AMBER Archive (2005)

Subject: AMBER: nmode error: GNORM is greater than the requested maximum

From: zhli_2000_at_126.com
Date: Wed Dec 14 2005 - 20:16:07 CST


Dear all,

     I meet the error message when using Nmode to calculate the binding
energy.
---------------------------------------------------------------------------
The error in nmode.out is :

 ***************** ***************** *****************
   step = 0
     F = -0.212557E+02 GRDMAX = 0.305431E+01 GNORM = 0.289946E-01
       E-NONB E-ELE E-HBOND E-BOND
    -0.46775E+04 -0.30152E+04 0.00000E+00
0.16089E+03
       E-ANGLE E-DIHED E-NB14 E-EEL14
     0.85853E+03 0.34060E+04 0.16563E+04
0.15898E+04
       E-POL E-3BOD
     0.00000E+00 0.00000E+00
 Root-mean-square gradient of input coords is 2.899455539563160E-002
 This is greater than the requested maximum: 1.000000000000000E-004
--------------------
 Its input file is:

  File generated by mm_pbsa.pl
       ntrun maxcyc ibelly drms
          1 100 0 0.10E-03
       rcut scnb scee dielc idiel
     99.00000 2.00000 1.20000 4.00000 0
      nsave dfpred bdwnhl smx emx alpha ndiag
         20 0.01000 0.10000 0.08000 0.30000 0.80000 10
 ipol = 0
 i3bod = 0
 nvect = 0
----------------------------------------------------------------------------

--

The input and output files in sander are the following, respectively.

File generated by mm_pbsa.pl &cntrl ntxo = 0, ntf = 1, ntb = 0, dielc = 4, cut = 99.0, nsnb = 99999, scnb = 2.0, scee = 1.2, imin = 1, maxcyc = 30000, ncyc = 0, drms = 0.00001 &end &ewald eedmeth= 5, &end ---------------------

NSTEP ENERGY RMS GMAX NAME NUMBER 16900 -2.1176E+01 2.9894E-04 9.1639E-03 C16 7243

BOND = 160.8852 ANGLE = 858.6083 DIHED = 3405.9603 VDWAALS = -4677.5442 EEL = -3015.2109 HBOND = 0.0000 1-4 VDW = 1656.2817 1-4 EEL = 1589.8431 RESTRAINT = 0.0000

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

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

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

FINAL RESULTS

NSTEP ENERGY RMS GMAX NAME NUMBER 16926 -2.1176E+01 8.1965E-04 6.0189E-02 C17 7241

BOND = 160.8852 ANGLE = 858.6079 DIHED = 3405.9606 VDWAALS = -4677.5440 EEL = -3015.2106 HBOND = 0.0000 1-4 VDW = 1656.2817 1-4 EEL = 1589.8429 RESTRAINT = 0.0000

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How to deal with this problem? Please give me some suggestions. Thank you in advance!

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