
          -------------------------------------------------------
          Amber 10 SANDER                              2008
          -------------------------------------------------------

| Run on 05/28/2008 at 14:28:33
  [-O]verwriting output

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

 
 Here is the input file:
 
APBS visualization example                                                     
&cntrl                                                                         
   maxcyc=0, imin=1,                                                           
   cut=12.0,                                                                   
   igb=6, ntb=0                                                                
   ntpr=1,                                                                     
 /                                                                             
&apbs                                                                          
    apbs_debug = 0,                                                            
    apbs_print=1,                                                              
    calc_type = 0,                                                             
    grid = 0.5, 0.5, 0.5,                                                      
    srad = 0.7,                                                                
    wpot = 1, wchg = 1, wsmol =1,                                              
    sp_apbs=.true.,                                                            
&end                                                                           
                                                                               

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

| Flags:                                                                        
| New format PARM file being parsed.
| Version =    1.000 Date = 10/18/06 Time = 21:21:36
 NATOM  =      22 NTYPES =       7 NBONH =      12 MBONA  =       9
 NTHETH =      25 MTHETA =      11 NPHIH =      42 MPHIA  =      18
 NHPARM =       0 NPARM  =       0 NNB   =      99 NRES   =       3
 NBONA  =       9 NTHETA =      11 NPHIA =      18 NUMBND =       8
 NUMANG =      16 NPTRA  =      16 NATYP =       7 NPHB   =       0
 IFBOX  =       0 NMXRS  =      10 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real                1592
|     Hollerith            137
|     Integer            21004
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total               95 kbytes
| Duplicated    0 dihedrals
| Duplicated    0 dihedrals

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

ACE                                                                             

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     =  12.00000, 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  extdiel =  78.50000
     alpb  =        0
     scnb    =   2.00000, scee    =   1.20000

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

Energy minimization:
     maxcyc  =       0, ncyc    =      10, ntmin   =       1
     dx0     =   0.01000, drms    =   0.00010
|  INFO: Old style inpcrd file read


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

ACE                                                                             
 begin time read from input coords =     0.000 ps

iAPBS: Initializing APBS interface
iAPBS: Using charge/radii definition from prmtop file
iAPBS: Grid dime not specified, calculating ...
iAPBS: Requesting dime re-calculation on the fly
iAPBS: Grid values: 
iAPBS: fglen:   13.346  17.483   9.556
iAPBS: cglen:   13.346  17.483   9.556
iAPBS: dime:   33  33  33
iAPBS: grid:    0.500   0.500   0.500
iAPBS: Required memory (in MB):      6.854

 APBS calculation parameters:

Nonlinear traditional PBE
Single Debye-Hukel boundary conditions
Cubic-spline surface
Using cubic B-spline discretization
Grid dimension:  33  33  33
Coarse grid lengths:  13.346  17.483   9.556 A
Fine grid lengths:  13.346  17.483   9.556 A
Grid spacings:   0.500   0.500   0.500 A
Solute dielectric (pdie):   2.000
Solvent dielectric (sdie):  78.400
Temperature: 298.150 K
Surface sphere density (sdens):  10.000 grid points/A^2
Surface tension:   0.105 kJ/mol/A
Using charge/radii information from prmtop file

 Number of triangulated 3-point waters found:        0

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



   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1       2.3630E+02     5.3610E+00     1.8943E+01     N           7

 BOND    =        0.0206  ANGLE   =        0.3620  DIHED      =        8.1071
 VDWAALS =        2.8120  EEL     =      -80.1238  EPB        =      244.2636
 1-4 VDW =        5.0157  1-4 EEL =       48.9355  RESTRAINT  =        0.0000
 ENPOLAR =        6.9045


  Maximum number of minimization cycles reached.


                    FINAL RESULTS



   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1       2.3630E+02     5.3610E+00     1.8943E+01     N           7

 BOND    =        0.0206  ANGLE   =        0.3620  DIHED      =        8.1071
 VDWAALS =        2.8120  EEL     =      -80.1238  EPB        =      244.2636
 1-4 VDW =        5.0157  1-4 EEL =       48.9355  RESTRAINT  =        0.0000
 ENPOLAR =        6.9045

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

|    Read coords time           0.01 ( 1.47% of Total)
|             Gen Born time              0.00 ( 0.01% of Nonbo)
|             PB Nonbond                 0.50 (100.0% of Nonbo)
|          Nonbond force              0.50 (100.0% of Force)
|          Bond/Angle/Dihedral        0.00 ( 0.02% of Force)
|          Other                      0.00 ( 0.01% of Force)
|       Force time                 0.50 (100.0% of Runmd)
|    Runmd Time                 0.50 (89.67% of Total)
|    Other                      0.05 ( 8.85% of Total)
| Total time                 0.55 (100.0% of ALL  )

| Highest rstack allocated:          0
| Highest istack allocated:          0
|           Job began  at 14:28:33.049  on 05/28/2008
|           Setup done at 14:28:33.106  on 05/28/2008
|           Run   done at 14:28:33.602  on 05/28/2008
|     wallclock() was called      22 times
