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

| Run on 09/07/2012 at 21:04:18
  [-O]verwriting output

File Assignments:
|  MDIN: sander_com.in                                                         
| MDOUT: sander_com.1.out                                                      
|INPCRD: ./snapshot/snapshot_com.crd.1                                         
|  PARM: ./ras-raf.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 MS                                  
 &cntrl                                                                        
  ntf    = 1,       ntb    = 0,       dielc  = 1.0,                            
  idecomp= 2,                                                                  
  igb    = 2,       saltcon= 0.00,                                             
  offset = 0.09,                                                               
  intdiel= 1.0,     extdiel= 80.0,                                             
  gbsa   = 2,       surften= 1.0,                                              
  cut    = 999.0,   nsnb   = 99999,                                            
  scnb   = 2.0,     scee   = 1.2,                                              
                                                                               
  imin   = 1,       maxcyc = 1,       ncyc   = 0,                              
 &end                                                                          
Residues considered as REC                                                     
RRES 1 166                                                                     
END                                                                            
Residues considered as LIG                                                     
LRES 167 242                                                                   
END                                                                            
Residues to print                                                              
RES 1 166 167 242                                                              
END                                                                            
END                                                                            

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

| Flags:                                                                        
| New format PARM file being parsed.
| Version =    1.000 Date = 08/28/12 Time = 15:57:59
 NATOM  =    3862 NTYPES =      14 NBONH =    1931 MBONA  =    1959
 NTHETH =    4377 MTHETA =    2642 NPHIH =    8903 MPHIA  =    8693
 NHPARM =       0 NPARM  =       0 NNB   =   21240 NRES   =     242
 NBONA  =    1959 NTHETA =    2642 NPHIA =    8693 NUMBND =      69
 NUMANG =     163 NPTRA  =     262 NATYP =      34 NPHB   =       0
 IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real              266903
|     Hollerith          23416
|     Integer           546250
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total             4310 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 =       2, rbornstat=      0

Potential function:
     ntf     =       1, ntb     =       0, igb     =       2, nsnb    =   99999
     ipol    =       0, gbsa    =       2, 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  extdiel =  80.00000
     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
