[AMBER] problem in minimisation

From: Hyma vathi <hymavathi.niper.gmail.com>
Date: Wed, 17 Mar 2010 20:34:12 +0530

Dear Amber users,

I am trying to minimise a protein which has cofactor NAP and ligand. I was
able to generate the prmtop and inpcrd files but upon minimisation, the
process is getting aborted and it is giving the following output. Can
anyone please give where the error is, I am attaching the files along with
this mail. Thank you in advance.
This is the min.in file
minimise protein
 &cntrl
  imin=1,
  maxcyc=1000,
  ncyc=500,
  ntb=1,
  ntr=1,
  cut=10.0
/
Hold protein fixed
500
RES 1 317
END
END

Out file

  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 = 10571808
| TOTAL SIZE OF NONBOND LIST = 10571808


   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 NaN NaN 1.4117E+11 H56 5054

 BOND = 279.7583 ANGLE = 1287.0123 DIHED =
3080.5897
 VDWAALS = NaN EEL = NaN HBOND =
0.0000
 1-4 VDW = 1576.5396 1-4 EEL = 14107.7055 RESTRAINT =
0.0000


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Received on Wed Mar 17 2010 - 08:30:04 PDT
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