What does your MMPBSA input file look like? Unless you are specifically
setting the variable use_sander=1 in your input file, then you are using an
outdated MMPBSA (the new version with AmberTools 1.5 uses a new, faster nab
program to do the GB and PB calculations instead of sander). I'm guessing,
too, that if this issue has been fixed, it is fixed in AmberTools 1.5 (and
will not be addressed in earlier versions AFAIK). Thus, you should install
AmberTools 1.5 if you haven't already, and try using the nab program instead
of sander if you have.
Hope this helps,
Jason
On Wed, Jul 20, 2011 at 4:01 AM, <zw258.cam.ac.uk> wrote:
> Bill Miller III wrote:
>
>> 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<http://lists.ambermd.org/mailman/listinfo/amber>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> ------------------------------**------------------------------**
>>> ------------
>>>
>>>
>>>> ______________________________**_________________
>>>>>>> AMBER mailing list
>>>>>>> AMBER.ambermd.org
>>>>>>> http://lists.ambermd.org/**mailman/listinfo/amber<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<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<http://ambermd.org/bugfixes/AmberTools/1.5/bugfix.all>
>>> Zhi
>>>
>>> ______________________________**_________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/**mailman/listinfo/amber<http://lists.ambermd.org/mailman/listinfo/amber>
>>>
>>>
>>>
>>
>>
>>
>>
>>
> Yes, I re-run the calculation and it still stop on the same frame (frame 8)
> of the complex.
> Output file is attached.
> Zhi
>
>
> -------------------------------------------------------
> Amber 11 SANDER 2010
> -------------------------------------------------------
>
> | Run on 07/20/2011 at 08:53:00
> [-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
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 20 2011 - 10:30:02 PDT
