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          Amber 9  SANDER                              2006
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| PMEMD implementation of SANDER, Release 9

| Run on 05/16/2011 at 18:13:45

  [-O]verwriting output

File Assignments:
|   MDIN: md.in3                                                                
|  MDOUT: md1-1.out                                                             
| INPCRD: md1.rst                                                               
|   PARM: ../prmtop/nt-wi.top                                                   
| RESTRT: md1-1.rst                                                             
|   REFC: ../prmtop/nt-wi.crd                                                   
|  MDVEL: mdvel                                                                 
|   MDEN: mden                                                                  
|  MDCRD: md1-1.mdcrd                                                           
| MDINFO: mdinfo                                                                
|LOGFILE: logfile                                                               

 
 Here is the input file:
 
MD                                                                             
 &cntrl                                                                        
  imin = 0, irest = 1, ntx = 7,                                                
  ntb = 2, pres0 = 1.0, ntp = 1,                                               
  taup = 2.0,                                                                  
  cut = 10, ntr = 1,                                                           
  ntc = 2, ntf = 2,                                                            
  tempi = 300.0, temp0 = 300.0,                                                
  ntt = 3, gamma_ln = 1.0,                                                     
  nstlim = 250000, dt = 0.002,                                                 
  ntpr = 250, ntwx = 250, ntwr = 5000                                          
 /                                                                             
Restrained Atoms                                                               
0.025                                                                          
RES 12 12                                                                      
RES 16 16                                                                      
RES 40 40                                                                      
RES 43 43                                                                      
RES 61 61                                                                      
END                                                                            
END                                                                            


 
| ERROR:   Could not read coords from md1.rst