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
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Received on Tue Jul 19 2011 - 15:30:02 PDT
