If you re-run MMPBSA.py does it always stop on the same frame (frame 8) of
the complex?
-Bill
On Tue, Jul 19, 2011 at 6:02 PM, Zhi Wang <zw258.cam.ac.uk> wrote:
> On 2011-7-20 5:54, Bill Miller III wrote:
> > Are you using AmberTools 1.5 with all patches applied?
> >
> > -Bill
> >
> > On Tue, Jul 19, 2011 at 1:31 PM, Bill Miller III<brmilleriii.gmail.com
> >wrote:
> >
> >> Sorry, you are correct. I have a different version of AmberTools. We are
> >> currently in the process of getting a patch for AmberTools 1.5 to fix
> this
> >> problem.
> >>
> >> -Bill
> >>
> >>
> >> On Tue, Jul 19, 2011 at 8:47 AM,<zw258.cam.ac.uk> wrote:
> >>
> >>> Bill Miller III wrote:
> >>>> This is a problem that a couple of other people have seen (myself
> >>> included).
> >>>> Mengjuei has written a patch for this error that worked for me. I have
> >>>> attached the patch. Apply it just as you would any other Amber bugfix,
> >>> and
> >>>> then recompile. That should fix your problem.
> >>>>
> >>>> -Bill
> >>>>
> >>>> On Tue, Jul 19, 2011 at 4:03 AM,<zw258.cam.ac.uk> wrote:
> >>>>
> >>>>
> >>>>> Hello!
> >>>>>
> >>>>> I am working on a simulation of a GPCR in membrane. My topology files
> >>> were
> >>>>> generated by CHAMBER as I am using CHARMM force field.
> >>>>>
> >>>>> Using MMPBSA.py, it failed at PB calculation stage. Following is the
> >>> error
> >>>>> messages and _MMPBSA_complex_pb.mdout file is attached.
> >>>>>
> >>>>> Thanks a lot.
> >>>>> Regards,
> >>>>> Zhi
> >>>>>
> >>>>>
> >>>>> ******************************
> >>>>> Reading command-line arguments and input files...
> >>>>> Loading and checking parameter files for compatibility...
> >>>>> ptraj found! Using /home/zw258/code/AMBER/**amber11/bin/ptraj
> >>>>> sander found! Using /home/zw258/code/AMBER/**amber11/bin/sander for
> GB
> >>>>> calculations
> >>>>> sander found! Using /home/zw258/code/AMBER/**amber11/bin/sander for
> PB
> >>>>> calculations
> >>>>> Preparing trajectories for simulation...
> >>>>> 1000 frames were read in and processed by ptraj for use in
> calculation.
> >>>>>
> >>>>> Beginning GB calculations with sander...
> >>>>> calculating complex contribution...
> >>>>> calculating receptor contribution...
> >>>>> calculating ligand contribution...
> >>>>>
> >>>>> Beginning PB calculations with sander...
> >>>>> calculating complex contribution...
> >>>>> Error: sander error during PB calculations!
> >>>>> NOTE: All files have been retained for debugging purposes. Type
> >>> MMPBSA.py
> >>>>> --clean to erase these files.
> >>>>> *************************************
> >>>>>
> >>>>>
> >>>>> -------------------------------------------------------
> >>>>> Amber 11 SANDER 2010
> >>>>> -------------------------------------------------------
> >>>>>
> >>>>> | Run on 07/18/2011 at 21:32:26
> >>>>> [-O]verwriting output
> >>>>>
> >>>>> File Assignments:
> >>>>> | MDIN: _MMPBSA_pb.mdin
> >>>>> | MDOUT: _MMPBSA_complex_pb.mdout
> >>>>> |INPCRD: _MMPBSA_dummycomplex.inpcrd.1
> >>>>> | PARM: complex_vmd.prmtop
> >>>>> |RESTRT: _MMPBSA_.restrt
> >>>>> | REFC: refc
> >>>>> | MDVEL: mdvel
> >>>>> | MDEN: mden
> >>>>> | MDCRD: mdcrd
> >>>>> |MDINFO: mdinfo
> >>>>> | MTMD: mtmd
> >>>>> |INPDIP: inpdip
> >>>>> |RSTDIP: rstdip
> >>>>>
> >>>>> |INPTRA: _MMPBSA_complex.mdcrd
> >>>>> |
> >>>>>
> >>>>> Here is the input file:
> >>>>>
> >>>>> File generated by MMPBSA.py
> >>>>> &cntrl
> >>>>> nsnb=99999, ipb=1, ntb=0, cut=999.0,
> >>>>> imin=5, igb=10,
> >>>>> /
> >>>>> &pb
> >>>>> istrng=100.0, sprob=1.4, maxitn=1000,
> >>>>> fillratio=4.0, radiopt=0, dbfopt=1,
> >>>>> cavity_surften=0.00542,
> >>>>> /
> >>>>>
> >>>>>
> >>>>>
> >>>
> --------------------------------------------------------------------------------
> >>>>> 1. RESOURCE USE:
> >>>>>
> >>>>>
> >>>
> --------------------------------------------------------------------------------
> >>>>> | Flags:
> >>>>> PB Info in pb_read(): npopt has been overwritten with inp
> >>>>> | New format PARM file being parsed.
> >>>>> | Version = 1.000 Date = 06/11/03 Time = 12:02:08
> >>>>> NATOM = 5068 NTYPES = 36 NBONH = 2545 MBONA = 2596
> >>>>> NTHETH = 5722 MTHETA = 3538 NPHIH = 9541 MPHIA = 4639
> >>>>> NHPARM = 0 NPARM = 0 NNB = 28000 NRES = 314
> >>>>> NBONA = 2596 NTHETA = 3538 NPHIA = 4639 NUMBND = 72
> >>>>> NUMANG = 163 NPTRA = 302 NATYP = 36 NPHB = 0
> >>>>> IFBOX = 1 NMXRS = 24 IFCAP = 0 NEXTRA = 0
> >>>>> NCOPY = 0
> >>>>>
> >>>>> Implicit solvent radii are modified Bondi radii (mbondi)
> >>>>> | Force field information read from topology file:
> >>>>> | CHARMM 31 *> CHARMM22 All-Hydrogen Topology File for
> Proteins
> >>> and
> >>>>> Lipi
> >>>>> |
> >>>>> |CHARMM: CHARMM force field in use.
> >>>>> |CHARMM: Overriding default value of chngmask.
> >>>>> |CHARMM: Setting chngmask = 0.
> >>>>>
> >>>>> | Memory Use Allocated
> >>>>> | Real 341238
> >>>>> | Hollerith 15520
> >>>>> | Integer 257185
> >>>>> | Max Pairs 1
> >>>>> | nblistReal 0
> >>>>> | nblist Int 0
> >>>>> | Total 3731 kbytes
> >>>>>
> >>>>> | Note: 1-4 EEL scale factors are being read from the topology file.
> >>>>>
> >>>>> | Note: 1-4 VDW scale factors are being read from the topology file.
> >>>>> | Duplicated 0 dihedrals
> >>>>> | Duplicated 0 dihedrals
> >>>>> |CHARMM: Reticulating splines.
> >>>>>
> >>>>> BOX TYPE: RECTILINEAR
> >>>>>
> >>>>>
> >>>>>
> >>>
> --------------------------------------------------------------------------------
> >>>>> 2. CONTROL DATA FOR THE RUN
> >>>>>
> >>>>>
> >>>
> --------------------------------------------------------------------------------
> >>>>>
> >>>>>
> >>>>> General flags:
> >>>>> imin = 5, nmropt = 0
> >>>>>
> >>>>> Nature and format of input:
> >>>>> ntx = 1, irest = 0, ntrx = 1
> >>>>>
> >>>>> Nature and format of output:
> >>>>> ntxo = 1, ntpr = 50, ntrx = 1, ntwr
> =
> >>>>> 500
> >>>>> iwrap = 0, ntwx = 0, ntwv = 0, ntwe
> =
> >>>>> 0
> >>>>> ioutfm = 0, ntwprt = 0, idecomp = 0,
> rbornstat=
> >>>>> 0
> >>>>>
> >>>>> Potential function:
> >>>>> ntf = 1, ntb = 0, igb = 10, nsnb
> =
> >>>>> 99999
> >>>>> ipol = 0, gbsa = 0, iesp = 0
> >>>>> dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
> >>>>>
> >>>>> Frozen or restrained atoms:
> >>>>> ibelly = 0, ntr = 0
> >>>>>
> >>>>> Energy minimization:
> >>>>> maxcyc = 1, ncyc = 10, ntmin = 1
> >>>>> dx0 = 0.01000, drms = 0.00010
> >>>>> | INFO: Old style inpcrd file read
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>
> --------------------------------------------------------------------------------
> >>>>> 3. ATOMIC COORDINATES AND VELOCITIES
> >>>>>
> >>>>>
> >>>
> --------------------------------------------------------------------------------
> >>>>> trajectory generated by ptraj
> >>>>> begin time read from input coords = 0.000 ps
> >>>>>
> >>>>> Number of triangulated 3-point waters found: 0
> >>>>>
> >>>>>
> >>>>>
> >>>
> --------------------------------------------------------------------------------
> >>>>> 4. RESULTS
> >>>>>
> >>>>>
> >>>
> --------------------------------------------------------------------------------
> >>>>> POST-PROCESSING OF TRAJECTORY ENERGIES
> >>>>> trajectory generated by ptraj
> >>>>> minimizing coord set # 1
> >>>>> Total surface charge -6.9062
> >>>>> Reaction field energy -3785.5658
> >>>>> Cavity solvation energy 95.2130
> >>>>>
> >>>>>
> >>>>> Maximum number of minimization cycles reached.
> >>>>>
> >>>>>
> >>>>> FINAL RESULTS
> >>>>>
> >>>>>
> >>>>>
> >>>>> NSTEP ENERGY RMS GMAX NAME
> >>> NUMBER
> >>>>> 1 -3.8663E+03 1.7229E+01 1.2763E+02 C
> 3019
> >>>>>
> >>>>> BOND = 1099.3618 ANGLE = 2514.9576 DIHED =
> >>>>> 1727.1072
> >>>>> UB = 307.7066 IMP = 144.9070 CMAP =
> >>>>> -343.5526
> >>>>> VDWAALS = -2140.7162 EEL = -16166.5478 EPB =
> >>>>> -3785.5698
> >>>>> 1-4 VDW = 1116.7688 1-4 EEL = 11564.0399 RESTRAINT =
> >>>>> 0.0000
> >>>>> ECAVITY = 95.2130 EDISPER = 0.0000
> >>>>> minimization completed, ENE= -.38663245E+04 RMS= 0.172292E+02
> >>>>> minimizing coord set # 2
> >>>>> Total surface charge -7.1518
> >>>>> Reaction field energy -4178.5283
> >>>>> Cavity solvation energy 96.6241
> >>>>>
> >>>>>
> >>>>> Maximum number of minimization cycles reached.
> >>>>>
> >>>>>
> >>>>> FINAL RESULTS
> >>>>>
> >>>>>
> >>>>>
> >>>>> NSTEP ENERGY RMS GMAX NAME
> >>> NUMBER
> >>>>> 1 -4.3244E+03 2.7545E+01 1.2338E+03 NE2
> 15
> >>>>>
> >>>>> BOND = 1091.2305 ANGLE = 2567.0512 DIHED =
> >>>>> 1750.6803
> >>>>> UB = 302.8783 IMP = 170.6923 CMAP =
> >>>>> -377.5378
> >>>>> VDWAALS = -2142.6715 EEL = -16029.9812 EPB =
> >>>>> -4178.5495
> >>>>> 1-4 VDW = 1063.7607 1-4 EEL = 11361.4440 RESTRAINT =
> >>>>> 0.0000
> >>>>> ECAVITY = 96.6241 EDISPER = 0.0000
> >>>>> minimization completed, ENE= -.43243786E+04 RMS= 0.275451E+02
> >>>>> minimizing coord set # 3
> >>>>> Total surface charge -7.1933
> >>>>> Reaction field energy -4846.2793
> >>>>> Cavity solvation energy 97.5741
> >>>>>
> >>>>>
> >>>>> Maximum number of minimization cycles reached.
> >>>>>
> >>>>>
> >>>>> FINAL RESULTS
> >>>>>
> >>>>>
> >>>>>
> >>>>> NSTEP ENERGY RMS GMAX NAME
> >>> NUMBER
> >>>>> 1 -5.0565E+03 4.1209E+01 2.3276E+03 HE22
> 17
> >>>>>
> >>>>> BOND = 1026.2478 ANGLE = 2471.6314 DIHED =
> >>>>> 1770.7979
> >>>>> UB = 297.7850 IMP = 158.3008 CMAP =
> >>>>> -370.6401
> >>>>> VDWAALS = -2134.3262 EEL = -16138.2931 EPB =
> >>>>> -4846.2582
> >>>>> 1-4 VDW = 1107.2937 1-4 EEL = 11503.3707 RESTRAINT =
> >>>>> 0.0000
> >>>>> ECAVITY = 97.5741 EDISPER = 0.0000
> >>>>> minimization completed, ENE= -.50565163E+04 RMS= 0.412091E+02
> >>>>> minimizing coord set # 4
> >>>>> Total surface charge -6.9240
> >>>>> Reaction field energy -3781.5458
> >>>>> Cavity solvation energy 99.0276
> >>>>>
> >>>>>
> >>>>> Maximum number of minimization cycles reached.
> >>>>>
> >>>>>
> >>>>> FINAL RESULTS
> >>>>>
> >>>>>
> >>>>>
> >>>>> NSTEP ENERGY RMS GMAX NAME
> >>> NUMBER
> >>>>> 1 -4.0487E+03 1.7492E+01 2.6532E+02 HH21
> 931
> >>>>>
> >>>>> BOND = 1037.5461 ANGLE = 2512.4890 DIHED =
> >>>>> 1781.7092
> >>>>> UB = 314.0055 IMP = 156.7151 CMAP =
> >>>>> -383.6738
> >>>>> VDWAALS = -2112.4389 EEL = -16363.8438 EPB =
> >>>>> -3781.5560
> >>>>> 1-4 VDW = 1111.3562 1-4 EEL = 11579.9868 RESTRAINT =
> >>>>> 0.0000
> >>>>> ECAVITY = 99.0276 EDISPER = 0.0000
> >>>>> minimization completed, ENE= -.40486770E+04 RMS= 0.174922E+02
> >>>>> minimizing coord set # 5
> >>>>> Total surface charge -6.8066
> >>>>> Reaction field energy -4132.0448
> >>>>> Cavity solvation energy 100.1397
> >>>>>
> >>>>>
> >>>>> Maximum number of minimization cycles reached.
> >>>>>
> >>>>>
> >>>>> FINAL RESULTS
> >>>>>
> >>>>>
> >>>>>
> >>>>> NSTEP ENERGY RMS GMAX NAME
> >>> NUMBER
> >>>>> 1 -4.0752E+03 2.3701E+01 1.0820E+03 HN
> 279
> >>>>>
> >>>>> BOND = 1068.4239 ANGLE = 2542.4866 DIHED =
> >>>>> 1752.5624
> >>>>> UB = 312.9327 IMP = 160.5512 CMAP =
> >>>>> -355.1272
> >>>>> VDWAALS = -2108.7107 EEL = -16070.2489 EPB =
> >>>>> -4131.9348
> >>>>> 1-4 VDW = 1099.9538 1-4 EEL = 11553.7967 RESTRAINT =
> >>>>> 0.0000
> >>>>> ECAVITY = 100.1397 EDISPER = 0.0000
> >>>>> minimization completed, ENE= -.40751746E+04 RMS= 0.237006E+02
> >>>>> minimizing coord set # 6
> >>>>> Total surface charge -7.2589
> >>>>> Reaction field energy -4482.6135
> >>>>> Cavity solvation energy 99.3138
> >>>>>
> >>>>>
> >>>>> Maximum number of minimization cycles reached.
> >>>>>
> >>>>>
> >>>>> FINAL RESULTS
> >>>>>
> >>>>>
> >>>>>
> >>>>> NSTEP ENERGY RMS GMAX NAME
> >>> NUMBER
> >>>>> 1 -4.5157E+03 2.4632E+01 7.3786E+02 HE3
> 578
> >>>>>
> >>>>> BOND = 1025.8814 ANGLE = 2598.7656 DIHED =
> >>>>> 1750.0536
> >>>>> UB = 311.4308 IMP = 176.1615 CMAP =
> >>>>> -365.6693
> >>>>> VDWAALS = -2110.0325 EEL = -16196.9724 EPB =
> >>>>> -4482.6283
> >>>>> 1-4 VDW = 1113.6909 1-4 EEL = 11564.3343 RESTRAINT =
> >>>>> 0.0000
> >>>>> ECAVITY = 99.3138 EDISPER = 0.0000
> >>>>> minimization completed, ENE= -.45156704E+04 RMS= 0.246318E+02
> >>>>> minimizing coord set # 7
> >>>>> Total surface charge -7.8574
> >>>>> Reaction field energy -4675.2626
> >>>>> Cavity solvation energy 97.6558
> >>>>>
> >>>>>
> >>>>> Maximum number of minimization cycles reached.
> >>>>>
> >>>>>
> >>>>> FINAL RESULTS
> >>>>>
> >>>>>
> >>>>>
> >>>>> NSTEP ENERGY RMS GMAX NAME
> >>> NUMBER
> >>>>> 1 -4.8040E+03 3.0581E+01 1.2089E+03 HG2
> 2176
> >>>>>
> >>>>> BOND = 1088.3925 ANGLE = 2590.6020 DIHED =
> >>>>> 1749.6480
> >>>>> UB = 324.7064 IMP = 153.5049 CMAP =
> >>>>> -378.3257
> >>>>> VDWAALS = -2159.4928 EEL = -16136.6875 EPB =
> >>>>> -4675.3001
> >>>>> 1-4 VDW = 1089.9328 1-4 EEL = 11451.3271 RESTRAINT =
> >>>>> 0.0000
> >>>>> ECAVITY = 97.6558 EDISPER = 0.0000
> >>>>> minimization completed, ENE= -.48040366E+04 RMS= 0.305811E+02
> >>>>> minimizing coord set # 8
> >>>>> Total surface charge -7.0924
> >>>>> Reaction field energy -5413.4434
> >>>>> Cavity solvation energy 99.0459
> >>>>>
> >>>>>
> >>>>> Maximum number of minimization cycles reached.
> >>>>>
> >>>>>
> >>>>> FINAL RESULTS
> >>>>>
> >>>>>
> >>>>>
> >>>>> NSTEP ENERGY RMS GMAX NAME
> >>> NUMBER
> >>>>> 1 -5.5510E+03 5.6513E+01 3.0241E+03 NH1
> 36
> >>>>>
> >>>>> BOND = 1076.6077 ANGLE = 2616.8717 DIHED =
> >>>>> 1724.5112
> >>>>> UB = 307.8197 IMP = 151.2331 CMAP =
> >>>>> -359.5713
> >>>>> VDWAALS = -2143.2190 EEL = -16160.7416 EPB =
> >>>>> -5413.3831
> >>>>> 1-4 VDW = 1075.5702 1-4 EEL = 11474.2433 RESTRAINT =
> >>>>> 0.0000
> >>>>> ECAVITY = 99.0459 EDISPER = 0.0000
> >>>>> minimization completed, ENE= -.55510124E+04 RMS= 0.565131E+02
> >>>>> minimizing coord set # 9
> >>>>> -8.9359999999999999 7.5970000000000004
> >>> 42.517000000000003
> >>>>> pb_fdfrc(): Atom out of focusing box 42 65
> >>> 182
> >>>>> _______________________________________________
> >>>>> 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
> >>>>
> >>> Thanks for the patch. However, I can not successfully install it. May I
> >>> ask which version of Amber and AmberTools this patch is for?
> >>>
> >>> **********install message****************
> >>> zw258.shed:~/code/AMBER/amber11$ patch -p0< ../focusing.patch
> >>> patching file AmberTools/src/pbsa/interface.c
> >>> Hunk #1 FAILED at 11.
> >>> Hunk #2 FAILED at 76.
> >>> Hunk #3 FAILED at 116.
> >>> 3 out of 3 hunks FAILED -- saving rejects to file
> >>> AmberTools/src/pbsa/interface.c.rej
> >>> patching file AmberTools/src/pbsa/interface.h
> >>> Reversed (or previously applied) patch detected! Assume -R? [n] ^C
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >> --
> >> Bill Miller III
> >> Quantum Theory Project,
> >> University of Florida
> >> Ph.D. Graduate Student
> >> 352-392-6715
> >>
> >
> >
> Yes, I am using AmberTools1.5 and patched bugfix.all which is downloaded
> from http://ambermd.org/bugfixes/AmberTools/1.5/bugfix.all
> Zhi
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue Jul 19 2011 - 18:00:02 PDT
