After setting my $PATH to include the right directories, I tried
"make test.mmmpbsa_py" (3 m's) with the release candidate, MAC OSx 10.5.8
gnu compilers.
Here is the output from mmpbsa.out:
Warning: igb=5 should be used with either mbondi2 or bondi pbradii set. Yours
are modified Bondi radii (mbondi)
sander(17488) malloc: *** mmap(size=1117442048) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
sander(17489) malloc: *** mmap(size=1135009792) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
sander(17501) malloc: *** mmap(size=1116864512) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
sander(17502) malloc: *** mmap(size=1134432256) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Error: No potential terms in sander output! Check output files.
ptraj found! Using /home/case/test/amber11/bin/ptraj
sander found! Using /home/case/test/amber11/bin/sander (serial only!)
Checking mutant topology files...
Preparing trajectories with ptraj...
2 frames were read in and processed by ptraj for use in calculation.
Mutating complex mdcrd for alanine scanning...
Starting sander calls
Starting gb calculation...
Starting pb calculation...
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
It's hard to tell if the program is indeed trying to allocate lots of memory
(more than my machine has), or if the malloc sizes are in error.
Also, it took way more than "a couple of minutes" to run, but maybe that's
because of the errors(?)
...dac
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Received on Mon Mar 29 2010 - 12:30:03 PDT
