[AMBER] RESTARTED DUE TO LINMIN FAILURE

From: Chris Chris <alpharecept.yahoo.com>
Date: Sun, 14 Oct 2012 21:55:55 -0700 (PDT)

I am trying to minimize a strecture that contains an anzyme and it's substrate. The complex was created by using Vina to dock the substrate to the enzyme. I followed the steps in the antechamber tutorial to make the inpcrd and prmtop files.

I tried the same exact protein without the docked ligand and it ran without error. The message below says I should try turning off SHAKE, but will that affact my results down the road here?

my min.in file:

min 1st time for ctz 2ps 
 &cntrl
  imin=1,maxcyc=5000,ncyc=500,
  cut=8.0,ntb=1,
  ntc=2,ntf=2,
  ntpr=100,
  ntr=1, 
 /
Putting restraints on residues 1-305
500.0
RES 1 306
END
END


 NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    500       2.6120E+05     4.0553E+03     5.6572E+05     HD21     1590

 BOND    =    31311.4597  ANGLE   =    30018.2823  DIHED      =     2992.1159
 VDWAALS =    98941.5229  EEL     =  -109489.5411  HBOND      =        0.0000
 1-4 VDW =   181774.5442  1-4 EEL =    13899.4160  RESTRAINT  =    11752.4888
 EAMBER  =   249447.8000

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

     Coordinate resetting cannot be accomplished,
     deviation is too large
     iter_cnt, my_bond_idx, i and j are :       5     780    1589    1590
  *** Especially for minimization, try ntc=1 (no shake)
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Received on Sun Oct 14 2012 - 22:00:03 PDT
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