Hello,
could anybody please explain the meaning/reason of this error ?
------
VASSERT: ASSERTION FAILURE! filename
/opt/amber12/apbs/contrib/iapbs/src/apbs_driver.c, line 80, (apbsgrid[i]
!= ((void *)0))
------
Considering relevant part of the "apbs_driver.c" file it seems like
memory allocation related issue
(please see below). I have obtained this error during
MMPBSA.py/sander.APBS analysis
of my complex (protein (REC) + small hyperbranched anionic polymer (LIG)).
It is whole really strange as the complex and receptor energies were
calculated without any problem and the calculation was stopped just during
calculation of the small (comparing to receptor) ligand.
The machine I am using have 64GB RAM and during the whole complex
calculation just few
GBs were used so even if the error seems like memmory allocation issue it
should have some
another reason than insufficient RAM. Moreover and this is pretty strange,
calculation
of another geometry of the same RECEPTOR + LIGAND pair (ligand just placed
in another part of receptor than in previous case) proceeded without any
problems (with the same COM.prmtop, REC.prmtop, LIG.prmtop files). So we
have here ligand molecule which for one set of conformations is
non-problematic for sander.APBS (taken from one complex) and just with
slight change in analysed conformations (taken from the another complex
geometry) there are problems even if there
are of course no atoms/charges overlaps or another problems (the
structures are from the end of 80ns simulation).
Moreover for "problematic" set of LIG conformations ( i.e. frames from
_MMPBSA_ligand.mdcrd.0 ) was possible without any problems calculate
surface electrostatic potential using APBS (apbs module in Chimera UCSF).
When I tried for the curiosity nonlinear PB (nonlin=1) for the
problematic complex, the situation was the same and just some warnings
Vc_vecpmg: trapped exp overflows: 2
Vc_vecpmg: trapped exp overflows: 2
Vc_vecpmg: trapped exp overflows: 1
Vc_vecpmg: trapped exp overflows: 1
Vc_vecpmg: trapped exp overflows: 1
....
were added into the mmpbsa.out file but these seems not to be problem
(they appeared during successfully finished complex and receptor
calculation) but then again appeared the probrem with ligand calculation
and the same error was written at the end of the mmpbsa.out file.
I would appreciate any suggestions, ideas what to try (e.g. to adjust some
apbs internal parameters).
I guess that to delete/comment problematic command "VASSERT( apbsgrid[i]
!= VNULL );" in "apbs_driver.c" and recompile is not a good idea :))
though I would like to do it as this error seems to me really absurd.
Thanks in advance for any comments !
Best wishes,
Marek
-------------------apbs_driver.c---part----------------------------------------
// Memory must be allocated for the outputs if they are to be returned
in-memory.
if( apbsgrid_meta[0] > 0 ) {
is_grid2file = 0;
VASSERT( apbsgrid != VNULL );
for(i=0; i<apbsgrid_meta[0]; i++) {
VASSERT( apbsgrid[i] != VNULL ); ****LINE 80****
}
}
------------------------------------------------------------------
------mmpbsa.out content---------
------mmpbsa.out content---------
------mmpbsa.out content---------
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /opt/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /opt/amber12/bin/cpptraj
sander.APBS found! Using /opt/amber12/bin/sander.APBS
Preparing trajectories for simulation...
3 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning PB calculations with /opt/amber12/bin/sander.APBS
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
VASSERT: ASSERTION FAILURE! filename
/opt/amber12/apbs/contrib/iapbs/src/apbs_driver.c, line 80, (apbsgrid[i]
!= ((void *)0))
File "/opt/amber12/bin/MMPBSA.py", line 91, in <module>
app.run_mmpbsa()
File "/opt/amber12/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/opt/amber12/bin/MMPBSA_mods/calculation.py", line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/opt/amber12/bin/MMPBSA_mods/calculation.py", line 428, in run
self.prmtop) + '\n\t'.join(error_list) + '\n')
CalcError: /opt/amber12/bin/sander.APBS failed with prmtop
../../prmtop/LIG.prmtop!
Exiting. All files have been retained.
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
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Received on Thu May 09 2013 - 18:00:02 PDT
