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

| Run on 05/22/2009 at 08:42:01
  [-O]verwriting output

File Assignments:
|  MDIN: sander_com.in                                                         
| MDOUT: sander_com.1.out                                                      
|INPCRD: ./1xkk_com.crd.1                                                      
|  PARM: ../com.prmtop                                                         
|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  MM GB                                     
 &cntrl                                                                        
  ntf    = 1,       ntb    = 0,       dielc  = 1.0,                            
  idecomp= 0,                                                                  
  igb    = 2,       saltcon= 0.00,                                             
  offset = 0.09,                                                               
  intdiel= 1.0,     extdiel= 80.0,                                             
  gbsa   = 0,       surften= 1.0,                                              
  cut    = 999.0,   nsnb   = 99999,                                            
  scnb   = 2.0,     scee   = 1.2,                                              
                                                                               
  imin   = 1,       maxcyc = 1,       ncyc   = 0,                              
 &end                                                                          

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

| Flags:                                                                        
| New format PARM file being parsed.
| Version =    1.000 Date = 04/20/09 Time = 10:14:26
 NATOM  =    4798 NTYPES =      17 NBONH =    2425 MBONA  =    2427
 NTHETH =    5528 MTHETA =    3287 NPHIH =   10255 MPHIA  =    6417
 NHPARM =       0 NPARM  =       0 NNB   =   26587 NRES   =     290
 NBONA  =    2427 NTHETA =    3287 NPHIA =    6417 NUMBND =      65
 NUMANG =     133 NPTRA  =      46 NATYP =      45 NPHB   =       0
 IFBOX  =       0 NMXRS  =      67 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real              307671
|     Hollerith          29080
|     Integer           260109
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total             3533 kbytes
| Duplicated    0 dihedrals
| Duplicated    0 dihedrals

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

1XKK                                                                            

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     =       2, nsnb    =   99999
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     = 999.00000, intdiel =   1.00000
     saltcon =   0.00000, offset  =   0.09000, gbalpha=    0.80000
     gbbeta  =   0.00000, gbgamma =   2.90912, surften =   1.00000
     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  =       1, ncyc    =       0, ntmin   =       1
     dx0     =   0.01000, drms    =   0.00010
|  INFO: Old style inpcrd file read


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


  FATAL: NATOM mismatch in coord and topology files