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.
>
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
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Received on Thu May 09 2013 - 19:00:02 PDT
