-------------------------------------------------------
          Amber 8  SANDER                 Scripps/UCSF 2004
          -------------------------------------------------------

| Run on 04/14/2006 at 14:44:10
  [-O]verwriting output

File Assignments:
|  MDIN: polyAT_vac_init_min.in.bad                                            
| MDOUT: badtest.out                                                           
|INPCRD: polyAT_vac.inpcrd                                                     
|  PARM: polyAT_vac.prmtop                                                     
|RESTRT: badtest.rst                                                           
|  REFC: refc                                                                  
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                  
| MDCRD: mdcrd                                                                 
|MDINFO: mdinfo                                                                
|INPDIP: inpdip                                                                
|RSTDIP: rstdip                                                                

 
 Here is the input file:
 
polyA-polyT 10-mer: initial minimisation prior to MD                           
 &cntrl                                                                        
  imin   = 1,                                                                  
  maxcyc = 500,                                                                
  ncyc   = 250,                                                                
  ntb    = 0,                                                                  
  igb    = 0,                                                                  
  cut    = 12                                                                  
 /                                                                             
                                                                               

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

| Flags: SGIFFT                                                                 
|    NONPERIODIC   ntb=0 and igb=0: Setting up nonperiodic simulation
|Largest sphere to fit in unit cell has radius =    39.759
| New format PARM file being parsed.
| Version =    1.000 Date = 02/19/04 Time = 15:33:29
 NATOM  =     638 NTYPES =      14 NBONH =     234 MBONA  =     452
 NTHETH =     554 MTHETA =     694 NPHIH =    1056 MPHIA  =    1238
 NHPARM =       0 NPARM  =       0 NNB   =    3544 NRES   =      20
 NBONA  =     452 NTHETA =     694 NPHIA =    1238 NUMBND =      32
 NUMANG =      59 NPTRA  =      39 NATYP =      24 NPHB   =       0
 IFBOX  =       0 NMXRS  =      33 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0


|     Memory Use     Allocated
|     Real               52165
|     Hollerith           3850
|     Integer           592617
|     Max Pairs         203203
|     Max Rstack         56380
|     Max Istack          3190
|       Total             3984 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     =       0, nsnb    =      25
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     =  12.00000, intdiel =   1.00000
     scnb    =   2.00000, scee    =   1.20000

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

Energy minimization:
     maxcyc  =     500, ncyc    =     250, ntmin   =       1
     dx0     =   0.01000, drms    =   0.00010

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

                                                                                
 begin time read from input coords =     0.000 ps

 Number of triangulated 3-point waters found:        0