I got error message on terminal:
mmpbsa_py_energy: malloc.c:2451: sYSMALLOc: Assertion `(old_top ==
(((mbinptr) (((char *) &((av)->bins[((1) - 1) * 2])) - __builtin_offsetof
(struct malloc_chunk, fd)))) && old_size == 0) || ((unsigned long)
(old_size) >= (unsigned long)((((__builtin_offsetof (struct malloc_chunk,
fd_nextsize))+((2 * (sizeof(size_t))) - 1)) & ~((2 * (sizeof(size_t))) -
1))) && ((old_top)->size & 0x1) && ((unsigned long)old_end & pagemask) ==
0)' failed.
CalcError: /home/zl/software/amber12/bin/mmpbsa_py_energy failed with
prmtop dh_fad_des.prmtop!
Exiting. All files have been retained.
In log file:
Loading and checking parameter files for compatibility...
Preparing trajectories for simulation...
100 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with
/home/zl/software/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
mmpbsa_py_energy found! Using /home/zl/software/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /home/zl/software/amber12/bin/cpptraj
in _MMPBSA_complesx_gb.mdout.0:
Reading parm file (dh_fad_des.prmtop)
title:
default_name
mm_options: e_debug=2
mm_options: gb=2
mm_options: rgbmax=25.000000
mm_options: gbsa=1
mm_options: surften=0.007200
mm_options: cut=999.000000
mm_options: epsext=78.300000
mm_options: kappa=0.103952
In _MMPBSA_gb.mdin:
GB
extdiel = 78.3
saltcon = 0.1
igb = 2
surften = 0.0072
rgbmax = 25.0
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Received on Wed Nov 06 2013 - 05:30:02 PST
