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

| Run on 05/28/2008 at 14:02:43
  [-O]verwriting output

File Assignments:
|  MDIN: mdin                                                                  
| MDOUT: cys.out                                                               
|INPCRD: ./prmtop-inpcrd/cys.inpcrd                                            
|  PARM: ./prmtop-inpcrd/cys.prmtop                                            
|RESTRT: restrt                                                                
|  REFC: refc                                                                  
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                  
| MDCRD: mdcrd                                                                 
|MDINFO: mdinfo                                                                
|INPDIP: inpdip                                                                
|RSTDIP: rstdip                                                                

 
 Here is the input file:
 
 test of iAPBS/sander solvation energies (based on pbsa_radi)                  
 &cntrl                                                                        
   ntx=1, irest=0,                                                             
   imin=1, maxcyc=0,                                                           
   ntpr=1, ntwr=100000,                                                        
   igb=6, ntb=0,                                                               
   ntc=1, ntf=1, tol=0.000001,                                                 
   ntt=0, temp0=300                                                            
 &end                                                                          
 &apbs                                                                         
    apbs_debug=0,                                                              
    apbs_print=0,                                                              
    grid=0.5, 0.5, 0.5,                                                        
    calc_type=0,                                                               
    cmeth=1,                                                                   
    bcfl=2,                                                                    
    srfm=1,                                                                    
    chgm=1,                                                                    
    pdie=1.0,                                                                  
    sdie=80.0,                                                                 
    srad = 1.4,                                                                
    radiopt=0,                                                                 
    calcforce=0, calcnpenergy=1,                                               
&end                                                                           

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

| Flags:                                                                        
| New format PARM file being parsed.
| Version =    1.000 Date = 09/05/04 Time = 11:20:33
 NATOM  =       6 NTYPES =       4 NBONH =       4 MBONA  =       1
 NTHETH =       7 MTHETA =       0 NPHIH =       3 MPHIA  =       0
 NHPARM =       0 NPARM  =       0 NNB   =      16 NRES   =       1
 NBONA  =       1 NTHETA =       0 NPHIA =       0 NUMBND =       3
 NUMANG =       3 NPTRA  =       1 NATYP =       4 NPHB   =       0
 IFBOX  =       0 NMXRS  =       6 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0


|     Memory Use     Allocated
|     Real                 532
|     Hollerith             39
|     Integer            20176
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total               83 kbytes
| Duplicated    0 dihedrals
| Duplicated    0 dihedrals

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

CYS                                                                             

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    =  100000
     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  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
--------------------------------------------------------------------------------

CYS                                                                             
 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

 APBS calculation parameters:

Nonlinear traditional PBE
Multiple Debye-Huckel boundary conditions
Smoothed molecular surface definition
Using cubic B-spline discretization
Grid dimension:  33  33  33
Coarse grid lengths:   8.388   9.078   7.439 A
Fine grid lengths:   8.388   9.078   7.439 A
Grid spacings:   0.500   0.500   0.500 A
Solute dielectric (pdie):   1.000
Solvent dielectric (sdie):  80.000
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       5.4871E+00     4.6203E-01     1.3514E+00     HG          5

 BOND    =        0.0001  ANGLE   =        0.0001  DIHED      =        0.0002
 VDWAALS =        0.0000  EEL     =        0.0000  EPB        =       -3.9117
 1-4 VDW =       -0.0063  1-4 EEL =        4.6089  RESTRAINT  =        0.0000
 ENPOLAR =        4.7958


  Maximum number of minimization cycles reached.


                    FINAL RESULTS



   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1       5.4871E+00     4.6203E-01     1.3514E+00     HG          5

 BOND    =        0.0001  ANGLE   =        0.0001  DIHED      =        0.0002
 VDWAALS =        0.0000  EEL     =        0.0000  EPB        =       -3.9117
 1-4 VDW =       -0.0063  1-4 EEL =        4.6089  RESTRAINT  =        0.0000
 ENPOLAR =        4.7958

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

|    Read coords time           0.00 ( 0.07% of Total)
|             PB Nonbond                 0.73 (100.0% of Nonbo)
|          Nonbond force              0.73 (100.0% of Force)
|          Bond/Angle/Dihedral        0.00 ( 0.01% of Force)
|       Force time                 0.73 (100.0% of Runmd)
|    Runmd Time                 0.73 (99.63% of Total)
|    Other                      0.00 ( 0.31% of Total)
| Total time                 0.73 (100.0% of ALL  )

| Highest rstack allocated:          0
| Highest istack allocated:          0
|           Job began  at 14:02:43.804  on 05/28/2008
|           Setup done at 14:02:43.807  on 05/28/2008
|           Run   done at 14:02:44.533  on 05/28/2008
|     wallclock() was called      22 times
