AMBER Archive (2002)

Subject: Molecular Dynamic procedure...

From: Andrei Leitão (ierdna_at_yahoo.com)
Date: Wed Oct 16 2002 - 10:48:10 CDT

 To the AMBER List members,

 I would like to know if anyone could give me an
information about a DNA molecular dynamic procedure.
 I am having problems with the molecular dynamic procedure
specified bellow:

5DNB, initial dynamics w/ belly on DNA, model1, 9.0 cut
 &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,
  nrun = 1,
  nstlim = 12500,
  ndfmin = 0, nscm = 0,
  init = 3, t = 0.0, dt = 0.002,

  temp0 = 300.0, tempi = 100.0,
  ig = 71277, heat = 0.0,
  ntt = 1,
  tautp = 0.2, tauts = 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 DNA fixed
500.0
RES 1 20
END
END

 I tried to change some of the key words above but the new
procedures had the same problem: there are variables that
are not in the namelist.
 If possible, I would like to have one archive that run
without problems to deal with because I did not find one
yet.
 Sorry if my question is not applicable here in this list
but I am starting working with AMBER.
 Thank you in advance.

=====
Andrei Leitão
Doutorando em Química Medicinal
Graduante Student in Medicinal Chemistry
NEQUIM - Núcleo de Estudos em Química Medicinal - Brasil
UFMG - Universidade Federal de Minas Gerais
NEQUIM - Medicinal Chemistry Group - Brazil
UFMG - Federal University of Minas Gerais

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