Thanks Robert !
I just sent you my LIG files (off line).
Best wishes,
Marek
Dne Fri, 10 May 2013 03:53:16 +0200 Robert Konecny <rok.ucsd.edu>
napsal/-a:
> Hi Marek,
>
> this error most likely suggests that something went wrong with the APBS
> grid setup, your ligand's geometry was perhaps not correctly processed.
>
> You can try to turn on or increase the debugging flag to see what is
> going
> on. Or you can send me your input files (off line) and I can take a look.
>
> Thanks,
>
> Robert
>
> On Fri, May 10, 2013 at 02:18:54AM +0200, Marek Maly wrote:
>> 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.
>>
>>
>> --
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Received on Fri May 10 2013 - 05:30:02 PDT
