Subject: AMBER question!!!

From: bxiong <[email-masked]>
Date: Mon, 14 Jan 2002 11:41:39 +0800

Dear CCLs:
I use the AmBER sander.MC Module and I used the Cap water, I do not know the control parameters , can someone give me a copy of the control.in ? 

By the way, I use the control.in and it quickly died. I do not know why.may be someone know what wrong of it, so I copy the log.out file to you to hope it useful.

Here is the input file:

# mc/md using sander                                                           
 &cntrl                                                                        
    irest=0, ntx=1,                                                            
    ibelly=0, imin=0,                                                          
    nstlim=3100, ntpr=10,                                                      
    t=0.0, dt=0.0020, vlimit=20.0,                                             
    ntt=1, temp0=300.0, dtemp=0.0, tautp=0.02,                                 
    ntb=0, ntf=2, igb=2,                                                       
    ntc=2, tol=0.0005, nsnb=20,                                                
    cut=9.0, scnb=2.0, scee=1.2,                                               
    ntwr=50, ntwx=500,                                                         
    imcdo = 0, ntr=1,                                                          
 &end                                                                          
 &ewald                                                                        
   nbflag=1,                                                                   
   skinnb = 1.0,                                                               
   eedmeth=4,                                                                  
   use_pme=0,                                                                  
   vdwmeth=0,                                                                  
   verbose=0,                                                                  
 &end                                                                          
 &cmcmd                                                                        
  imcsol = 0, imcfil = 1, imccp = 0, imcew = 0,                                
  imcrst = 0, EMCIF = 1.0, EMCNF = 0.0, IMCINT = 0 ,                           
  emcofe = 1.0d0, emcofn = 1.0d0,                                              
  imcfrs = 305, imclst = 306, imccur = 305,                                    
  imcns = 100, imcans = 200,                                                   
 &end                                                                          
Group input for restrained atoms                                               
5.0                                                                            
RES 1 304                                                                      
RES 307 328                                                                    
RES 334 336                                                                    
                                                              
RES 527 551                                                                    
END                                                                            
END                               

 begin time read from input coords =     0.000 ps

 Number of triangulated 3-point waters found:      383

 NSTEP =     0  TIME(PS) =    0.000  TEMP(K) =     0.00  PRESS =      0.00
 Etot   =  -13803.1934  EKtot   =       0.0000  EPtot      =  -13803.1934
 BOND   =     663.6023  ANGLE   =    1802.0128  DIHED      =    1726.4369
 1-4 NB =    1061.8815  1-4 EEL =   12051.2919  VDWAALS    =   -1983.7956
 EELEC  =  -29124.6232  EHBOND  =       0.0000  CONSTRAINT =       0.0000
 ------------------------------------------------------------------------------

 vlimit exceeded for step            2; vmax =    96.85260855818514    
 vlimit exceeded for step            3; vmax =    27.87656435858480    
 vlimit exceeded for step            4; vmax =    2123.093135853720    

     COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
     DEVIATION IS TOO LARGE
     NITER, NIT, LL, I AND J ARE :    0    1 2386 4798 4799

wish you can give me some suggestion!!!!

Best regards!
   
            [email-masked]

Xiong Bin  
Shanghai Institute of Materia Medica, C.A.S.
phone:021-64311833-222(office)