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

| Run on 11/04/2008 at 17:35:47
  [-O]verwriting output

File Assignments:
|  MDIN: fib_heat2.in                                                          
| MDOUT: fib_heat21.out                                                        
|INPCRD: fib_min221.rst                                                        
|  PARM: fib_lin.prmtop                                                        
|RESTRT: fib_heat21.rst                                                        
|  REFC: fib_min221.rst                                                        
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                  
| MDCRD: fib_heat21.mdcrd                                                      
|MDINFO: mdinfo                                                                
|INPDIP: inpdip                                                                
|RSTDIP: rstdip                                                                

 
 Here is the input file:
 
Stage 1 heating of dimerc40 0 to 300K                                          
 &cntrl                                                                        
  imin=0, irest=0, ntx=1,                                                      
  nstlim=100000, dt=0.002,gbsa =1,surften=0.005,                               
  ntc=2, ntf=2,ntr=1,                                                          
  ntt=3, gamma_ln =5.0,                                                        
  tempi=0.000, temp0=300.19,                                                   
  ntpr=500, ntwx=500, ntwr = 500,                                              
  ntb=0, igb=1,nmropt=1,                                                       
  cut=16                                                                       
  /                                                                            
  &wt type= 'REST', istep1 =0, istep2=0, value1=1.0, value2=1.0, /             
  &wt type='END' /                                                             
  DISANG=rst                                                                   
  END                                                                          
  hold the fibril fixed                                                        
  10.0                                                                         
  ATOM 1 900                                                                   
  END                                                                          
  END                                                                          

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

| Flags: MPI                                                                    
| New format PARM file being parsed.
| Version =    1.000 Date = 10/31/08 Time = 16:06:01
 NATOM  =    2452 NTYPES =      14 NBONH =    1248 MBONA  =    1215
 NTHETH =    2835 MTHETA =    1634 NPHIH =    5166 MPHIA  =    3101
 NHPARM =       0 NPARM  =       0 NNB   =   13398 NRES   =     169
 NBONA  =    1215 NTHETA =    1634 NPHIA =    3101 NUMBND =      32
 NUMANG =      66 NPTRA  =      33 NATYP =      23 NPHB   =       0
 IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real              157352
|     Hollerith          14883
|     Integer           241606
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total             2231 kbytes
| Duplicated    0 dihedrals
| Duplicated    0 dihedrals

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

                                                                                

General flags:
     imin    =       0, nmropt  =       1

Nature and format of input:
     ntx     =       1, irest   =       0, ntrx    =       1

Nature and format of output:
     ntxo    =       1, ntpr    =     500, ntrx    =       1, ntwr    =     500
     iwrap   =       0, ntwx    =     500, ntwv    =       0, ntwe    =       0
     ioutfm  =       0, ntwprt  =       0, idecomp =       0, rbornstat=      0

Potential function:
     ntf     =       2, ntb     =       0, igb     =       1, nsnb    =      25
     ipol    =       0, gbsa    =       1, iesp    =       0
     dielc   =   1.00000, cut     =  16.00000, 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
     alpb  =        0
     scnb    =   2.00000, scee    =   1.20000

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

Molecular dynamics:
     nstlim  =    100000, nscm    =      1000, nrespa  =         1
     t       =   0.00000, dt      =   0.00200, vlimit  =  20.00000

Langevin dynamics temperature regulation:
     ig      =   71277
     temp0   = 300.19000, tempi   =   0.00000, gamma_ln=   5.00000

SHAKE:
     ntc     =       2, jfastw  =       0
     tol     =   0.00001

NMR refinement options:
     iscale  =       0, noeskp  =       1, ipnlty  =       1, mxsub   =       1
     scalm   = 100.00000, pencut  =   0.10000, tausw   =   0.10000

    LOADING THE CONSTRAINED ATOMS AS GROUPS


   5.  REFERENCE ATOM COORDINATES

      
|  INFO: Old style inpcrd file read

    ----- READING GROUP     1; TITLE:
   END                                                                       

     rfree: Error decoding variable  1  3 from:
  hold 

     this indicates that your input contains 

      incorrect information

     field   1 was supposed to 

      have a (1=character, 2=integer, 3=decimal) value