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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, Chemical Physics, Chemical and Biomedical Engineering University of California, Irvine, CA 92697-3900 > > 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 >> >> >> >> _______________________________________________ >> >> AMBER mailing list >> >> 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 >> >> _______________________________________________ >> AMBER mailing list >> 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 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Jan 14 2015 - 10:00:04 PST