box type detection is now fixed for general triclinic cells. (2) Fixed segfault when reading trajectory with box coords when associated parm has no box informaton. (3) Fix potential write of binary characters to Amber trajectory files when using "outtraj". (4) General improvement in output and debugging messages.
bugfix.2: MMPBSA.py failed to mutate the residues ILE, THR, and VAL. Also, setup.sh in mmpbsa_py failed to set AMBERHOME to the correct value if it was not set at all. Fixes both issues

bugfix.3: Adds variable 1-4 scaling to tleap

bugfix.4: Cpptraj (V1.0.8 -> V1.0.9): Fix bug that could result in long wait times during file type detection.

bugfix.5: Fix atom type definition for iodine in antechamber (Amber types)

bugfix.6: AT15_Amber11.py: Inform users of tests that are expected to fail and/or cause an error with AmberTools 1.5 + Amber11.

bugfix.7: readparm.py: add support for chamber-created prmtop files and fix LJ indexing issues for extracting original radii/well depths from the A/BCOEF arrays.

bugfix.8: Support for FedoraCore 15 and other machines using gcc 4.6.

bugfix.9: Ptraj: Fixes problem reading compressed Amber Trajectories with offset values > 1.

bugfix.10: Cpptraj: Restart/mol2/pdb output frame numbers now match datafile frame numbers. Also fix read of broken Amber trajectories.

bugfix.11: configure: Fix configuration for installation of native Windows version of pmemd.
bugfix.12: Fix H1-CT-C -O and related angles to ensure wild cards don't contribute.

bugfix.13: Patch to configure to work with Amber 11 GPU updates (bugfix 17 in Amber 11)

bugfix.14: Fix reading of gzipped Amber trajectories in ptraj/cpptraj with uncompressed size > 4GB.

bugfix.15: Fix segmentation faults of some pbsa tests when building with Intel compilers version 12.

bugfix.16: Cpptraj: Fix potential segmentation fault during Per-residue RMSD calc ('rmsd perres').

bugfix.17: MMPBSA.py: Fix bug that prevents alanine scanning from working properly with MM/3D-RISM.

bugfix.18: Ptraj: Several bugfixes. (1) Fix bug in 'closest' where wrong distances calcd if no box info present. (2) Fix minor memory error in 'secstruct'. (3) Correct behavior of 'vector principal' when 'x|y|z' not specified. (4) Fix segfaults in 'watershell' command.

bugfix.19: Fix case where even valid options for inp are flagged as illegal choices in MMPBSA.py

bugfix.20: Don't mix the ildn and ff99SBnmr fixes, so that leaprc.ff99SBnmr matches the original paper.

bugfix.21: Fixes excess chemical potential polar/apolar decomposition in 3D-RISM calculations and a few other minor 3D- and 1D-RISM bugs.

bugfix.22: Fixes compilation for some compilers by appling missing 'save' attribute.

bugfix.23: PBSA: A new box was not created for the second snapshot when imin = 5; Box dimensions are inputted only when a ligand is present, so in other cases, a new box is always created.

bugfix.24: configure: Automagically apply AT15_Amber11.py when necessary (if Amber 11 exists alongside AmberTools 1.5). Can be disabled via -nopatch.

bugfix.25: Miscellaneous fixes to MTK++ and MCPB.

bugfix.26: Cpptraj => V1.1.2. Fix reading of restart files with # atoms > 5 digits.

bugfix.27: MMPBSA.py: Fix parsing of Normal Mode entropy output

bugfix.28: MMPBSA.py: Fix calculation of standard deviations for normal mode entropy calculations.

Version 1.4

1.4 April, 2010 (git tag: v_11)

bugfix.all: This patch script contains all bug fixes for AmberTools version 1.4 in a single patch script. You can patch your AmberTools 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 < 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 AmberTools.
In order to enable the DFTB tests for sqm (introduced with bugfix.8) you have to run:
cd $AMBERHOME
chmod ugo+x AmberTools/test/check_slko_files.x

Remember that DFTB will only work if you install the DFTB integral (Slater-Koster) parameter files.
bugfix.1: Update atom types in gaff.dat; remove some unused parameters.
bugfix.2: Fix a bug that can cause segfaults in sleap from the addions command.
bugfix.3: Update tleap and xleap to avoid some segfaults on Fedora Core 12/13 and possibly Ubuntu 10.04.
bugfix.4: Fix to parallel ptraj when compressed trajectories are input.
bugfix.5: Fix to 3D-RISM results for ionic solvents (like NaCl in water).
bugfix.6: The gbsa=1 option gives bad results when mme2() is used.
bugfix.7: Fix possible data overflow in pbsa.
bugfix.8: Enable DFTB in sqm.
bugfix.9: Fixes issues in ptraj. 1) ptraj could not properly process large compressed and uncompressed trajectory files. 2) the cluster command could trigger a segmentation fault.
bugfix.10: Second derivative calculations in NAB would fail with 6-fold dihedrals.
bugfix.11: Enable d orbitals in the DFTB code.
bugfix.12: Fixes bug in ptraj where reading an input file with no EOL would cause a segmentation fault.
bugfix.13: Adds missing parameters for disulfide bonds in the amoeba force field.
bugfix.14: Fixes performance issues with sqm. Calculations will be 30% faster after application of this patch.
bugfix.15: Fixes issues in ptraj. 1) output of cluster trajectory could cause a segfault when trajectory became too large. 2) Fixes minor bug in secstruct (DSSP) command where turn populations would be slightly off for residues lacking one or more backbone atoms (H, C, N, or O) such as PRO or terminal residues.
bugfix.16: Fixes reading of large (>2GB) files in ptraj. Without this patch very large Amber Trajectories may become corrupted (Note: NetCDF trajectories do not have this issue).
bugfix.17: Makes the interface of the addions command in sleap more similar to tleap's.
bugfix.18: Makes corrections or improvements to commands in sleap: saveAmberParm, savePdb, combine, sequence, set UNIT box, solvatebox, and check.
bugfix.19: Fixes issue where sleap didn't print negative dihedral force constants.
bugfix.20: N-terminal proline charges in ff03 are incorrect. Also adds ACE N-terminal residue to all_aminont03.lib

Version 1.3

1.3 December, 2009 (CVS tag: at_1_3)

bugfix.all: This patch script contains all bug fixes for AmberTools version 1.3 in a single patch script. You can patch your AmberTools 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 < 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 AmberTools.
bugfix.1: Make an scf failure a fatal error for sqm, to minimze wasted computer time on a failed calculation.
bugfix.2: Allow the pbsa program to handle halogens in the GAFF force field.

Version 1.2

1.2 July, 2008 (CVS tag: at_1_2)

bugfix.all: This patch script contains all bug fixes for AmberTools version 1.2 in a single patch script. You can patch your AmberTools 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 < 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 AmberTools.
bugfix.1: antechamber test charmm ala2 output update for phase changes.
bugfix.2: NAB failed assertion for some dihedral phases, such as in ff99bsc0.
bugfix.3: fixes to ptraj related to netcdf, remd and compressed files
bugfix.4: fixes buffer overrun when writing mol2 files in LEaP
bugfix.5: remove some duplicate parameters in gaff.dat
bugfix.6: fixes issues with ptraj failing to identify some CHARMM PSF files.
bugfix.7: fixes issues with ptraj processing of REMD, netcdf trajectories
bugfix.8: more fixes related to bugfix.7
bugfix.9: don't allow dihedral phases that are not zero or pi (as in parmbsc0)
bugfix.10: patch the loadMol2 command in LEaP so that it won't choke on odd residue numbers
bugfix.11: fix to am1-bcc bond orders (and hence charges) for SO2 and NO2 groups
bugfix.12: update leaprc files to recognize atom and residue names in PDB 3 format

Version 1.0

1.0 April, 2008 (CVS tag: at_1_0)

bugfix.all: This patch script contains all bug fixes for AmberTools version 1.0 in a single patch script. You can patch your AmberTools 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 < 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 AmberTools.
bugfix.1: nblist.c in NAB won't compile with MPI turned on
bugfix.2: The readparm() routine will throw an error when MPI is turned on
bugfix.3: sleap will not read a leaprc file from an arbitrary path
bugfix.4: sleap does not recognize the closeness parameter in solvateBox
bugfix.5: sleap cleanups required for Mac OSX
bugfix.6: sleap fixes to addIons to work with solvated systems
bugfix.7: Fix to possible segfaults when doing clustering in ptraj