AMBER Archive (2008)

Subject: AMBER: nmode

From: James Thomas (james.protein_at_googlemail.com)
Date: Mon Mar 31 2008 - 13:48:43 CDT

Dear amber community

I am using nmode to do Newton-Raphson minimisation
The input protein is obtained from PDB, H atoms removed, then processed with
tleap to get the prmtop & inpcrd files.
However, the NR minimisation get terminated early and I am not sure how to
troubleshoot this.

Any suggestions?

Many thanks!

=====================
The input nmdin file:
&data
     ntrun=4,
     nsave=2,
     ndiag=2,
     cut=95.0,
     nprint=100,
     drms=0.00001,
     maxcyc=100,
     bdwnhl=0.01,
     dfpred=0.1,
     scnb=2.0,
     scee=2.0,
     nvect=200,
     ntxo=1,
 &end

================
The nmdout file:
 minimization for
nmode
       ntrun maxcyc ibelly drms
          4 100 0 0.10E-04
       rcut scnb scee dielc idiel
     95.00000 2.00000 2.00000 1.00000 0
      nsave dfpred bdwnhl smx emx alpha ndiag
          2 0.10000 0.01000 0.08000 0.30000 0.80000 2
 ipol = 0
 i3bod = 0
 nvect = 200
| New format PARM file being parsed.
| Version = 1.000 Date = 03/20/08 Time = 15:42:26

    PARM file has the title:

Total memory required : 301034923 real words

Total memory required : 17074060 integer words

Total memory required : 17712 4-character words

Maximum nonbond pairs 16701309

     Duplicated 0 dihedrals

     Duplicated 0 dihedrals

 Getting coordinates from file with title:

    Number of non-bonded pairs = 16669620
    Number of H-bonded pairs = 0

 ***************** ***************** *****************
   step = 0
     F = 0.153216E+06 GRDMAX = 0.177166E+07 GNORM = 0.219344E+05
       E-NONB E-ELE E-HBOND E-BOND
     0.15252E+06 -0.80776E+04 0.00000E+00 0.17805E+03
       E-ANGLE E-DIHED E-NB14 E-EEL14
     0.82970E+03 0.35161E+04 0.18596E+04 0.23887E+04
       E-POL E-3BOD
     0.00000E+00 0.00000E+00
     Coordinate origin is now the molecular center of mass
          b1 = ********** b2 =********** tlamba = **********
          rms of step length = ************
Stop in nonbon1, npr= 5767

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