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

| Run on 05/07/2007 at 11:59:19
  [-O]verwriting output

File Assignments:
|  MDIN: md_classical.in                                                       
| MDOUT: md_classical.out                                                      
|INPCRD: min_classical.rst                                                     
|  PARM: try.prmtop                                                            
|RESTRT: md_classical.rst                                                      
|  REFC: try.inpcrd                                                            
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                  
| MDCRD: md_classical.mdcrd                                                    
|MDINFO: mdinfo                                                                
|INPDIP: inpdip                                                                
|RSTDIP: rstdip                                                                


 Here is the input file:

300K constant temp MD                                                          
 &cntrl                                                                        
  imin=0, ntb=0,                                                               
  cut=18.0, ntc=1, ntf=1,                                                      
  tempi=0, temp0=300.0,                                                        
  ntt=3, gamma_ln=1.0,                                                         
  nstlim=100, dt=0.001,                                                        
  ntpr=1, ntwx=1, ntr=1,                                                       
  restraint_wt=100, restraintmask=1-20                                         
 /                                                                             
                                                                               

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

| Flags:                                                                        
|    NONPERIODIC   ntb=0 and igb=0: Setting up nonperiodic simulation
|Largest sphere to fit in unit cell has radius =    49.859
| New format PARM file being parsed.
| Version =    1.000 Date = 05/03/07 Time = 15:40:44
 NATOM  =    6377 NTYPES =      10 NBONH =    6354 MBONA  =      24
 NTHETH =      38 MTHETA =      31 NPHIH =      74 MPHIA  =      46
 NHPARM =       0 NPARM  =       0 NNB   =    8653 NRES   =    2114
 NBONA  =      24 NTHETA =      31 NPHIA =      46 NUMBND =      16
 NUMANG =      25 NPTRA  =      16 NATYP =      13 NPHB   =       1
 IFBOX  =       1 NMXRS  =      22 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0


|     Memory Use     Allocated
|     Real              333467
|     Hollerith          40378
|     Integer           160752
|     Max Pairs       17005333
|     nblistReal         76524
|     nblist Int        436501
|       Total            72120 kbytes
| Duplicated    0 dihedrals
| Duplicated    0 dihedrals

     BOX TYPE: RECTILINEAR

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

                                                                                

General flags:
     imin    =       0, 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    =       1, ntwv    =       0, ntwe    =       0
     ioutfm  =       0, ntwprt  =       0, idecomp =       0, rbornstat=      0

Potential function:
     ntf     =       1, ntb     =       0, igb     =       0, nsnb    =      25
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     =  18.00000, intdiel =   1.00000
     scnb    =   2.00000, scee    =   1.20000

Frozen or restrained atoms:
     ibelly  =       0, ntr     =       1

Molecular dynamics:
     nstlim  =       100, nscm    =      1000, nrespa  =         1
     t       =   0.00000, dt      =   0.00100, vlimit  =  20.00000

Langevin dynamics temperature regulation:
     ig      =   71277
     temp0   = 300.00000, tempi   =   0.00000, gamma_ln=   1.00000

    LOADING THE CONSTRAINED ATOMS AS GROUPS


   5.  REFERENCE ATOM COORDINATES

      
|  INFO: Old style inpcrd file read

Error in group input::atommask.f::selectElemMask
elementary mask does not start with : or @