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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 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/amberReceived on Mon Jan 12 2015 - 15:30:02 PST