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
>
--
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 - 15:00:03 PDT
