AMBER 6.0 Bug Fixes
6.0 November, 1999 (CVS tag: v6_0)
sander with generalized Born reports "unable to find bonded partner".
Machine.pgf77 and Machine.axp_f90 need LOADCC
defined to compile C programs.
sander_classic/forcemp.f may fail to compile.
the LES_CUT test may not run on MPI parallel machines.
the opls_parm.dat file is missing from the amber6/dat directory.
PME calculations with order>4 and polarizable potentials may
give inaccurate forces.
Advice for compiling/running sander under linux w/ MPICH.
tleap 'loses' an object if one tries to edit it
(edit only works with xleap).
xleap's Xraw pkg wn't compile on Unicos.
solvent temperature is incorrect in sander_classic with ntt=5 and MPI.
problems with compilation, NMR and nmode test cases on
Compaq (DEC) alpha machines.
compilation of ptraj on IBM rs6000, sp2 machines.
minor error in the NMR-related code "fantasian"
compiling ptraj on rs6000
occasional memory problem in computing correlation functions in ptraj
gibbs fails when PME is used on SGI machines (perhaps other platforms as well)
NMR refinements in sander fail on Linux with Portland Group Compiler
Sander doesn't exit gracefully when igb=0 and ntb=0
Parallel runs on sander may overflow memory for some machines
sander_classic may fail for shared memory parallel runs with explicit water
Leap exits when loading pdb with too many bonds on an atom.
Carnal prints bad restrt format on COORD GROUP,
runs out of file descriptors on COORD GROUP restrt & pdb.
The "amber.def" file is missing from the interface distribution.
Carnal dies on linux when closing STREAM file twice.
Carnal can die in PUCKER on ranges of residues.
Don't require hydrogens to follow heavy atoms in sander GB
updates to interface file sander_pme_namelist.def
nmode may dump core for large molecules
setting random velocities at beginning of MD in sander_classic is broken
another fix to the randomize velocities code, in sander & sander_classic
randomized velocities in gibbs give too cold a temperature