Ray,
It does give an InputError when I try to add in space=1.0 to the py script.
But setting space=1.0 in the pb.mdin and running mmpbsa_py_energy does
complete successfully- the memory usage drops to 18%, while it hovers near
54% when space=0.5 in pb.mdin. I'm guessing that the memory usage jumps
even more when running MMPBSA.py to the point that it crashes, since I was
also able to get it to successfully run on another computer with more
memory- is the lower memory usage why I'm able to run pb.mdin through
mmpbsa_py_energy?
Likewise, I realize the most obvious solution to this problem would be to
get more memory on my workstation, but out of curiosity could I run the
respective .mdin for the receptor/ligand/complex manually through
mmpbsa_py_energy as a work around as well?
But thanks for the insight!
Best,
Kenneth
On Tue, Jan 13, 2015 at 1:08 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Kenneth,
>
> It should also be "space=1.0" in the python script if Wes has put it
> in. If not, please insert it into the .mdin file to test it. Let us
> know what you find …
>
> Thanks a lot!
>
> 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 10:28 PM, Kenneth Huang
> <kennethneltharion.gmail.com> wrote:
> > 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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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > 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
>
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Received on Tue Jan 13 2015 - 21:00:02 PST
