AMBER Archive (2007)

Subject: AMBER: deformation of DNA duplex after MD simulation (AMBER9)

From: Chengwen Chen (chenchengwen_at_gmail.com)
Date: Sat Jan 20 2007 - 22:28:59 CST

Dear all,
I run MD for a DNA duplex with B-DNA produced by "nucgen" as starting
structure. The simulation is performed in explicit solvent model, and the
steps is almost identical to the AMBER8 tutorial for DNA provided by Ross
Walker.

After 1ns simulation, the DNA is enlongated with widened major
groove (almost doubled compared with starting strucutre). And the one of
the terminal basepair is opened.

Interestingly, another DNA duplex with different sequence produced by the
same method look fine.

What is the problem? Would distance restraints on hydrogen bonds of terminal
basepair make it better? Thank you.

The input file is listed as follow

duplex with 12bps, ff99,couter ion added: initial minimisation prior to MD,
 &cntrl
  imin = 1,
  ncyc = 1000,
  maxcyc = 2000,
  ntb = 1,
  cut = 10,
  ntr = 1,
 /
Hold the DNA fixed
500.0
RES 1 24
END
END

ff99, couter ion added: second minimisation prior to MD, mininmize the whole
system
 &cntrl
  imin = 1,
  ncyc = 2000,
  maxcyc = 5000,
  ntb = 1,
  cut = 10,
  ntr = 0,
 /

ff99,MD1, heating 10A cut off
 &cntrl
  imin = 0,
  irest = 0,
  ntx = 1,
  ntb = 1,
  ntpr = 100,
  ntwx = 100,
  ntwr = 1000,
  ntt = 3,
  gamma_ln = 1.0,
  tempi = 0.0,
  temp0 = 300.0,
  nstlim = 10000,
  dt = 0.002,
  cut = 10,
  ntc = 2,
  ntf = 2,
  ntr =1,
 /
Keep DNA fixed with weak restraints
10.0
RES 1 24
END
END

ff99,MD2, MD on 300K, 10A cut off
 &cntrl
  imin = 0,
  irest = 1,
  ntx = 5,
  ntb = 2,
  pres0 = 1.0,
  ntp =1,
  taup = 2.0,
  ntpr = 100,
  ntwx = 100,
  ntwr = 1000,
  ntt = 3,
  gamma_ln = 1.0,
  tempi = 300.0,
  temp0 = 300.0,
  nstlim = 50000,
  dt = 0.002,
  cut = 10,
  ntc = 2,
  ntf = 2,
  ntr = 0,
 /

ff99,producing step MD3, 10A cut off
 &cntrl
  imin = 0,
  irest = 1,
  ntx = 5,
  ntb = 2,
  pres0 = 1.0,
  ntp =1,
  taup = 2.0,
  ntpr = 100,
  ntwx = 100,
  ntwr = 1000,
  ntt = 3,
  gamma_ln = 1.0,
  tempi = 300.0,
  temp0 = 300.0,
  nstlim = 500000,
  dt = 0.002,
  cut = 10,
  ntc = 2,
  ntf = 2,
  ntr = 0,
 /

Best Wishes
Chen Chengwen

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