AMBER Archive (2002)

Subject: Molecular dynamic protocol...

From: Andrei Leitão (ierdna_at_yahoo.com)
Date: Fri Dec 27 2002 - 12:40:26 CST

 Hi AMBER users,

 I am having problems with input file from DNA molecular
dynamic.
 This message appears in the screen:
** Address Error **

End of diagnostics

[1] Exit 1 sander -O -i
aaa_md_ntra.in -o aaa_md_ntra.out -c aaa_min_ntr.restrt -p
...

 There are no errors in the prmtop file, but the output
archive shows the following message in the :
   ...
   5. REFERENCE ATOM COORDINATES

    ----- READING GROUP 1; TITLE:
  &wt

 It appears that the comand &wt is not correct. Here is my
file (this is very similar to the DNA tutorial one):

5DNB, initial dynamics (ntr) DNA, 25ps, 12.0 cut
 &cntrl
   ntx = 1, irest = 0, ntrx = 1,
ntxo = 1,
   ntpr = 100, ntwx = 500, ntwv = 0,
ntwe = 0,

   ntf = 2, ntb = 2,
   cut = 12.0, nsnb = 10,

   ibelly = 0, ntr = 1,

   imin = 0,
   nstlim = 2000,
   t = 0.0, dt = 0.001,

  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=2000,
                 value1=300.0, value2=300.0,

 &end
  &wt
   type='END',

 &end
Hold the DNA fixed
500.0
RES 1 14
END
END

 When I put the temperature parameters in the botton of the
file it worked well.

 Thank you very much...

=====
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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