AMBER Archive (2007)

Subject: AMBER: question about distance restraint on terminal WC of DNA duplex (AMBER9)

From: Chengwen Chen (chenchengwen_at_gmail.com)
Date: Fri Feb 09 2007 - 02:25:00 CST

Dear AMBER user:
I am modeling DNA duplexes in explicit model. Since one of the terminal
bases flipped out after MD simulation, I try to use distance restraint on
terminal WC of the duplex using weight of restraint at 1.0. But I am not
sure about the way I make the input file, and the value of restraint
weight. Is is large enough? I had tried 10.0, but the MD simulation quit
with error. Can you give me some suggestions?

md input file:
&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,
  nmropt = 1,
 /

&wt type='REST',value1=1.0,value2=1.0, /
&wt type='END' /
LISTOUT=POUT

DISANG=RST

RST file:
#
# 1 DC5 H42 24 DG3 O6 1.80 2.00
 &rst
  ixpk= 0, nxpk= 0, iat= 12, 535, r1= 1.30, r2= 1.80, r3= 2.00, r4= 2.50,
      rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
 &end
#
# 1 DC5 N3 24 DG3 H1 1.84 2.04
 &rst
  ixpk= 0, nxpk= 0, iat= 14, 545, r1= 1.34, r2= 1.84, r3= 2.04, r4= 2.54,
&end
#
# 1 DC5 N3 24 DG3 N1 2.85 3.05
 &rst
  ixpk= 0, nxpk= 0, iat= 14, 544, r1= 2.35, r2= 2.85, r3= 3.05, r4= 3.55,
&end
#
# 1 DC5 N4 24 DG3 O6 2.81 3.01
 &rst
  ixpk= 0, nxpk= 0, iat= 10, 535, r1= 2.31, r2= 2.81, r3= 3.01, r4= 3.51,
&end
#
# 1 DC5 O2 24 DG3 H22 1.75 1.95
 &rst
  ixpk= 0, nxpk= 0, iat= 16, 534, r1= 1.25, r2= 1.75, r3= 1.95, r4= 2.45,
&end
#
# 12 DC3 H42 13 DG5 O6 1.80 2.00
 &rst
  ixpk= 0, nxpk= 0, iat= 251, 272, r1= 1.30, r2= 1.80, r3= 2.00, r4= 2.50,
&end
#
# 12 DC3 N3 13 DG5 H1 1.84 2.04
 &rst
  ixpk= 0, nxpk= 0, iat= 253, 282, r1= 1.34, r2= 1.84, r3= 2.04, r4= 2.54,
&end
#
# 12 DC3 N3 13 DG5 N1 2.85 3.05
 &rst
  ixpk= 0, nxpk= 0, iat= 253, 281, r1= 2.35, r2= 2.85, r3= 3.05, r4= 3.55,
&end
#
# 12 DC3 N4 13 DG5 O6 2.81 3.01
 &rst
  ixpk= 0, nxpk= 0, iat= 249, 272, r1= 2.31, r2= 2.81, r3= 3.01, r4= 3.51,
&end
#
# 12 DC3 O2 13 DG5 H22 1.75 1.95
 &rst
  ixpk= 0, nxpk= 0, iat= 255, 271, r1= 1.25, r2= 1.75, r3= 1.95, r4= 2.45,
&end

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