AMBER Archive (2009)

Subject: [AMBER] LINMIN failure notice

From: Jio M (jiomm_at_yahoo.com)
Date: Fri Sep 18 2009 - 05:20:18 CDT

Dear Amber users;

I have ligand protein complex with waterbox.. I did minimisation with SHAKE then this LINMIN failure came...

but it was suggested to do first minimisation without SHAKE then second
minimisation with SHAKE..in this case I got no error in first
minimisation  but with SHAKE LINMIN failure again noticed.. what
is  reason and solution for this .......

min_noSHAKE.in

 &cntrl

  imin=1,maxcyc=1000,ncyc=500,

  cut=8.0,ntb=1,

  ntc=1,ntf=1,

  ntpr=100,

  ntr=1, restraintmask=':207-478',

  restraint_wt=2.0

 /

min.in file

&cntrl

  imin=1,maxcyc=1000,ncyc=500,

  cut=8.0,ntb=1,

  ntc=2,ntf=2,

  ntpr=100,

  ntr=1, restraintmask=':207-478',

  restraint_wt=2.0

 /

 4.  RESULTS

--------------------------------------------------------------------------------

 ---------------------------------------------------

 APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION

 using   5000.0 points per unit in tabled values

 TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff

| CHECK switch(x): max rel err =   0.2738E-14   at   2.422500

| CHECK d/dx switch(x): max rel err =   0.8314E-11   at   2.736960

 ---------------------------------------------------

| Local SIZE OF NONBOND LIST =     507119

| TOTAL SIZE OF NONBOND LIST =    7982221

   NSTEP      
ENERGY         
RMS           
GMAX        
NAME    NUMBER

      1     
-1.5371E+05     1.8408E+01    
6.1403E+01    
O        9015

 BOND    =     
139.7029  ANGLE   =     
585.9775  DIHED     
=     2697.3324

 VDWAALS =    26288.8749 
EEL     =  -196992.8151 
HBOND     
=        0.0000

 1-4 VDW =      935.1457  1-4 EEL
=    12636.5467  RESTRAINT 
=        1.3255

 EAMBER  =  -153709.2350

   NSTEP      
ENERGY         
RMS           
GMAX        
NAME    NUMBER

    100     
-1.5371E+05     1.8408E+01    
6.1382E+01    
O        9015

 BOND    =     
139.6206  ANGLE   =     
585.9935  DIHED     
=     2697.3411

 VDWAALS =    26285.6160 
EEL     =  -196988.8291 
HBOND     
=        0.0000

 1-4 VDW =      935.1360  1-4 EEL
=    12636.5486  RESTRAINT 
=        1.3329

 EAMBER  =  -153708.5731

   NSTEP      
ENERGY         
RMS           
GMAX        
NAME    NUMBER

    200     
-1.5371E+05     1.8408E+01    
6.1382E+01    
O        9015

 BOND    =     
139.6198  ANGLE   =     
585.9938  DIHED     
=     2697.3412

 VDWAALS =    26285.5845 
EEL     =  -196988.7917 
HBOND     
=        0.0000

 1-4 VDW =      935.1359  1-4 EEL
=    12636.5488  RESTRAINT 
=        1.3330

 EAMBER  =  -153708.5677

   NSTEP      
ENERGY         
RMS           
GMAX        
NAME    NUMBER

    300     
-1.5371E+05     1.8408E+01    
6.1382E+01    
O        9015

 BOND    =     
139.6190  ANGLE   =     
585.9939  DIHED     
=     2697.3413

 VDWAALS =    26285.5526 
EEL     =  -196988.7510 
HBOND     
=        0.0000

 1-4 VDW =      935.1358  1-4 EEL
=    12636.5484  RESTRAINT 
=        1.3331

 EAMBER  =  -153708.5599

   NSTEP      
ENERGY         
RMS           
GMAX        
NAME    NUMBER

    400     
-1.5371E+05     1.8408E+01    
6.1382E+01    
O        9015

 BOND    =     
139.6181  ANGLE   =     
585.9941  DIHED     
=     2697.3414

 VDWAALS =    26285.5202 
EEL     =  -196988.7128 
HBOND     
=        0.0000

 1-4 VDW =      935.1358  1-4 EEL
=    12636.5483  RESTRAINT 
=        1.3331

 EAMBER  =  -153708.5548

   NSTEP      
ENERGY         
RMS           
GMAX        
NAME    NUMBER

    500     
-1.5371E+05     1.8408E+01    
6.1382E+01    
O        9015

 BOND    =     
139.6174  ANGLE   =     
585.9943  DIHED     
=     2697.3415

 VDWAALS =    26285.4885 
EEL     =  -196988.6745 
HBOND     
=        0.0000

 1-4 VDW =      935.1357  1-4 EEL
=    12636.5485  RESTRAINT 
=        1.3332

 EAMBER  =  -153708.5486

     .... RESTARTED DUE TO LINMIN FAILURE ...

     .... RESTARTED DUE TO LINMIN FAILURE ...

     .... RESTARTED DUE TO LINMIN FAILURE ...

     .... RESTARTED DUE TO LINMIN FAILURE ...

   NSTEP      
ENERGY         
RMS           
GMAX        
NAME    NUMBER

    600     
-1.5371E+05     1.8408E+01    
6.1382E+01    
O        9015

 BOND    =     
139.6171  ANGLE   =     
585.9943  DIHED     
=     2697.3415

 VDWAALS =    26285.4794 
EEL     =  -196988.6632 
HBOND     
=        0.0000

 1-4 VDW =      935.1357  1-4 EEL
=    12636.5486  RESTRAINT 
=        1.3332

 EAMBER  =  -153708.5465

     .... RESTARTED DUE TO LINMIN FAILURE ...

     ***** REPEATED LINMIN FAILURE *****

     ***** SEE http://amber.scripps.edu/Questions/linmin.html FOR MORE INFO *****

                    FINAL RESULTS

   NSTEP      
ENERGY         
RMS           
GMAX        
NAME    NUMBER

    614     
-1.5371E+05     1.8408E+01    
6.1382E+01    
O        9015

 BOND    =     
139.6171  ANGLE   =     
585.9943  DIHED     
=     2697.3415

 VDWAALS =    26285.4781 
EEL     =  -196988.6617 
HBOND     
=        0.0000

 1-4 VDW =      935.1357  1-4 EEL
=    12636.5486  RESTRAINT 
=        1.3332

 EAMBER  =  -153708.5463

thanks:

Jiomm

      
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