This is, indeed, strange.
Can you send me a of files I can use to reproduce this problem off-list?
Thanks,
Jason
> On Jan 12, 2015, at 2:45 PM, Kenneth Huang <kennethneltharion.gmail.com> wrote:
>
> Dear all,
>
> I'm running into a frankly bizarre error with MMPBSA using AmberTools14.
> After generating my complex/ligand/receptor prmtop files with ante-MMPBSA
> using this command-
>
> ante-MMPBSA.py -p sol.prmtop -c com.prmtop -r rec.prmtop -l lig.prmtop -s
> ':WAT,:Na+' -n ':1-521,:1562-2082'
>
> I then tried testing a short, two frame test run in MMPBSA with my input as-
>
> &general
> startframe=269, endframe=270, interval=1, keep_files=2,
> receptor_mask=':522-1561:2083-2084', ligand_mask=':1-521:1562-2082',
> strip_mask=':WAT:Na+',
> /
> &gb
> igb=5,
> /
> &pb
> radiopt=0, indi=2.0,
> /
>
> Which then proceeded to crash with a CalcError failure with the complex.
> The log showed that it was crashing at GB calculations, but checking
> _MMPBSA_complex_gb.mdout.0 only provided this-
>
> Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)
>
> Processing frame 1
> iter Total bad vdW elect nonpolar genBorn
> frms
>
> So trying to see what exactly was causing the crash, I ran MMPBSA with
> use_sander=1 in the input. Strangely enough, the log file/outputs show it
> crashing with the same complex CalcError at PB instead of GB.
> _MMPBSA_complex_gb.mdout.0 is actually completing, or doing a very good job
> of looking as if it's successful- but checking _MMPBSA_complex_pb.mdout.0
> gives me this message-
>
> POST-PROCESSING OF TRAJECTORY ENERGIES
> Cpptraj Generated trajectory
>
> minimizing coord set # 1
> SA Bomb in sa_arc(): Allocates aborted 3 0 5014 5014 0 0
>
> I figured I'd try running mmpbsa_py_energy to see if I couldn't get a more
> clear idea of what the error was, but oddly enough running _MMPBSA_pb.mdin
> and _MMPBSA_gb.mdin with mmpbsa_py_energy both seem to complete without a
> problem-
>
> BOND = 6139.4423 ANGLE = 16044.7359 DIHED =
> 25743.7335
> VDWAALS = -16859.4284 EEL = -151313.2641 EGB =
> -19146.8926
> 1-4 VDW = 7348.3643 1-4 EEL = 82548.4930 RESTRAINT =
> 0.0000
> ESURF = 590.8814
>
> MM/GBSA processing done!
>
> BOND = 6139.4423 ANGLE = 16044.7359 DIHED =
> 25743.7335
> VDWAALS = -16859.4284 EEL = -75656.6320 EPB =
> -10359.5105
> 1-4 VDW = 7348.3643 1-4 EEL = 82548.4930 RESTRAINT =
> 0.0000
> ECAVITY = 15063.6475 EDISPER = -7396.2674
> MM/PBSA processing done!
>
> Total surface charge 7.9234
> Reaction field energy -10359.5105
> Cavity solvation energy 15063.6475
> Dispersion solvation energy -7396.2674
>
> I've tried running MMPBSA on a slightly different system that
> also uses requisite prmtop files using the same command for ante-MMPBSA,
> and the behavior is exactly the same. Yet when I run MMPBSA on a different
> system that uses prmtop files that I haven't made using ante-MMPBSA, it's
> able to run without a problem.
>
> At this point, I'm not really sure what to make of this error- I was
> initially thinking it might've been a problem with my mask selection for
> the ligand/receptor, but that mmpbsa_py_energy is actually able to give
> outputs has me wondering if there's something wrong with how I made the
> prmtops with ante-MMPBSA, or something else is going on entirely.
>
> Best,
>
> Kenneth
> --
> Ask yourselves, all of you, what power would hell have if those imprisoned
> here could not dream of heaven?
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 12 2015 - 12:30:02 PST
