AMBER 7.0 Bug Fixes

7.0	March, 2002 (CVS tag: v7_0)

• bugfix.1: Compiling with Intel or Portland group compilers hangs sander or nmode

• bugfix.2: LEaP may crash if given an unknown hybridization

• bugfix.3: ptraj doesn't read new format LES-type prmtop files correctly

• bugfix.4: protonate has an incorrect default location for the PROTON_INFO file

• bugfix.5: mm_pbsa gives "Something wrong with NGR..." error for some trajectories

• bugfix.6: Leap can assign non-0 charges when none are assigned in prep.in file.

• bugfix.7: GBSA calculations using the GAFF force field give a "bad atom type" error

• bugfix.8: LEaP balks at PDB files with more than 99999 atoms or more than 9999 residues

• bugfix.9: "make install" in mm_pbsa can fail for some C compilers

• bugfix.10: nmode exits with a return code of 0 even when there is insufficient memory

• bugfix.11: in antechamber, long atom and residue names in mol2 files are not properly truncated

• bugfix.12: anal does not correctly read the new format for restart files

• bugfix.13: protonate fails to add protons to some nucleic acid residues

• bugfix.14: the -aatm option in ambpdb is broken

• bugfix.15: carnal exits if loading pdb where prmtop has box

• bugfix.16: small changes to LEaP to allow compilation on FreeBSD and Mac OSX

• bugfix.17: Gasteiger charges in antechamber are not always correctly computed; some bond types in mol2 files are read in incorrectly

• bugfix.18: LEaP could fail on 64-bit architectures with 32-bit integers

• bugfix.19: the leaprc.ff02EP startup file does not load the correct protein libraries

• bugfix.20: the -nocorr option of makeDIST_RST is broken

• bugfix.21: addIons can crash or give incorrect ion positions

• bugfix.22: the NFREQ parameter in mm_pbsa is broken

• bugfix.23: check in sander for belly runs when igb>0 is not made

• bugfix.24: fix LEaP to give correct Born radii for the GAFF force field

• bugfix.25: this patch, along with buxfix.26, will allow one to successfully build roar-cp (in roar-2.1).

• bugfix.26: this patch, along with buxfix.25, will allow one to successfully build roar-cp (in roar-2.1).

• bugfix.27: add error trap to disable mm/pbsa energy decomposition on multiple structures

• bugfix.28: minor update to LEaP parser required for latest versions of bison

• bugfix.29: ptraj cut the last atom of an atom mask range

• bugfix.30: fix to the restart files used in roar-cp

• bugfix.31: randomized velocities in sander give too cold a temperature

• bugfix.32: randomized velocities in gibbs also give too cold a temperature

• bugfix.33: mm_pbsa.pl reads pdb file as space-separated format, not as fixed-column format

• bugfix.34: nmr-related intense program may fail to compile on some configurations

• bugfix.35: antechamber fails to assign correct atoms types for nitriles

• bugfix.36: LEaP does not compile with DEBUG defined

• bugfix.37: LEaP does not build with LeapDebugLib defined as YES

• bugfix.38: sander can give "too many subcells" error for small periodic systems

• bugfix.39: protonate puts atoms names in the wrong column when using PROTON_INFO.Brook

• bugfix.40: quasih only allows 3*natom/2 frequencies to be calculated

• bugfix.41: nmanal doesn't read input prmtop files correctly

• bugfix.42: parallel sander minimization with shake may not shake all waters

• bugfix.43: sander free energies don't correctly include long-range van der Waals corrections

• bugfix.44: changes to allow amber to run on Mac OSX with the NAGF95 compiler

• bugfix.45: some Linux distributions (SuSE, others?) may fail to compile LEaP

• bugfix.46: LEaP may crash when removing or erasing atoms.

• bugfix.47: LEaP may crash when writing a prmtop for a unit with unbonded hydrogens.

• bugfix.48: nmode thinks that the number of atoms in the prmtop and coordinate files differ

• bugfix.49: carnal can give TABLE errors with certain inputs

• bugfix.50: gibbs doesn't read in CAP information correctly from the prmtop file