AMBER Archive (2003)

Subject: Questions about output archive and micromolecules

From: Andrei Leitão (ierdna_at_yahoo.com)
Date: Mon Jun 30 2003 - 15:17:46 CDT

 Dear Amber users,

 I am performing DNA dynamics and my input file is listed
bellow:

 &cntrl

  ntx = 1, irest = 0, ntrx = 1, ntxo
  = 1,
  ntpr = 1000, ntwx = 1000, ntwv = 1000, ntwe
  = 1000,
  ntwprt = 0,

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

  ibelly = 0, ntr = 0,

  imin = 0,

  nstlim = 500000,
  t = 0.0, dt = 0.001,

  temp0 = 300.0, tempi = 100.0,
  ig = 71277, heat = 0.0,
  ntt = 1,
  vlimit = 20.0,

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

  ntc = 2, tol = 0.00001,

 &end
 &ewald
 &end
 &wt
   type='TEMP0', istep1=0, istep2=50000,
                 value1=100.0, value2=300.0,
 &end
 &wt
   type='TEMP0', istep1=20000, istep2=500000,
                 value1=300.0, value2=300.0,
 &end

 The output and restrt files format are O.K. although I
noticed a message in the output archive:

check COM velocity, temp: 0.000000 0.00(Removed)

 I would like to know if there was any problem during my
dynamic or if my protocol is wrong because I did not see it
before.

 I have another question:
 I tried to do a molecular dynamic with a micromolecule
(and after that I will perform another one including the
DNA) and AMBER did not understand my input pdb file when I
used the Xleap program to generate the inpcrd and prmtop
files. Is there any kind of example in the AMBER homepage
that I could follow? I did not find a good one because I
have a X-ray structure (the structure was checked).
 There are two examples in tutorial part (crown ether in
vacuum and methane in water box) but none of them has a
case that pdb files with micro and macromolecules are used
together.

 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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