AMBER Archive (2007)

Subject: AMBER: Distance Restraints Problem

From: Esther Brugger (esther_brugger_at_yahoo.com)
Date: Tue Jan 02 2007 - 16:00:16 CST

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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