1168308155421 Progress log (SimTK ISIM)
1168308155453 Started Mon Jan 08 18:02:35 PST 2007
1168308155453 
1168308155453 Loading ion conditions...
1168308155765 Ion conditions loaded.
1168308278031 
Loading structure from file:/C:/Documents%20and%20Settings/Administrator/Desktop/24dup.pqr...
1168308278265 Measuring size of molecule in file C:\DOCUME~1\ADMINI~1\LOCALS~1\Temp\ISIM7122\working\expanded\24dup.pqr...
1168308278296 Running psize.py...
1168308278296 Using molecule structure file C:\DOCUME~1\ADMINI~1\LOCALS~1\Temp\ISIM7122\working\expanded\24dup.pqr
1168308278640 Environment variable settings
PROCESSOR_ARCHITECTURE=x86
LOGONSERVER=\\SIMBIOS-SCHMIDT
HOMEDRIVE=C:
SESSIONNAME=Console
HOMEPATH=\Documents and Settings\Administrator
TMP=C:\DOCUME~1\ADMINI~1\LOCALS~1\Temp
windir=C:\WINDOWS
PROCESSOR_IDENTIFIER=x86 Family 15 Model 4 Stepping 1, GenuineIntel
SystemDrive=C:
USERPROFILE=C:\Documents and Settings\Administrator
SonicCentral=C:\Program Files\Common Files\Sonic Shared\Sonic Central\
PATHEXT=.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH
CommonProgramFiles=C:\Program Files\Common Files
=::=::\
NUMBER_OF_PROCESSORS=1
COMPUTERNAME=SIMBIOS-SCHMIDT
ComSpec=C:\WINDOWS\system32\cmd.exe
OS=Windows_NT
CLIENTNAME=Console
USERNAME=Administrator
TEMP=C:\DOCUME~1\ADMINI~1\LOCALS~1\Temp
ALLUSERSPROFILE=C:\Documents and Settings\All Users
USERDOMAIN=SIMBIOS-SCHMIDT
PROCESSOR_LEVEL=15
SystemRoot=C:\WINDOWS
APPDATA=C:\Documents and Settings\Administrator\Application Data
Path=C:\Program Files\Java\jre1.5.0_10\bin;C:\Program Files\Mozilla Firefox\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\OpenAFS\Common;C:\Program Files\OpenAFS\Client\Program;"C:\Program Files\Java\jre1.5.0_10\bin"
FP_NO_HOST_CHECK=NO
PROCESSOR_REVISION=0401
ProgramFiles=C:\Program Files

Issuing command: <C:\DOCUME~1\ADMINI~1\LOCALS~1\Temp\ISIM7122\working\psize.exe --GMEMCEIL=2000 24dup.pqr >
1168308278875 Issued command
1168308279265 

NOTE: The recommended settings from
psize are NOT necessarily exactly what will be used when
running APBS.

1168308279265 

Psize Standard Output:

1168308279265 Default constants used (./psize.py --help for more information):
{'CFAC': 1.7, 'TFAC_SPARC': 0.00050000000000000001, 'OFAC': 0.10000000000000001, 'SPACE': 0.5, 'TFAC_ALPHA': 9.0000000000000006e-005, 'REDFAC': 0.25, 'FADD': 20, 'GMEMCEIL': 2000, 'TFAC_XEON': 0.00029999999999999997, 'GMEMFAC': 160}

################# MOLECULE INFO ####################
Number of ATOM entries = 1518
Number of HETATM entries (ignored) = 0
Total charge = -46.000 e
Dimensions = 23.231 x 24.766 x 82.200 A
Center = 0.358 x 1.605 x 38.363 A
Lower corner = -11.258 x -10.778 x -2.737 A
Upper corner = 11.973 x 13.988 x 79.463 A

############## GENERAL CALCULATION INFO #############
Coarse grid dims = 39.493 x 42.102 x 139.740 A
Fine grid dims = 39.493 x 42.102 x 102.200 A
Num. fine grid pts. = 65 x 65 x 193
Fine mesh spacing = 0.617073 x 0.657847 x 0.532292 A
Estimated mem. required for sequential solve = 124.424 MB
Number of focusing operations = 2

################# ESTIMATED REQUIREMENTS ####################
Memory per processor                   = 124.424 MB
Grid storage requirements (ASCII)      = 74.654 MB
Grid storage requirements (XDR)        = 6.221 MB
Time to solve on 667 MHz EV67 Alpha    = 146.777 sec
Time to solve on 500 MHz PIII Xeon     = 489.255 sec
Time to solve on 400 MHz UltraSparc II = 815.425 sec

1168308279265 

Psize Standard Error:

1168308279265 1168308293843 Starting APBS task...
1168308293843 Unpacking APBS executable...
1168308293968 Creating APBS input file...
1168308293968 APBS input file:
1168308293968 

********************

1168308293968 read 
    mol pqr 24dup.pqr
end

elec
    mg-manual
    dime  97 97 97
    nlev 4
    glen 149.513 149.513 149.513
    gcent mol 1
    mol 1
    npbe
    bcfl sdh
    ion  1 0.000 2.0   # Zero ionic strength for initial run
    ion -1 0.000 2.0
    pdie 2
    sdie 78.36
    srfm smol
    chgm spl2
    srad 1.4
    swin 0.3
    temp 298
    gamma 0.105
    calcenergy no
    calcforce no
    write pot dx macroionPotential
end

quit
1168308293968 

******************

1168308293984 Running APBS...
1168308294046 Progress file not found.
1168308315156 Progress file not found.
1168308323578 Standard error stream: 

1168308323578 ************************************ 

1168308323578 asc_getToken: Error occurred (bailing out).
Vio_scanf: Format problem with input.
1168308323578 

************************************ 

1168308323578 Standard output stream: 

1168308323578 ************************************ 

1168308323578 

    ----------------------------------------------------------------------
    APBS -- Adaptive Poisson-Boltzmann Solver
    Version 0.3.2
    
    Nathan A. Baker (baker@biochem.wustl.edu)
    Dept. Biochemistry and Molecular Biophysics
    Center for Computational Biology
    Washington University in St. Louis
    
    Additional contributing authors listed in the code documentation.
    
    Copyright (c) 2002-2004.  Washington University in St. Louis.
    All Rights Reserved.
    Portions Copyright (c) 1999-2002.  The Regents of the University of 
    California.
    Portions Copyright (c) 1995.  Michael Holst.
    
    This program is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation; either version 2 of the License, or
    (at your option) any later version.
    
    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
    
    You should have received a copy of the GNU General Public License
    along with this program; if not, write to the Free Software
    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307 USA
    ----------------------------------------------------------------------
    APBS uses PMG and FEtk to solve the Poisson-Boltzmann equation
    numerically.  FEtk and PMG are developed and maintained by the Holst
    Research Group at UC San Diego.  PMG is designed to solve the nonlinear
    Poisson-Boltzmann equation and similar problems with linear space and
    time complexity through the use of box methods, inexact Newton methods,
    and algebraic multilevel methods.  FEtk is designed to solve general
    coupled systems of nonlinear partial differential equations accurately
    and efficiently using adaptive multilevel finite element methods,
    inexact Newton methods, and algebraic multilevel methods.  More
    information about PMG and FEtk may be found at <http://www.FEtk.ORG>.
    ----------------------------------------------------------------------

This executable compiled on May 17 2006 at 15:33:26

Parsing input file apbs_molecule.in...
Parsed input file.
Got PQR paths for 1 molecules
Reading PQR-format atom data from 24dup.pqr.
  1518 atoms
  Centered at (3.575e-001, 1.605e+000, 3.836e+001)
  Net charge -4.60e+001 e
Preparing to run 1 PBE calculations.
----------------------------------------
CALCULATION #1: MULTIGRID
  Setting up problem...
  Vpbe_ctor:  Using max ion radius (2 A) for exclusion function
  Debye length:  0 A
  Current memory usage:  177.458 MB total, 177.458 MB high water
  Using cubic spline charge discretization.
  Grid dimensions: 97 x 97 x 97
  Grid spacings: 1.557 x 1.557 x 1.557
  Grid lengths: 149.513 x 149.513 x 149.513
  Grid center: (0.358, 1.605, 38.363)
  Multigrid levels: 4
  Molecule ID: 1
  Nonlinear traditional PBE
  Single Debye-Huckel sphere boundary conditions
  2 ion species (0.000 M ionic strength):
    2.000 A-radius, 1.000 e-charge, 0.000 M concentration
    2.000 A-radius, -1.000 e-charge, 0.000 M concentration
  Solute dielectric: 2.000
  Solvent dielectric: 78.360
  Using "molecular" surface definition; harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature:  298.000 K
  Surface tension:  0.105 kJ/mol/A^2
  Potential to be written to macroionPotential.dx
  Solving PDE (see io.mc* for details)...
  Writing potential to macroionPotential.dx
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying 1 molecules
Final memory usage:  0.000 MB total, 177.458 MB high water

Thanks for using APBS!

1168308323578 

************************************ 

1168308323578 APBS process completed successfully
1168308323593 Unpacking ISIM executable...
1168308323640 ISIM input file:
1168308323640 

********************

1168308323640 #GENERAL

FORM                          S
RADIUS                       74.75664683592476  
LENGTH                        180.0   /*redundant, since 'S' is selected*/
TEMPERATURE                  298.0
MEDIUM_PERMITTIVITY          78.36000061035156
GENERAL_MODE                  N

#ENDGENERAL

#TECHNICAL

TOTAL_STEPS                   5000
MINIMIZATION_STEPS            35
CREATION_DESTRUCTION_CYCLES   10    
SHUFFLING_STEPS               10
SHUFFLING_MODE                N
SO_MANY_ARE_SOME              40      /*redundant, since 'N' is selected*/
MAXIMUM_DISPLACEMENT          2.0
PARAMETRIZATION_MINIMUM       50
RANDOM_SEED                   4357

#ENDTECHNICAL

#ANALYSIS

EQUILIBRATION_STEPS           200
GRID_RESOLUTION               100           
COORDINATES_OUTPUT            1000
NUMBER_DENSITIES_OUTPUT       1000
CHARGE_DENSITY_OUTPUT         1000
POTENTIAL_OUTPUT              1000
PAIR_CORRELATION_OUTPUT       6200
POTENTIAL_FREQUENCY           100
PAIR_CORRELATION_FREQUENCY    6200
PAIR_CORRELATION_RESOLUTION   0.3
PAIR_CORRELATION_SHELLS       5

#ENDANALYSIS

#IONS

MODEL                         H
TYPES                         3
Cl  40.0  -1.0  3.0  0.0
Mg  10.0  2.0  2.0  0.0
Na  20.0  1.0  1.0  0.0

#ENDIONS

#MACROMOLECULE

TYPE_ID                               P    
STERIC_MODE                           S    
BORN_ION_CHARGE                       30.0                /*redundant, since 'P' is selected*/
BORN_ION_RADIUS                       10.0                /*redundant, since 'P' is selected*/
PQR_FILENAME                          24dup.pqr
PQR_DX_POTENTIAL_FILENAME             macroionPotential.dx
PQR_GRID_RESOLUTION                   60
PQR_OUTSIDE_MESH_MODE                 1

#ENDMACROMOLECULE

1168308323640 

******************

1168308323656 Creating ISIM excess potential files...
1168308323671 Running ISIM...
1168308330734 Ok Step=<     100> 0.00e+000  _scalefactor=1.8Step 100 of 5000
1168308331609 Ok Step=<     200> 1.33e+002  _scalefactor=1.8Step 200 of 5000
1168308332890 Ok Step=<     300> 1.24e+002  _scalefactor=1.8Step 300 of 5000
1168308336984 Progress file found.
1168308338531 Ok Step=<     400> 2.68e+002  _scalefactor=1.8Step 400 of 5000
1168308344406 Ok Step=<     500> 3.41e+002  _scalefactor=1.8Step 500 of 5000
1168308350890 Ok Step=<    -600> 3.86e+002  _scalefactor=1.8Step 600 of 5000
1168308352187 Ok Step=<     700> 3.43e+002  _scalefactor=1.62Step 700 of 5000
1168308358093 Ok Step=<     800> 3.75e+002  _scalefactor=1.62Step 800 of 5000
1168308359125 Progress file found.
1168308364156 Ok Step=<     900> 4.02e+002  _scalefactor=1.62Step 900 of 5000
1168308370453 Ok Step=<    1000> 4.24e+002  _scalefactor=1.62Step 1000 of 5000
1168308380796 Progress file found.
1168308384656 Ok Step=<    1100> 4.92e+002  _scalefactor=1.62Step 1100 of 5000
1168308390703 Ok Step=<    1200> 5.02e+002  _scalefactor=1.62Step 1200 of 5000
1168308396578 Ok Step=<    1300> 5.07e+002  _scalefactor=1.62Step 1300 of 5000
1168308401421 Progress file found.
1168308402031 Ok Step=<    1400> 5.10e+002  _scalefactor=1.62Step 1400 of 5000
1168308407875 Ok Step=<    1500> 5.16e+002  _scalefactor=1.62Step 1500 of 5000
1168308413718 Ok Step=<    1600> 5.19e+002  _scalefactor=1.62Step 1600 of 5000
1168308419171 Ok Step=<    1700> 5.21e+002  _scalefactor=1.62Step 1700 of 5000
1168308422000 Progress file found.
1168308424625 Ok Step=<    1800> 5.21e+002  _scalefactor=1.62Step 1800 of 5000
1168308430453 Ok Step=<    1900> 5.24e+002  _scalefactor=1.62Step 1900 of 5000
1168308436703 Ok Step=<    2000> 5.26e+002  _scalefactor=1.62Step 2000 of 5000
1168308442562 Progress file found.
1168308450968 Ok Step=<    2100> 5.58e+002  _scalefactor=1.62Step 2100 of 5000
1168308456875 Ok Step=<    2200> 5.59e+002  _scalefactor=1.62Step 2200 of 5000
1168308463406 Ok Step=<    2300> 5.63e+002  _scalefactor=1.62Step 2300 of 5000
1168308464515 Progress file found.
1168308470734 Ok Step=<    2400> 5.64e+002  _scalefactor=1.62Step 2400 of 5000
1168308477921 Ok Step=<    2500> 5.65e+002  _scalefactor=1.62Step 2500 of 5000
1168308484000 Ok Step=<    2600> 5.64e+002  _scalefactor=1.62Step 2600 of 5000
1168308487140 Progress file found.
1168308489875 Ok Step=<    2700> 5.65e+002  _scalefactor=1.62Step 2700 of 5000
1168308495546 Ok Step=<    2800> 5.65e+002  _scalefactor=1.62Step 2800 of 5000
1168308501453 Ok Step=<    2900> 5.65e+002  _scalefactor=1.62Step 2900 of 5000
1168308508437 Ok Step=<    3000> 5.66e+002  _scalefactor=1.62Step 3000 of 5000
1168308509750 Progress file found.
1168308522218 Ok Step=<    3100> 5.86e+002  _scalefactor=1.62Step 3100 of 5000
1168308528546 Ok Step=<    3200> 5.86e+002  _scalefactor=1.62Step 3200 of 5000
1168308531781 Progress file found.
1168308533906 Ok Step=<    3300> 5.85e+002  _scalefactor=1.62Step 3300 of 5000
1168308539937 Ok Step=<    3400> 5.85e+002  _scalefactor=1.62Step 3400 of 5000
1168308545359 Ok Step=<    3500> 5.84e+002  _scalefactor=1.62Step 3500 of 5000
1168308550656 Ok Step=<    3600> 5.82e+002  _scalefactor=1.62Step 3600 of 5000
1168308553937 Progress file found.
1168308556296 Ok Step=<    3700> 5.82e+002  _scalefactor=1.62Step 3700 of 5000
1168308562000 Ok Step=<    3800> -5.80e+002  _scalefactor=1.62Step 3800 of 5000
1168308568812 Ok Step=<    3900> -5.50e+002  _scalefactor=1.62Step 3900 of 5000
1168308574000 Ok Step=<    4000> -5.23e+002  _scalefactor=1.62Step 4000 of 5000
1168308576328 Progress file found.
1168308587437 Ok Step=<    4100> -4.81e+002  _scalefactor=1.62Step 4100 of 5000
1168308593953 Ok Step=<    4200> -4.54e+002  _scalefactor=1.62Step 4200 of 5000
1168308598500 Progress file found.
1168308600218 Ok Step=<    4300> -4.29e+002  _scalefactor=1.62Step 4300 of 5000
1168308606453 Ok Step=<    4400> -4.06e+002  _scalefactor=1.62Step 4400 of 5000
1168308612484 Ok Step=<    4500> -3.83e+002  _scalefactor=1.62Step 4500 of 5000
1168308618421 Ok Step=<    4600> -3.61e+002  _scalefactor=1.62Step 4600 of 5000
1168308620578 Progress file found.
1168308624250 Ok Step=<    4700> -3.41e+002  _scalefactor=1.62Step 4700 of 5000
1168308630359 Ok Step=<    4800> -3.20e+002  _scalefactor=1.62Step 4800 of 5000
1168308635859 Ok Step=<    4900> -3.02e+002  _scalefactor=1.62Step 4900 of 5000
1168308641968 Ok Step=<    5000> -2.84e+002  _scalefactor=1.62Step 5000 of 5000
1168308642843 Progress file found.
1168308654187 ISIM Process succeeded.
1168308654187 Standard error stream: 

1168308654187 ************************************ 

1168308654187 1168308654187 

************************************ 

1168308654187 Standard output stream: 

1168308654187 ************************************ 

1168308654187 
ISIM, working copy

1168308654187 

************************************ 

1168308654187 Contents of ISIM.Err file:
1168308654187 **********************************************************************
1168308654187 
1168308654187 
1168308654187 			ERROR-FILE FOR JOB STARTED ON
1168308654187 			Mon Jan 08 18:05:23 2007
1168308654187 
1168308654187 
1168308654187 **********************************************************************
1168308654187 
1168308654187 
1168308654187 
1168308654187 asc_getToken: Error occurred (bailing out).
1168308654187 Vio_scanf: Format problem with input.
1168308654187 asc_getToken: Error occurred (bailing out).
1168308654203 Vio_scanf: Format problem with input.
1168308654203 minimzSteps=       36	  -256.18	  -35.476	        0	   -220.7 END OF MIN
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -36.3936) not found in hiearchy!
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -34.8834) not found in hiearchy!
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -33.3732) not found in hiearchy!
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -31.8629) not found in hiearchy!
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -30.3527) not found in hiearchy!
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -28.8425) not found in hiearchy!
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -27.3322) not found in hiearchy!
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -25.822) not found in hiearchy!
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -24.3118) not found in hiearchy!
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -22.8015) not found in hiearchy!
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -21.2913) not found in hiearchy!
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -19.7811) not found in hiearchy!
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -18.2708) not found in hiearchy!
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -16.7606) not found in hiearchy!
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -15.2504) not found in hiearchy!
1168308654203 Vmgrid_value:  Point (-74.3991, -73.1516, -13.7401) not found in hiearchy!

contiuing for 2MB

ending with

1168309320265 Vmgrid_value:  Point (-74.3991, -29.3548, 4.38271) not found in hiearchy!
1168309320265 Vmgrid_value:  Point (-74.3991, -29.3548, 5.89294) not found in hiearchy!
1168309320265 Vmgrid_value:  Point (-74.3991, -29.3548, 7.40318) not found in hiearchy!
1168309320328 Vmgrid_value:  Point (-74.3991, -29.3548, 8.91341) not found in hiearchy!
1168309320375 Vmgrid_value:  Point (-74.3991, -29.3548, 10.4236) not found in hiearchy!
1168309320546 Vmgrid_value:  Point (-74.3991, -29.3548, 11.9339) not found in hiearchy!
1168309320578 Vmgrid_value:  Point (-74.3991, -29.3548, 13.4441) not found in hiearchy!
1168309320671 Vmgrid_value:  Point (-74.3991, -29.3548, 14.9544) not found in hiearchy!
1168309320687 Vmgrid_value:  Point (-74.3991, -29.3548, 16.4646) not found in hiearchy!
1168309320781 Vmgrid_value:  Point (-74.3991, -29.3548, 17.9748) not found in hiearchy!
1168309320781 Vmgrid_value:  Point (-74.3991, -29.3548, 19.4851) not found in hiearchy!
1168309320781 Vmgrid_value:  Point (-74.3991, -29.3548, 20.9953) not found in hiearchy!
1168309320781 Vmgrid_value:  Point (-74.3991, -29.3548, 22.5055) not found in hiearchy!
1168309320781 Vmgrid_value:  Point (-74.3991, -29.3548, 24.0158) not found in hiearchy!