AMBER Archive (2003)

Subject: Sander_classic output: NAN

From: pantelo_at_okstate.edu
Date: Mon Jul 14 2003 - 11:07:19 CDT

I am running a simple minimization of RB69, Pol-alpha, using sander_classic. Below is my input file. I am using .prmtop and .inpcrd files before any water or ions have been added. I am having a problem with my output file numbers. After the first run, I get "nan" values for everything. Do you think it is a problem with my structure or with my input file?

Input:

Relaxation of Hydrogen holding all heavy atoms still
 &cntrl
  ntpr=1,
  ntf=1, idiel=0, dielc=1, scnb=2, scee=1.2, cut=10.0
  imin=1, maxcyc=100, ncyc=100, ntmin=1, ntwe=10, ntwxm=0,
  ntr=1, ntwx=1, ntwem=0,
 &end
 Group input for restraining the Protein and DNA heavy atoms
 5000
 FIND
 * * M *
 SEARCH
 RES 1 934
 END
END

Output after one step:

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 nan nan 3.9408E+08 O 16661

 BOND = 903.6790 ANGLE = 2606.6465 DIHED = 8287.9576
 VDWAALS = 23532619.7971 EEL = -24232.1835 HBOND = 0.0000
 1-4 VDW = nan 1-4 EEL = inf CONSTRAINT = 0.0000

Thank you,
Angela Pantelogianis