
          -------------------------------------------------------
          Amber 9  SANDER                              2006
          -------------------------------------------------------

| Run on 09/24/2007 at 15:23:10
  [-O]verwriting output

File Assignments:
|  MDIN: iapbs.in                                                              
| MDOUT: iapbs.2.amber.out                                                     
|INPCRD: pgb.rst                                                               
|  PARM: prmtop                                                                
|RESTRT: restrt                                                                
|  REFC: refc                                                                  
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                  
| MDCRD: mdcrd                                                                 
|MDINFO: mdinfo                                                                
|INPDIP: inpdip                                                                
|RSTDIP: rstdip                                                                

 
 Here is the input file:
 
 test of PB reaction field on protein g solvated in a sphere (iAPBS)           
&cntrl                                                                         
   ntx=1, irest=0,                                                             
   imin=1, ntmin=2, maxcyc=0,                                                  
   ntpr=1, igb=6, ntb=0,                                                       
   ntc=1, ntf=1, tol=0.000001,                                                 
 /                                                                             
&apbs                                                                          
    apbs_debug=0, apbs_print=1,                                                
    grid = 0.5, 0.5, 0.5,                                                      
    calc_type=0,     cmeth=1,                                                  
 bcfl=2, srfm=0,                                                               
 chgm=0, srad =1.4, swin =0.3,                                                 
 pdie=1.0,  sdie=80.0,                                                         
 calcforce=0,                                                                  
 radiopt=2, pqr='pgb-amber.pqr',                                               
&end                                                                           

--------------------------------------------------------------------------------
   1.  RESOURCE   USE: 
--------------------------------------------------------------------------------

| Flags:                                                                        
| New format PARM file being parsed.
| Version =    1.000 Date = 03/08/04 Time = 15:34:25
 NATOM  =     855 NTYPES =      13 NBONH =     419 MBONA  =     442
 NTHETH =     951 MTHETA =     600 NPHIH =    1716 MPHIA  =    1040
 NHPARM =       0 NPARM  =       0 NNB   =    4698 NRES   =      56
 NBONA  =     442 NTHETA =     600 NPHIA =    1040 NUMBND =      30
 NUMANG =      65 NPTRA  =      26 NATYP =      21 NPHB   =       0
 IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0


|     Memory Use     Allocated
|     Real               55051
|     Hollerith           5188
|     Integer            61665
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              691 kbytes
| Duplicated    0 dihedrals
| Duplicated    0 dihedrals

--------------------------------------------------------------------------------
   2.  CONTROL  DATA  FOR  THE  RUN
--------------------------------------------------------------------------------

                                                                                

General flags:
     imin    =       1, nmropt  =       0

Nature and format of input:
     ntx     =       1, irest   =       0, ntrx    =       1

Nature and format of output:
     ntxo    =       1, ntpr    =       1, 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     =       6, nsnb    =      25
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     =   8.00000, intdiel =   1.00000
     saltcon =   0.00000, offset  =   0.09000, gbalpha=    1.00000
     gbbeta  =   0.00000, gbgamma =   0.00000, surften =   0.00500
     rdt     =   0.00000, rgbmax  =  25.00000
     alpb  =        0
     scnb    =   2.00000, scee    =   1.20000

Frozen or restrained atoms:
     ibelly  =       0, ntr     =       0

Energy minimization:
     maxcyc  =       0, ncyc    =      10, ntmin   =       2
     dx0     =   0.01000, drms    =   0.00010
|  INFO: Old style inpcrd file read


--------------------------------------------------------------------------------
   3.  ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

                                                                                
 begin time read from input coords =     0.000 ps

iAPBS: Initializing APBS interface
iAPBS: Reading radii definition from pqr filename: pgb-amber.pqr                                                                                                                                                                                                                                                   
iAPBS: Grid dime not specified, calculating ...
iAPBS: Requesting recalculating dime during caclulations.
iAPBS: Grid values: 
fglen:   40.582  53.930  51.807
cglen:   40.582  57.681  54.072
dime:   65  97  97
grid:    0.500   0.500   0.500
Required memory (in MB):    116.651

 APBS calculation parameters:

Nonlinear traditional PBE
Multiple Debye-Huckel boundary conditions
Molecular surface definition
Using trilinear interpolation (linear splines)
Grid dimension:  65  97  97
Coarse grid lengths:  40.582  57.681  54.072
Fine grid lengths:  40.582  53.930  51.807
Grid spacings:   0.500   0.500   0.500
Solute dielectric (pdie):   1.000
Solvent dielectric (sdie):  80.000
Temperature: 298.150
sdens:  10.000
Surface tension:   0.105
radiopt is set to 2

 Number of triangulated 3-point waters found:        0

--------------------------------------------------------------------------------
   4.  RESULTS
--------------------------------------------------------------------------------



   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1      -2.1135E+03     2.8943E+00     2.2881E+01     CG        606

 BOND    =       15.9232  ANGLE   =       72.0306  DIHED      =      259.6946
 VDWAALS =     -400.2516  EEL     =    -4454.9764  EPB        =     -942.1228
 1-4 VDW =      182.2148  1-4 EEL =     3058.2617  RESTRAINT  =        0.0000
 ENPOLAR =       95.6782


  Maximum number of minimization cycles reached.


                    FINAL RESULTS



   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1      -2.1135E+03     2.8943E+00     2.2881E+01     CG        606

 BOND    =       15.9232  ANGLE   =       72.0306  DIHED      =      259.6946
 VDWAALS =     -400.2516  EEL     =    -4454.9764  EPB        =     -942.1228
 1-4 VDW =      182.2148  1-4 EEL =     3058.2617  RESTRAINT  =        0.0000
 ENPOLAR =       95.6782

--------------------------------------------------------------------------------
   5.  TIMINGS
--------------------------------------------------------------------------------

|    Read coords time           0.00 ( 0.02% of Total)
|                Calc gb off-diag           0.01 (99.85% of Gen B)
|                Other                      0.00 ( 0.15% of Gen B)
|             Gen Born time              0.01 ( 0.02% of Nonbo)
|             PB Nonbond                25.02 (100.0% of Nonbo)
|          Nonbond force             25.02 (100.0% of Force)
|       Force time                25.02 (100.0% of Runmd)
|    Runmd Time                25.02 (100.0% of Total)
|    Other                      0.01 ( 0.05% of Total)
| Total time                25.04 (100.0% of ALL  )

| Highest rstack allocated:          0
| Highest istack allocated:          0
|           Job began  at 15:23:10.515  on 09/24/2007
|           Setup done at 15:23:10.531  on 09/24/2007
|           Run   done at 15:23:35.557  on 09/24/2007
|     wallclock() was called      22 times
