# AMBER: Distance Restraints Problem

From: Esther Brugger <esther_brugger.yahoo.com>
Date: Tue, 2 Jan 2007 14:00:16 -0800 (PST)

Dear ALL,

Recently, I want to add distance restraints in the MD simulation. I read the manual and searched the problems on the website, but I still have some difficulties to write the input file.
(1) Is it correct if I put ntc=2, ntf=2 in this distance restraints MD simulation? or I shouldn't use it in this restraint calcuation.
Here is the input file:
NPT MD 100ps with Distance Restrains
&cntrl
nmropt=1, pencut = -0.001,
ntb = 2, pres0 = 1, ntp = 1,
taup = 2.0, cut = 12,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 50000, dt = 0.002, vlimit=20,
ntpr = 100, ntwx = 100, ntwr = 1000
/
& wt type = 'END'/
DISANG=DIST.RST

(2) I have 5 residues, in each residue, the restrainted H number is the same (if I didn't say it clearly, you may see the list following, probably you can understand it), how can I describe it in a easy way in DISANG file?

1 MIC H118 1 MIC H129 2.00 5.00
1 MIC H79 1 MIC H90 2.00 5.00
1 MIC H40 1 MIC H51 2.00 5.00
1 MIC H 1 MIC H11 2.00 5.00

2 MIC H118 2 MIC H129 2.00 5.00
2 MIC H79 2 MIC H90 2.00 5.00
2 MIC H40 2 MIC H51 2.00 5.00
2 MIC H 2 MIC H11 2.00 5.00

3 MIC H118 3 MIC H129 2.00 5.00
3 MIC H79 3 MIC H90 2.00 5.00
3 MIC H40 3 MIC H51 2.00 5.00
3 MIC H 3 MIC H11 2.00 5.00

4 MIC H118 4 MIC H129 2.00 5.00
4 MIC H79 4 MIC H90 2.00 5.00
4 MIC H40 4 MIC H51 2.00 5.00
4 MIC H 4 MIC H11 2.00 5.00

5 MIC H118 5 MIC H129 2.00 5.00
5 MIC H79 5 MIC H90 2.00 5.00
5 MIC H40 5 MIC H51 2.00 5.00
5 MIC H 5 MIC H11 2.00 5.00

(3) Here is the file of my DISANG file, I really wish someone can help me to write it in a simple way.
# 1 1 MIC H118 1 MIC H129 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 234, 253, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50,
rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
&end
#
# 2 1 MIC H79 1 MIC H90 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 183, 168, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 3 1 MIC H40 1 MIC H51 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 116, 101, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 4 1 MIC H 1 MIC H11 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 36, 17, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 5 2 MIC H118 2 MIC H129 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 502, 521, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 6 2 MIC H79 2 MIC H90 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 451, 168, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 7 2 MIC H40 2 MIC H51 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 384, 369, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 8 2 MIC H 2 MIC H11 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 304, 285, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 9 3 MIC H118 3 MIC H129 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 770, 789, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 10 3 MIC H79 3 MIC H90 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 719, 704, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 11 3 MIC H40 3 MIC H51 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 652, 637, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 12 3 MIC H 3 MIC H11 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 572, 553, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 13 4 MIC H118 4 MIC H129 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 1038, 1057, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 14 4 MIC H79 4 MIC H90 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 987, 972, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 15 4 MIC H40 4 MIC H51 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 920, 905, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 16 4 MIC H 4 MIC H11 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 840, 821, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 17 5 MIC H118 5 MIC H129 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 1306, 1325, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 18 5 MIC H79 5 MIC H90 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 1255, 1240, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 19 5 MIC H40 5 MIC H51 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 1188, 1173, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end
#
# 20 5 MIC H 5 MIC H11 2.00 5.00
&rst
ixpk= 0, nxpk= 0, iat= 1108, 1089, r1= 1.50, r2= 2.00, r3= 5.00, r4= 5.50, &end

Thanks a lot for your any kind help!
Happy New Year!

Esther B.

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Received on Wed Jan 03 2007 - 06:07:29 PST
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