AMBER 5.0 Bug Fixes

5.0	November, 1997 (RCS 7.0)

• bugfix.1: corrected version of octree.c for LEaP

• bugfix.2: fix to non-Ewald periodic boundary condition code in sander

• bugfix.3: minor update to Makefile for fantasian

• bugfix.4: minor update to Makefile for spasms

• bugfix.5: fix pointer problem in gibbs when "cap" of water used

• bugfix.6: fix gibbs Makefile typo for "bigsource"

• bugfix.7: patches for compiling leap on rs6000

• bugfix.8: patches for compiling leap on SGI Irix 6.4

• bugfix.9: xleap crash in addIons (possibly other crashes too)

• bugfix.10: sander: failures when polarization is used

• bugfix.11: sander: memory allocation failures not detected

• bugfix.12: roar: updates to permit compilation on more machines

• bugfix.13: carnal: failure to detect main-chain atoms in BACKBONE

• bugfix.14: carnal: DISTRIBUTION DIST NORM fails with 1 group (intra-group distances).

• bugfix.15: carnal: STATIC fails when expecting box from pdb or box-less restrt

• bugfix.16: roar: fix compile problem for Dec Alpha machines.

• bugfix.17: sander: problem with PME on some (non-SGI, non-Cray) parallel machines

• bugfix.18: parm96.dat: 'missing' improper torsions, deleted ions fixed parm96.dat

• bugfix.19: ions9*.lib: can't see ions with unit editor fixed ions91.lib fixed ions94.lib

• bugfix.20: Leap: update unitio.c to avoid possible crash in saveAmberParm

• bugfix.21: Sample Machine.g77 file to aid compilation with that compiler.

• bugfix.22: Leap: solvateBox can result in solute being off-center in box.

• bugfix.23: xleap: speed enhancement to counter slowdown introduced by bugfix.9

• bugfix.24: carnal: TORSION BACKBONE error when looped molecule followed by non-looped terminal one

• bugfix.25: xleap: "Add H and Build" exits on atom with undefined hybridization.

• bugfix.26: xleap: "edit Na+" crashes on DEC Alpha

• bugfix.27: sander/SGI: enable polarization on parallel machines.

• bugfix.28: ALL/Solaris: new Machine files for Solaris Machine.sun / Machine.sun_hpc_mpi

• bugfix.29: Exit handling in mexit.f for g77/f2c compilation.

• bugfix.30: Sander: MPI parallel implementation of PME

• bugfix.31: Leap: sometimes crashes: "Unmatched Exec Push/Pop, ..."

• bugfix.32: Leap: bug (crash) in solvate routines, activated by bugfix.31

• bugfix.33: Leap: compilation on IRIX 6.5

• bugfix.34: Carnal: crashes when reading restrt with box for STATIC.

• bugfix.35: Leap: on IRIX 6.5, floating-point numbers printed to screen are all 0.00000.

• bugfix.36: Leap: compilation on Cray T3E

• bugfix.37: Leap: possible crash on saveAmberParm when torsions are commented

• bugfix.38: Leap: redundant bond in a prep.in LOOP section causes exit in loadpdb.

• bugfix.39: Leap: solvateCap bug crashes DEC alpha, may cause imperfect cap on other machines.

• bugfix.40: Carnal: writing pdb files w/ residues > 9999, coordinates get pushed to the right and some viewers can't load the file.

• bugfix.41: Leap: crashes when deleting a water added by a solvate cmd.

• bugfix.42: xleap: crashes on Dec when moving molecule or closing edit window.

• bugfix.43: xleap: bug that might cause crashes in 'relax selection'.

• bugfix.44: xleap: bug that might cause crashes in Unit Editor 'build' commands.

• bugfix.45: sander: fixes three body list generation for more than one ion.

• bugfix.46: xleap: bug that might cause crash when using 'load' windows.

• bugfix.47: xleap: adding a row to a parm atom table shifts columns.

• bugfix.48: Leap: wrong torsion term parameter chosen when duplicates without wildcard atom types are loaded from multiple parmsets.

• bugfix.49: Leap: solvateOct with single cutoff results in wrong scaleup of box for diagonal clearance.