On 2011-7-21 1:03, Jason Swails wrote:
> 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 outdated MMPBSA (the new version with AmberTools 1.5 uses a new, faster nab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
>>
>>
>
Yes, I set the variable use_sander=1 in my input file. I did this as
your suggested in the previous email.
*********************
Ah, it appears as though nab cannot handle a chamber-created topology file,
which makes sense. The CHARMM-specific potential terms are not coded into
nab.
To fix this, you*must* have Amber11, and put the variable "use_sander=1" in
your MMPBSA.py input file.
Does this work?
All the best,
Jason
***************************
I will send a test case to Bill later.
Thanks for you help.
Zhi
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Received on Wed Jul 20 2011 - 13:00:03 PDT
