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

| Run on 03/04/2008 at 15:27:54
  [-O]verwriting output

File Assignments:
|  MDIN: Gamma_wat_min1.in                                                     
| MDOUT: Gamma_wat_min1.out                                                    
|INPCRD: Gamma_wat.inpcrd                                                      
|  PARM: Gamma_wat.prmtop                                                      
|RESTRT: Gamma_wat_min1.rst                                                    
|  REFC: refc                                                                  
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                  
| MDCRD: mdcrd                                                                 
|MDINFO: mdinfo                                                                
|INPDIP: inpdip                                                                
|RSTDIP: rstdip                                                                

 
 Here is the input file:
 
 Nef WT_wat_min1.in                                                            
NefWT 206aa: initial minimization solvent + ions                               
&cntrl                                                                         
 imin =1,                                                                      
 maxcyc=1000,                                                                  
 ncyc  = 500,                                                                  
 ntb   = 1,                                                                    
 ntr   = 1,                                                                    
 cut   = 10                                                                    
/                                                                              
Hold the Nef fixed                                                             
500.0                                                                          
RES 1 204                                                                      
END                                                                            
END                                                                            
                                                                               

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

| Flags: MPI                                                                    
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius =    40.553
| New format PARM file being parsed.
| Version =    1.000 Date = 02/29/08 Time = 11:52:38
 NATOM  =   65086 NTYPES =      16 NBONH =   63453 MBONA  =    1684
 NTHETH =    3561 MTHETA =    2292 NPHIH =    6758 MPHIA  =    4236
 NHPARM =       0 NPARM  =       0 NNB   =  100198 NRES   =   20835
 NBONA  =    1684 NTHETA =    2292 NPHIA =    4236 NUMBND =      43
 NUMANG =      89 NPTRA  =      39 NATYP =      30 NPHB   =       1
 IFBOX  =       1 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0


|     Memory Use     Allocated
|     Real             5585414
|     Hollerith         411353
|     Integer          3766018
|     Max Pairs       18744768
|     Max Rstack       3204818
|     Max Istack        325430
|       Total           159484 kbytes
| Duplicated    0 dihedrals
| Duplicated    0 dihedrals

     BOX TYPE: RECTILINEAR

--------------------------------------------------------------------------------
   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     =       1, igb     =       0, nsnb    =      25
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     =  10.00000, intdiel =   1.00000
     scnb    =   2.00000, scee    =   1.20000

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

Energy minimization:
     maxcyc  =    1000, ncyc    =     500, ntmin   =       1
     dx0     =   0.01000, drms    =   0.00010

Ewald parameters:
     verbose =       0, ew_type =       0, nbflag  =       1, use_pme =       1
     vdwmeth =       1, eedmeth =       1, netfrc  =       1
     Box X =  111.689   Box Y =   86.834   Box Z =   81.106
     Alpha =   90.000   Beta  =   90.000   Gamma =   90.000
     NFFT1 =  120       NFFT2 =   90       NFFT3 =   81
     Cutoff=   10.000   Tol   =0.100E-04
     Ewald Coefficient =  0.27511
     Interpolation order =    4

  Unit   10 Error on OPEN: refc