AMBER 6.0 Bug Fixes

6.0	November, 1999 (CVS tag: v6_0)

• bugfix.1: sander with generalized Born reports "unable to find bonded partner".

• bugfix.2: Machine.pgf77 and Machine.axp_f90 need LOADCC defined to compile C programs.

• bugfix.3: sander_classic/forcemp.f may fail to compile.

• bugfix.4: the LES_CUT test may not run on MPI parallel machines.

• bugfix.5: the opls_parm.dat file is missing from the amber6/dat directory.

• bugfix.6: PME calculations with order>4 and polarizable potentials may give inaccurate forces.

• bugfix.7: Advice for compiling/running sander under linux w/ MPICH.

• bugfix.8: tleap 'loses' an object if one tries to edit it (edit only works with xleap).

• bugfix.9: xleap's Xraw pkg wn't compile on Unicos.

• bugfix.10: solvent temperature is incorrect in sander_classic with ntt=5 and MPI.

• bugfix.11: problems with compilation, NMR and nmode test cases on Compaq (DEC) alpha machines.

• bugfix.12: compilation of ptraj on IBM rs6000, sp2 machines.

• bugfix.13: minor error in the NMR-related code "fantasian"

• bugfix.14: compiling ptraj on rs6000

• bugfix.15: occasional memory problem in computing correlation functions in ptraj

• bugfix.16: gibbs fails when PME is used on SGI machines (perhaps other platforms as well)

• bugfix.17: NMR refinements in sander fail on Linux with Portland Group Compiler

• bugfix.18: Sander doesn't exit gracefully when igb=0 and ntb=0

• bugfix.19: Parallel runs on sander may overflow memory for some machines

• bugfix.20: sander_classic may fail for shared memory parallel runs with explicit water

• bugfix.21: Leap exits when loading pdb with too many bonds on an atom.

• bugfix.22: Carnal prints bad restrt format on COORD GROUP, runs out of file descriptors on COORD GROUP restrt & pdb.

• bugfix.23: The "amber.def" file is missing from the interface distribution.

• bugfix.24: Carnal dies on linux when closing STREAM file twice.

• bugfix.25: Carnal can die in PUCKER on ranges of residues.

• bugfix.26: Don't require hydrogens to follow heavy atoms in sander GB

• bugfix.27: updates to interface file sander_pme_namelist.def

• bugfix.28: nmode may dump core for large molecules

• bugfix.29: setting random velocities at beginning of MD in sander_classic is broken

• bugfix.30: another fix to the randomize velocities code, in sander & sander_classic

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