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

| Run on 09/29/2009 at 16:47:00
  [-O]verwriting output

File Assignments:
|  MDIN: iapbs.in                                                              
| MDOUT: iapbs_com.1.out                                                       
|INPCRD: ./snapshots/snap_com.crd.1                                            
|  PARM: ./com.top                                                             
|RESTRT: restrt                                                                
|  REFC: refc                                                                  
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                  
| MDCRD: mdcrd                                                                 
|MDINFO: mdinfo                                                                
|INPDIP: inpdip                                                                
|RSTDIP: rstdip                                                                

|INPTRA: inptraj                                                               
|

 Here is the input file:

File generated by mm_pbsa.pl. Using iAPBS                                      
 &cntrl                                                                        
  ntf    = 1,       ntb    = 0,                                                
  igb    = 6,       dielc  = 1.0,                                              
  cut    = 999.0,   nsnb   = 99999,                                            
  scnb   = 2.0,     scee   = 1.2,                                              
  imin   = 1,       maxcyc = 0,       ntmin  = 2,                              
 &end                                                                          
 &apbs                                                                         
  apbs_print=0, apbs_debug=0, calc_type = 0,                                   
  grid = 0.5, 0.5, 0.5,                                                        
  radiopt = 2, pqr='pqr',                                                      
  sdie = 80.0, pdie = 1.0, srad=1.4,                                           
  cmeth=1, bcfl=2, srfm=1, chgm=1,                                             
  nion = 0,                                                                    
  swin=0.3, gamma=0.105,                                                       
  calcenergy=1, calcforce=0, calcnpenergy=1                                    
 &end                                                                          

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

| Flags:                                                                        
| New format PARM file being parsed.
| Version =    1.000 Date = 07/27/09 Time = 16:15:41
 NATOM  =    3222 NTYPES =      14 NBONH =    1659 MBONA  =    1593
 NTHETH =    3786 MTHETA =    2163 NPHIH =    7132 MPHIA  =    5045
 NHPARM =       0 NPARM  =       0 NNB   =   17932 NRES   =     199
 NBONA  =    1593 NTHETA =    2163 NPHIA =    5045 NUMBND =      62
 NUMANG =     140 NPTRA  =      63 NATYP =      43 NPHB   =       0
 IFBOX  =       0 NMXRS  =      99 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are Bondi radii (bondi)                                                             

|     Memory Use     Allocated
|     Real              206639
|     Hollerith          19533
|     Integer           186401
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total             2418 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    =      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     =       6, nsnb    =   99999
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     = 999.00000, 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   =       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 charge/radii definition from pqr filename: pqr                                                                                                                                                                                                                                                             
Wrong number of atoms in PQR file!