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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 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/amberReceived on Tue Jan 13 2015 - 10:30:02 PST