Ray,
Is there a corresponding keyword to determine space=1.0 in the MMPBSA
input, or is it only present in the PB input from _MMPBSA_pb.mdin? If the
latter, I've been able to run PB.in with space=0.5 through mmpbsa_py_energy
directly without issue. But if it is a very possible memory related issue,
why would it be that it crashes on PB only when I've chosen to use sander,
yet without sander being used it'll crash at GB instead? I've been working
under the assumption that GB does go through some surface calculations, but
not nearly as rigorous as those that PB employs.
I will see what I can do about testing it out on a different workstation
with more available memory to see what happens, though.
Best,
Kenneth
On Mon, Jan 12, 2015 at 6:26 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Looks like there is not enough memory on your compute node to compute
> the expensive SES surface for PB …
>
> If the error goes away when you set space = 1.0 (i.e. 1 Angstrom
> instead of 0.5 Angstrom), it'd confirm my guess.
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor,
> Biochemistry, Molecular Biophysics, Chemical Physics,
> Chemical and Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Mon, Jan 12, 2015 at 12:10 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
> > 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?
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
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Received on Mon Jan 12 2015 - 22:30:03 PST
