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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>> ------------------------------------------------------------------------
>>
>>>>>> _______________________________________________
>>>>>> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> 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
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Received on Wed Jul 20 2011 - 01:30:02 PDT
