AMBER Archive (2003)

Subject: namelist read: variable not in namelist

From: Majid moghaddam (erfani_m_at_yahoo.com)
Date: Tue Mar 18 2003 - 04:18:46 CST

Hello
I am trying to run an MD with fixed solute( a peptide
) in water. I used md_ntr.in from the tutorial ( DNA,
equilibrating and runing...) to make input file for
sander with changing number of residues and name of
molecule as follow:

 &cntrl

  nmropt = 1,
  ntx = 1, irest = 0, ntrx = 1,
ntxo = 1,
  ntpr = 100, ntwx = 500, ntwv = 0,
ntwe = 0,

  ntf = 2, ntb = 2,
  cut = 9.0, nsnb = 10,

  ibelly = 0, ntr = 1,

  imin = 0,
  nstlim = 12500,
  nscm = 0,
  t = 0.0, dt = 0.002,

  temp0 = 300.0, tempi = 100.0,
  ig = 71277, heat = 0.0,
  ntt = 1,
  tautp = 0.2,
  vlimit = 15.0,

  ntp = 1, pres0 = 1.0, comp = 44.6,
  taup = 0.2, npscal = 1,

  ntc = 2, tol = 0.00001,

 &end
 &wt
   type='TEMP0', istep1=0, istep2=500,
                 value1=100.0, value2=300.0,
 &end
 &wt
   type='TEMP0', istep1=500, istep2=12500,
                 value1=300.0, value2=300.0,
 &end
 &wt
   type='END',
 &end
 &rst
   iat=0,
 &end
Hold the protein fixed
500.0
RES 1 29
END
END

The following message appeared and program stoped.

namelist read: variable not in namelist
apparent state: unit 5 named md_ntr.in
last format: list io
lately reading sequential formatted external IO
Aborted

I would appreciate if you help me.
Majid Erfani Moghaddam

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