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

| Run on 05/12/2005 at 13:17:42
  [-O]verwriting output

File Assignments:
|  MDIN: v_res.in                                                              
| MDOUT: v_res.out                                                             
|INPCRD: min1.restrt                                                           
|  PARM: ljt2.prmtop                                                           
|RESTRT: v_res.restrt                                                          
|  REFC: min1.restrt                                                           
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                  
| MDCRD: v_res.mdcrd                                                           
|MDINFO: v_res.mdinfo                                                          
|INPDIP: inpdip                                                                
|RSTDIP: rstdip                                                                

 
 Here is the input file:
 
molecular dynamics run                                                         
 &cntrl                                                                        
     nmropt=1, vlimit=20                                                       
    imin=0,irest=0,ntx=1,                                                      
    tempi=0.0,temp0=300,tautp=0.5                                              
    ntt=1,npscal=1,nsnb=25                                                     
    ntp=0,ntb=1,ntr=1                                                          
    ntc=2,ntf=2,scee=1.2,                                                      
    nstlim=20000,dt=0.002,                                                     
    ntwx=500,ntpr=25,ntwr=500,                                                 
    cut=12.0,                                                                  
 &end                                                                          
 &wt                                                                           
   type='TEMP0',istep1=0,istep2=2500,                                          
                value1=0.0,value2=50.0,                                        
 &end                                                                          
 &wt                                                                           
   type='TEMP0',istep1=2500,istep2=5000,                                       
                value1=50.0,value2=100.0,                                      
 &end                                                                          
&wt                                                                            
   type='TEMP0',istep1=5000,istep2=7500,                                       
                value1=100.0,value2=150.0,                                     
 &end                                                                          
 &wt                                                                           
   type='TEMP0',istep1=7500,istep2=10000,                                      
                value1=150.0,value2=200.0,                                     
 &end                                                                          
 &wt                                                                           
   type='TEMP0',istep1=10000,istep2=15000,                                     
                value1=200.0,value2=300.0,                                     
 &end                                                                          
 &wt                                                                           
   type='TEMP0',istep1=15000,istep2=25000,                                     
                value1=300.0,value2=300.0,                                     
 &end                                                                          
 &wt                                                                           
   type='END',                                                                 
 &end                                                                          
 &rst                                                                          
   iat=0,                                                                      
 &end                                                                          
Restrain the Protein heavy atoms I                                             
50.0                                                                           
FIND                                                                           
 *  C   *  *                                                                   
 *  CA  *  *                                                                   
 *  CB  *  *                                                                   
 *  CC  *  *                                                                   
 *  CD  *  *                                                                   
 *  CK  *  *                                                                   
 *  CM  *  *                                                                   
 *  CN  *  *                                                                   
 *  CQ  *  *                                                                   
SEARCH                                                                         
RES 1  342                                                                     
END                                                                            
Restrain the Protein heavy atoms II                                            
50.0                                                                           
FIND                                                                           
 *  CR  *  *                                                                   
 *  CT  *  *                                                                   
 *  CV  *  *                                                                   
 *  CW  *  *                                                                   
 *  C*  *  *                                                                   
 *  CY  *  *                                                                   
 *  CZ  *  *                                                                   
 *  N   *  *                                                                   
 *  NA  *  *                                                                   
SEARCH                                                                         
RES 1  342                                                                     
END                                                                            
Restrain the Protein heavy atoms III                                           
50.0                                                                           
FIND                                                                           
 *  NC  *  *                                                                   
 *  N2  *  *                                                                   
 *  N3  *  *                                                                   
 *  NT  *  *                                                                   
 *  N*  *  *                                                                   
 *  NY  *  *                                                                   
 *  NB  *  *                                                                   
 *  O   *  *                                                                   
 *  O2  *  *                                                                   
SEARCH                                                                         
RES 1  342                                                                     
END                                                                            
Restrain the Protein heavy atoms III                                           
50.0                                                                           
FIND                                                                           
 *  OH  *  *                                                                   
 *  OS  *  *                                                                   
 *  P   *  *                                                                   
 *  S   *  *                                                                   
 *  SH  *  *                                                                   
SEARCH                                                                         
RES 1  342                                                                     
END                                                                            
Restrain the lig heavy atoms I                                                 
50.0                                                                           
FIND                                                                           
 *  ca  *  *                                                                   
 *  c   *  *                                                                   
 *  ce  *  *                                                                   
 *  c3  *  *                                                                   
 *  n2  *  *                                                                   
 *  o   *  *                                                                   
 *  os  *  *                                                                   
 *  oh  *  *                                                                   
SEARCH                                                                         
RES 343                                                                        
END                                                                            
END                                                                            

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

| Flags: SGIFFT                                                                 
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius =    28.920
| New format PARM file being parsed.
| Version =    1.000 Date = 04/23/05 Time = 05:06:30
 NATOM  =   23273 NTYPES =      18 NBONH =   20653 MBONA  =    2678
 NTHETH =    5858 MTHETA =    3643 NPHIH =   11126 MPHIA  =    7856
 NHPARM =       0 NPARM  =       0 NNB   =   52782 NRES   =    6368
 NBONA  =    2678 NTHETA =    3643 NPHIA =    7856 NUMBND =      57
 NUMANG =     116 NPTRA  =      53 NATYP =      42 NPHB   =       1
 IFBOX  =       2 NMXRS  =      29 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0


|     Memory Use     Allocated
|     Real             1701900
|     Hollerith         146008
|     Integer          1669885
|     Max Pairs       21287037
|     Max Rstack       1456536
|     Max Istack        116365
|       Total           115375 kbytes
| Duplicated    0 dihedrals
| Duplicated    0 dihedrals

     BOX TYPE: TRUNCATED OCTAHEDRON

--------------------------------------------------------------------------------
   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    =      25, 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     =       1, 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     =       1

Molecular dynamics:
     nstlim  =   20000, nscm    =    1000, nrespa  =       1
     t       =   0.00000, dt      =   0.00200, vlimit  =  20.00000

Berendsen (weak-coupling) temperature regulation:
     temp0   = 300.00000, tempi   =   0.00000, tautp   =   0.50000

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

Ewald parameters:
     verbose =       0, ew_type =       0, nbflag  =       1, use_pme =       1
     vdwmeth =       1, eedmeth =       1, netfrc  =       1
     Box X =   70.838   Box Y =   70.838   Box Z =   70.838
     Alpha =  109.471   Beta  =  109.471   Gamma =  109.471
     NFFT1 =   72       NFFT2 =   72       NFFT3 =   72
     Cutoff=   12.000   Tol   =0.100E-04
     Ewald Coefficient =  0.22664
     Interpolation order =    4

    LOADING THE CONSTRAINED ATOMS AS GROUPS


   5.  REFERENCE ATOM COORDINATES

      
    ----- READING GROUP     1; TITLE:
  &rst                                                                       

     GROUP    1 HAS HARMONIC CONSTRAINTS    -4.00000

     rfree: Error decoding variable  2  2 from:
Restrain the 

     this indicates that your input contains 

      incorrect information

     field   2 was supposed to 

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