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
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Received on Tue Jul 19 2011 - 11:00:03 PDT
