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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Received on Sun Feb 11 2007 - 06:07:29 PST
