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Diffstat (limited to 'sim/src/sim-params.txt')
| -rwxr-xr-x | sim/src/sim-params.txt | 498 |
1 files changed, 0 insertions, 498 deletions
diff --git a/sim/src/sim-params.txt b/sim/src/sim-params.txt deleted file mode 100755 index 9a8b9530d..000000000 --- a/sim/src/sim-params.txt +++ /dev/null @@ -1,498 +0,0 @@ -# -# Copyright 2007 Nanorex, Inc. See LICENSE file for details. -# $Id$ -# - -# This file should be placed in your ~/Nanorex directory. It is read -# by the simulator before each simulation or minimization run. You -# should be able to edit and save it between runs and see the new -# results in later runs. - -# The element, stretch, and bend lines define new force field -# parameters which override or extend the force field compiled into -# the simulator. - -# Angle values can be entered in either degrees or radians. The units -# line lets you specify which. You can switch between the two as often -# as you like. The default is: -# -#units radians - -units degrees - -# format for element lines -# -# Z (int) number of protons, or atomType index -# grp (int) group number in periodic table (not currently used) -# groups 9-22 are lanthanides -# groups 8-31 are transition metals -# per (int) period in periodic table (not currently used) -# sym (string) abbreviated symbol name (one-three characters) -# sym values are used in stretch and bend records -# name (string) full name, for printing -# mass (double) in yg (yoctograms, or 1e-24 g) -# rvdW (double) van der Waals radius, in 1e-10 m or angstroms or 0.1 nm -# evdW (double) van der Waals stiffness, in zJ (zepto Joules, or milli atto Joules, or 1e-21 J) -# NOTE: specifing an evdW value < .1 will cause the value to be calculated based on number of protons -# rcov (double) covalent radius in pm (1e-12 m) -# used to generate unspecified bond parameters -# chrg (double) charge in mulitples of proton charge -# -# Z grp per par sym name mass rvdW evdW bnds rcov chrg virt - -element 997 0 0 All PAM5 All-PAM5-Pseudo-Atoms 0.0 0.0 0.0 0 0 0 0 -element 996 0 0 PAM5 P5S PAM5-Sugars 0.0 0.0 0.0 0 0 0 0 -element 995 0 0 PAM5 P5P PAM5-Phosphates 0.0 0.0 0.0 0 0 0 0 -element 994 0 0 PAM5 P5G PAM5-Major-Grooves 0.0 0.0 0.0 0 0 0 0 -element 993 0 0 PAM5 P5V PAM5-Virtual-Atoms 0.0 0.0 0.0 0 0 0 0 -element 992 0 0 PAM5 P5d PAM5-depricated 0.0 0.0 0.0 0 0 0 0 -element 991 0 0 All PAM3 All-PAM3-Pseudo-Atoms 0.0 0.0 0.0 0 0 0 0 - -element 200 0 0 P5d Ax5 DNA-Pseudo-Axis 167.0 0.0 0.0 4 100 0 0 700 -element 201 0 0 P5S Ss5 DNA-Pseudo-Sugar 167.0 0.0 0.0 3 170 0 0 800 -element 202 0 0 P5P Pl5 DNA-Pseudo-Phosphate 167.0 0.0 0.0 2 170 0 0 900 -element 203 0 0 P5d Sj5 DNA-Pseudo-Sugar-Junction 167.0 0.0 0.0 3 170 0 0 810 -element 204 0 0 P5d Ae5 DNA-Pseudo-Axis-End 167.0 0.0 0.0 1 100 0 0 701 -element 205 0 0 P5d Pe5 DNA-Pseudo-Phosphate-End 167.0 0.0 0.0 1 170 0 0 901 -element 206 0 0 P5d Sh5 DNA-Pseudo-Sugar-End 167.0 0.0 0.0 1 170 0 0 902 -element 207 0 0 P5d Hp5 DNA-Pseudo-Hairpin 167.0 0.0 0.0 2 100 0 0 820 -element 208 0 0 P5G Gv5 DNA-Pseudo-Groove 167.0 0.0 0.0 2 100 0 0 820 -element 209 0 0 P5G Gr5 DNA-Pseudo-Groove-End 167.0 0.0 0.0 2 100 0 0 820 - -element 220 0 0 P5V vDa1 virtual-DNA-planeA-num1 0.0 0.0 0.0 1 100 0 1 -element 221 0 0 P5V vDa2 virtual-DNA-planeA-num2 0.0 0.0 0.0 1 100 0 1 -element 222 0 0 P5V vDa3 virtual-DNA-planeA-num3 0.0 0.0 0.0 1 100 0 1 -element 223 0 0 P5V vDa4 virtual-DNA-planeA-num4 0.0 0.0 0.0 1 100 0 1 -element 224 0 0 P5V vDa5 virtual-DNA-planeA-num5 0.0 0.0 0.0 1 100 0 1 -element 225 0 0 P5V vDa6 virtual-DNA-planeA-num6 0.0 0.0 0.0 1 100 0 1 -element 226 0 0 P5V vDa7 virtual-DNA-planeA-num7 0.0 0.0 0.0 1 100 0 1 -element 227 0 0 P5V vDa8 virtual-DNA-planeA-num8 0.0 0.0 0.0 1 100 0 1 - -element 230 0 0 P5V vDb1 virtual-DNA-planeB-num1 0.0 0.0 0.0 1 100 0 1 -element 231 0 0 P5V vDb2 virtual-DNA-planeB-num2 0.0 0.0 0.0 1 100 0 1 -element 232 0 0 P5V vDb3 virtual-DNA-planeB-num3 0.0 0.0 0.0 1 100 0 1 -element 233 0 0 P5V vDb4 virtual-DNA-planeB-num4 0.0 0.0 0.0 1 100 0 1 -element 234 0 0 P5V vDb5 virtual-DNA-planeB-num5 0.0 0.0 0.0 1 100 0 1 -element 235 0 0 P5V vDb6 virtual-DNA-planeB-num6 0.0 0.0 0.0 1 100 0 1 -element 236 0 0 P5V vDb7 virtual-DNA-planeB-num7 0.0 0.0 0.0 1 100 0 1 -element 237 0 0 P5V vDb8 virtual-DNA-planeB-num8 0.0 0.0 0.0 1 100 0 1 - -element 240 0 0 P5V vDn virtual-DNA-non-bonded 0.0 0.0 0.0 0 100 0 1 - -element 300 0 0 PAM3 Ax3 PAM3-Axis 167.0 0.0 0.0 4 100 0 0 700 -element 301 0 0 PAM3 Ss3 PAM3-Sugar 167.0 0.0 0.0 3 170 0 0 800 -element 302 0 0 PAM3 Pl3 PAM3-Phosphate-Link 167.0 3.6 10.0 2 170 -1 0 900 -element 303 0 0 PAM3 Sj3 PAM3-Sugar-Junction 167.0 0.0 10.0 3 170 0 0 810 -element 304 0 0 PAM3 Ae3 PAM3-Axis-End 167.0 0.0 0.0 1 100 0 0 701 -element 305 0 0 PAM3 Se3 PAM3-Sugar-End 167.0 3.6 10.0 1 170 -2 0 901 -element 306 0 0 PAM3 Sh3 PAM3-Sugar-Hydroxyl 167.0 0.0 0.0 1 170 0 0 902 -element 307 0 0 PAM3 Hp3 PAM3-Hairpin 167.0 0.0 0.0 2 100 0 0 820 - -# format for vdw lines -# -# rvdW (double) van der Waals radius in pm or 1e-12 m -# evdW (double) van der Waals energy in zJ or 1e-21 J -# cutoffRadiusStart (double) start of smooth transition in pm -# cutoffRadiusEnd (double) end of smooth transition in pm -# name (string) symbol-v-symbol -# The atomType (number of protons) of the first symbol must be <= the second. -# -# The vdw potential is multiplied by a smooth transition function -# between cutoffRadiusStart and cutoffRadiusEnd. Beyond -# cutoffRadiusEnd the vdw potential is identically zero. If -# cutoffRadiusEnd < cutoffRadiusStart, this transition is disabled, -# and the potential is shifted so that it is zero at cutoffRadiusEnd. -# If cutoffRadiusStart < 0, it is set to rvdW. If cutoffRadiusEnd < -# 0, it is set to rvdW * VanDerWaalsCutoffFactor (specified by -# --vdw-cutoff-factor). Setting cutoffRadiusEnd to rvdW, and -# cutoffRadiusStart to any larger value selects only the repulsive -# interaction. -# -# rvdW evdW start end name - -vdw 200.0 10.0 100.0 7.2 vDn-v-vDn - -vdw 7.2 10.0 100.0 7.2 Pl3-v-Pl3 -vdw 7.2 10.0 100.0 7.2 Pl3-v-Se3 -vdw 7.2 10.0 100.0 7.2 Se3-v-Se3 - -# format for stretch lines -# -# ks (double) in N/m -# r0 (double) equilibrium distance, in pm, or 1e-12 m -# de (double) in aJ, or 1e-18 J -# beta (double) in 1e10 m^-1 -# set to sqrt(ks / (2.0 * de)) / 10.0 if value here is less than zero -# inflectionR (double) r value in pm where d^2(Lippincott(r)) / dr^2 == 0 -# inflectionR is end of interpolation table during minimization -# set to r0*1.5 if value here is less than zero -# qual (int) quality of parameter (use of a parameter with quality < 5 produces a warning) -# quad (int) flag, non-zero if this stretch should be quadratic instead of Lippincott/Morse -# bondName (string) symbol-bondOrder-symbol -# bondOrders are: (1, a, g, 2, 3) a is aromatic, g is graphitic -# The atomType (number of protons) of the first symbol must be <= the second. -# -# ks r0 de beta inflectionR qual quad bondName - -stretch 4.00 318.00 1.0000 -1 -1 9 1 Ax5-1-Ax5 -stretch 50.00 676.00 1.0000 -1 -1 9 1 Ax5-1-Ss5 -stretch 50.00 676.00 1.0000 -1 -1 9 1 Ax5-1-Sj5 -stretch 4.00 364.00 1.0000 -1 -1 9 1 Ss5-1-Pl5 -stretch 4.00 400.00 1.0000 -1 -1 9 1 Pl5-1-Sj5 -stretch 4.00 180.00 1.0000 -1 -1 9 1 H-1-Ax5 -stretch 4.00 200.00 1.0000 -1 -1 9 1 H-1-Ss5 -stretch 4.00 200.00 1.0000 -1 -1 9 1 H-1-Pl5 -stretch 4.00 180.00 1.0000 -1 -1 9 1 Ax5-1-Ae5 -stretch 4.00 200.00 1.0000 -1 -1 9 1 Ss5-1-Sh5 -stretch 4.00 364.00 1.0000 -1 -1 9 1 Ss5-1-Pe5 -stretch 4.00 357.00 1.0000 -1 -1 9 1 Pl5-1-Hp5 -stretch 4.00 357.00 1.0000 -1 -1 9 1 Pe5-1-Hp5 -stretch 4.00 200.00 1.0000 -1 -1 9 1 Sh5-1-Hp5 -stretch 4.00 200.00 1.0000 -1 -1 9 1 H-1-Hp5 - -stretch 50.00 1239.60 1.0000 -1 -1 9 1 Ss5-1-Ss5 -stretch 50.00 1064.70 1.0000 -1 -1 9 1 Gv5-1-Ss5 -stretch 50.00 1064.70 1.0000 -1 -1 9 1 Gr5-1-Ss5 -stretch 0.00 300.00 1.0000 -1 -1 9 1 Gv5-1-Gv5 -stretch 0.00 300.00 1.0000 -1 -1 9 1 Gv5-1-Gr5 - - -stretch 4.00 318.00 1.0000 -1 -1 9 1 Ax3-1-Ax3 -stretch 4.00 318.00 1.0000 -1 -1 9 1 Ax3-1-Ae3 -stretch 50.00 870.00 1.0000 -1 -1 9 1 Ax3-1-Ss3 -stretch 50.00 870.00 1.0000 -1 -1 9 1 Ax3-1-Sj3 -stretch 50.00 870.00 1.0000 -1 -1 9 1 Ax3-1-Se3 -stretch 4.00 318.00 1.0000 -1 -1 9 1 Ae3-1-Ax3 -stretch 4.00 318.00 1.0000 -1 -1 9 1 Ae3-1-Ae3 -stretch 50.00 870.00 1.0000 -1 -1 9 1 Ae3-1-Ss3 -stretch 50.00 870.00 1.0000 -1 -1 9 1 Ae3-1-Sj3 -stretch 50.00 870.00 1.0000 -1 -1 9 1 Ae3-1-Se3 -stretch 4.00 400.00 1.0000 -1 -1 9 1 Pl3-1-Sj3 -stretch 4.00 180.00 1.0000 -1 -1 9 1 H-1-Ax3 -stretch 4.00 200.00 1.0000 -1 -1 9 1 H-1-Ss3 -stretch 4.00 200.00 1.0000 -1 -1 9 1 H-1-Pl3 -stretch 4.00 200.00 1.0000 -1 -1 9 1 Ss3-1-Sh3 -stretch 4.00 357.00 1.0000 -1 -1 9 1 Se3-1-Hp3 -stretch 50.00 870.00 1.0000 -1 -1 9 1 Se3-1-Ae3 -stretch 4.00 200.00 1.0000 -1 -1 9 1 Sh3-1-Hp3 -stretch 4.00 200.00 1.0000 -1 -1 9 1 H-1-Hp3 -stretch 4.00 625.00 1.0000 -1 -1 9 1 Ss3-1-Ss3 -stretch 4.00 625.00 1.0000 -1 -1 9 1 Ss3-1-Sj3 -stretch 4.00 625.00 1.0000 -1 -1 9 1 Se3-1-Ss3 -stretch 4.00 625.00 1.0000 -1 -1 9 1 Ss3-1-Se3 -stretch 50.00 870.00 1.0000 -1 -1 9 1 Ss3-1-Ae3 -stretch 4.00 625.00 1.0000 -1 -1 9 1 Se3-1-Sj3 -stretch 4.00 670.00 1.0000 -1 -1 9 1 Sj3-1-Sj3 - -# format for bend lines -# -# ktheta (double) in aJ / rad^2 (1e-18 J/rad^2) -# theta0 (double) in radians -# qual (int) quality of parameter (use of a parameter with quality < 5 produces a warning) -# name (string) symbol-bondOrder-symbol.hybridization-bondOrder-symbol -# bondOrders are: (1, a, g, 2, 3) a is aromatic, g is graphitic -# atoms in group 3 have a default hybridization of sp2 -# other atoms have a default hybridization of sp3 -# an info line in the mmp file can change the hybridization -# possible values are: (sp, sp2, sp2_g, sp3, sp3d) -# sp2_g is graphitic, sp3d is not supported yet -# -# ktheta theta0 qual bondName - -# 180 degree along Axis -bend 0.18 180.000 9 Ax5-1-Ax5.sp3-1-Ax5 -#bend 0.18 180.000 9 H-1-Ax5.sp3-1-Ax5 #duplicate, H is sugar -#bend 0.18 180.000 9 H-1-Ax5.sp3-1-Ae5 #duplicate, H is sugar -bend 0.18 180.000 9 Ax5-1-Ax5.sp3-1-Ae5 -bend 0.18 180.000 9 Ae5-1-Ax5.sp3-1-Ae5 - -# 90 degree Axis to Sugar -bend 1.0 90.000 9 Ax5-1-Ax5.sp3-1-Ss5 -bend 1.0 90.000 9 Ax5-1-Ax5.sp3-1-Sj5 -#bend 1.0 90.000 9 H-1-Ax5.sp3-1-Ss5 #duplicate, H is sugar -bend 1.0 90.000 9 Ss5-1-Ax5.sp3-1-Ae5 -bend 1.0 90.000 9 H-1-Ax5.sp3-1-Ax5 -bend 1.0 90.000 9 H-1-Ax5.sp3-1-Ae5 -bend 1.0 90.000 9 H-1-Ax5.sp3-1-H - -# 133 degree minor groove -bend 1.0 133.000 9 Ss5-1-Ax5.sp3-1-Ss5 -bend 1.0 133.000 9 Ss5-1-Ax5.sp3-1-Sj5 -bend 1.0 133.000 9 Sj5-1-Ax5.sp3-1-Sj5 -bend 1.0 133.000 9 H-1-Ax5.sp3-1-Ss5 -bend 1.0 133.000 9 H-1-Ax5.sp3-1-Sj5 - -# 121 degree Axis Sugar Phosphate -bend 0.04 121.000 9 Ax5-1-Ss5.sp3-1-Pl5 -bend 0.04 121.000 9 Ax5-1-Ss5.sp3-1-Pe5 -bend 0.04 121.000 9 Ax5-1-Ss5.sp3-1-Sh5 -bend 0.04 121.000 9 H-1-Ss5.sp3-1-Ax5 - -# 127 degree Phosphate Sugar Phosphate -bend 0.04 127.000 9 Pl5-1-Ss5.sp3-1-Pl5 -bend 0.04 127.000 9 Pl5-1-Ss5.sp3-1-Pe5 -bend 0.04 127.000 9 Pl5-1-Ss5.sp3-1-Sh5 -bend 0.04 127.000 9 Pe5-1-Ss5.sp3-1-Pe5 -bend 0.04 127.000 9 Pe5-1-Ss5.sp3-1-Sh5 -bend 0.04 127.000 9 Sh5-1-Ss5.sp3-1-Sh5 -bend 0.04 127.000 9 H-1-Ss5.sp3-1-Pl5 -bend 0.04 127.000 9 H-1-Ss5.sp3-1-Pe5 -bend 0.04 127.000 9 H-1-Ss5.sp3-1-Sh5 -bend 0.04 127.000 9 H-1-Ss5.sp3-1-H - -# 127 degree Phosphate Hairpin Phosphate -bend 0.04 127.000 9 Pl5-1-Hp5.sp3-1-Pl5 -bend 0.04 127.000 9 Pl5-1-Hp5.sp3-1-Pe5 -bend 0.04 127.000 9 Pl5-1-Hp5.sp3-1-Sh5 -bend 0.04 127.000 9 Pe5-1-Hp5.sp3-1-Pe5 -bend 0.04 127.000 9 Pe5-1-Hp5.sp3-1-Sh5 -bend 0.04 127.000 9 Sh5-1-Hp5.sp3-1-Sh5 -bend 0.04 127.000 9 H-1-Hp5.sp3-1-Pl5 -bend 0.04 127.000 9 H-1-Hp5.sp3-1-Pe5 -bend 0.04 127.000 9 H-1-Hp5.sp3-1-Sh5 -bend 0.04 127.000 9 H-1-Hp5.sp3-1-H - -# 115 degree Axis JunctionSugar Phosphate -bend 0.04 115.000 9 Ax5-1-Sj5.sp3-1-Pl5 -bend 0.04 115.000 9 Ax5-1-Sj5.sp3-1-Pe5 -bend 0.04 115.000 9 Ax5-1-Sj5.sp3-1-Sh5 -bend 0.04 115.000 9 H-1-Sj5.sp3-1-Ax5 - -# 110 degree Phosphate JunctionSugar Phosphate -bend 0.04 110.000 9 Pl5-1-Sj5.sp3-1-Pl5 -bend 0.04 110.000 9 Pl5-1-Sj5.sp3-1-Pe5 -bend 0.04 110.000 9 H-1-Sj5.sp3-1-Pl5 -bend 0.04 110.000 9 H-1-Sj5.sp3-1-H -bend 0.04 110.000 9 H-1-Sj5.sp3-1-Pe5 -bend 0.04 110.000 9 Pe5-1-Sj5.sp3-1-Pe5 - -# 127 degree Phosphate JunctionSugar end -bend 0.04 127.000 9 Pl5-1-Sj5.sp3-1-Sh5 -bend 0.04 127.000 9 Pe5-1-Sj5.sp3-1-Sh5 -bend 0.04 127.000 9 Sh5-1-Sj5.sp3-1-Sh5 -bend 0.04 127.000 9 H-1-Sj5.sp3-1-Sh5 - -# 92.5 degree Sugar Phosphate Sugar -bend 0.04 92.500 9 Ss5-1-Pl5.sp3-1-Ss5 -bend 0.04 92.500 9 Ss5-1-Pl5.sp3-1-Sh5 -bend 0.04 92.500 9 Ss5-1-Pl5.sp3-1-Hp5 -bend 0.04 92.500 9 Sh5-1-Pl5.sp3-1-Sh5 -bend 0.04 92.500 9 Sh5-1-Pl5.sp3-1-Hp5 -bend 0.04 92.500 9 Hp5-1-Pl5.sp3-1-Hp5 -bend 0.04 92.500 9 H-1-Pl5.sp3-1-Ss5 -bend 0.04 92.500 9 H-1-Pl5.sp3-1-Sh5 -bend 0.04 92.500 9 H-1-Pl5.sp3-1-Hp5 -bend 0.04 92.500 9 H-1-Pl5.sp3-1-H - -# 92.5 degree Sugar Phosphate JunctionSugar -bend 0.04 92.500 9 Ss5-1-Pl5.sp3-1-Sj5 -bend 0.04 92.500 9 Sj5-1-Pl5.sp3-1-Sh5 -bend 0.04 92.500 9 Sj5-1-Pl5.sp3-1-Hp5 -bend 0.04 92.500 9 H-1-Pl5.sp3-1-Sj5 - -# 115.8 degree JunctionSugar Phosphate JunctionSugar -bend 0.04 115.800 9 Sj5-1-Pl5.sp3-1-Sj5 - -# PAM3 Bend Parameters ####################################3 - -# 180 degree along Axis -bend 0.18 180.000 9 Ax3-1-Ax3.sp3-1-Ax3 -#bend 0.18 180.000 9 H-1-Ax3.sp3-1-Ax3 #duplicate, H is sugar -#bend 0.18 180.000 9 H-1-Ax3.sp3-1-Ae3 #duplicate, H is sugar -bend 0.18 180.000 9 Ax3-1-Ax3.sp3-1-Ae3 -bend 0.18 180.000 9 Ae3-1-Ax3.sp3-1-Ae3 - -# 90 degree Axis to Sugar -bend 1.0 90.000 9 Ax3-1-Ax3.sp3-1-Ss3 -bend 1.0 90.000 9 Ax3-1-Ax3.sp3-1-Sj3 -bend 1.0 90.000 9 Ax3-1-Ax3.sp3-1-Se3 -bend 1.0 90.000 9 Ax3-1-Ae3.sp3-1-Ss3 -bend 1.0 90.000 9 Ax3-1-Ae3.sp3-1-Sj3 -bend 1.0 90.000 9 Ax3-1-Ae3.sp3-1-Se3 -bend 1.0 90.000 9 Ss3-1-Ax3.sp3-1-Ae3 -bend 1.0 90.000 9 Sj3-1-Ax3.sp3-1-Ae3 -bend 1.0 90.000 9 Ss3-1-Ae3.sp3-1-Ae3 -bend 1.0 90.000 9 Sj3-1-Ae3.sp3-1-Ae3 -bend 1.0 90.000 9 Ae3-1-Ax3.sp3-1-Se3 -bend 1.0 90.000 9 Ae3-1-Ae3.sp3-1-Se3 -#bend 1.0 90.000 9 H-1-Ax3.sp3-1-Ss3 #duplicate, H is sugar -#bend 1.0 90.000 9 H-1-Ax3.sp3-1-Sj3 #duplicate, H is sugar -#bend 1.0 90.000 9 H-1-Ax3.sp3-1-Se3 #duplicate, H is sugar -bend 1.0 90.000 9 H-1-Ax3.sp3-1-Ax3 -bend 1.0 90.000 9 H-1-Ax3.sp3-1-Ae3 -bend 1.0 90.000 9 H-1-Ax3.sp3-1-H -#bend 1.0 90.000 9 H-1-Ae3.sp3-1-Ss3 #duplicate, H is sugar -#bend 1.0 90.000 9 H-1-Ae3.sp3-1-Sj3 #duplicate, H is sugar -#bend 1.0 90.000 9 H-1-Ae3.sp3-1-Se3 #duplicate, H is sugar -bend 1.0 90.000 9 H-1-Ae3.sp3-1-Ax3 -bend 1.0 90.000 9 H-1-Ae3.sp3-1-Ae3 -bend 1.0 90.000 9 H-1-Ae3.sp3-1-H - -# 133 degree minor groove -bend 1.0 133.000 9 Ss3-1-Ax3.sp3-1-Ss3 -bend 1.0 133.000 9 Ss3-1-Ax3.sp3-1-Sj3 -bend 1.0 133.000 9 Ss3-1-Ax3.sp3-1-Se3 -bend 1.0 133.000 9 Sj3-1-Ax3.sp3-1-Sj3 -bend 1.0 133.000 9 H-1-Ax3.sp3-1-Ss3 -bend 1.0 133.000 9 H-1-Ax3.sp3-1-Sj3 -bend 1.0 133.000 9 H-1-Ax3.sp3-1-Se3 -bend 1.0 133.000 9 Ss3-1-Ae3.sp3-1-Ss3 -bend 1.0 133.000 9 Ss3-1-Ae3.sp3-1-Sj3 -bend 1.0 133.000 9 Ss3-1-Ae3.sp3-1-Se3 -bend 1.0 133.000 9 Sj3-1-Ae3.sp3-1-Sj3 -bend 1.0 133.000 9 H-1-Ae3.sp3-1-Ss3 -bend 1.0 133.000 9 H-1-Ae3.sp3-1-Sj3 -bend 1.0 133.000 9 H-1-Ae3.sp3-1-Se3 - -# 74.58 degree Axis Sugar Sugar -bend 0.04 74.580 9 Ax3-1-Ss3.sp3-1-Ss3 -bend 0.04 74.580 9 Ax3-1-Ss3.sp3-1-Se3 -bend 0.04 74.580 9 Ax3-1-Ss3.sp3-1-Sh3 -bend 0.04 74.580 9 H-1-Ss3.sp3-1-Ax3 - -# 74.58 degree Axis-end Sugar Sugar -bend 0.04 74.580 9 Ss3-1-Se3.sp3-1-Ae3 -bend 0.04 74.580 9 Ss3-1-Ss3.sp3-1-Ae3 -bend 0.04 74.580 9 Ae3-1-Ss3.sp3-1-Sh3 -bend 0.04 74.580 9 Ae3-1-Ss3.sp3-1-Se3 -bend 0.04 74.580 9 H-1-Ss3.sp3-1-Ae3 - -# 108 degree for Axis JunctionSugar JunctionSugar -bend 0.04 108.000 9 Ax3-1-Sj3.sp3-1-Sj3 -bend 0.04 108.000 9 Ae3-1-Sj3.sp3-1-Sj3 - -# 149 degree Sugar Sugar Sugar -bend 0.04 149.000 9 Ss3-1-Ss3.sp3-1-Ss3 -bend 0.04 149.000 9 Ss3-1-Ss3.sp3-1-Sj3 -bend 0.04 149.000 9 Ss3-1-Ss3.sp3-1-Se3 -bend 0.04 149.000 9 Ss3-1-Ss3.sp3-1-Sh3 -bend 0.04 149.000 9 Se3-1-Ss3.sp3-1-Se3 -bend 0.04 149.000 9 Se3-1-Ss3.sp3-1-Sh3 -bend 0.04 149.000 9 Sh3-1-Ss3.sp3-1-Sh3 -bend 0.04 149.000 9 H-1-Ss3.sp3-1-Ss3 -bend 0.04 149.000 9 H-1-Ss3.sp3-1-Sj3 -bend 0.04 149.000 9 H-1-Ss3.sp3-1-Se3 -bend 0.04 149.000 9 H-1-Ss3.sp3-1-Sh3 -bend 0.04 149.000 9 H-1-Ss3.sp3-1-H - -# 149 degree for Sugar JunctionSugar JunctionSugar -bend 0.04 149.000 9 Ss3-1-Sj3.sp3-1-Sj3 - -# 74.58 degree Axis JunctionSugar Sugar -bend 0.04 74.580 9 Ax3-1-Sj3.sp3-1-Ss3 -bend 0.04 74.580 9 Ax3-1-Sj3.sp3-1-Se3 -bend 0.04 74.580 9 Ax3-1-Sj3.sp3-1-Sh3 -bend 0.04 74.580 9 H-1-Sj3.sp3-1-Ax3 - -# 74.58 degree Axis-end JunctionSugar Sugar -bend 0.04 74.580 9 Ae3-1-Sj3.sp3-1-Ss3 -bend 0.04 74.580 9 Ae3-1-Sj3.sp3-1-Se3 -bend 0.04 74.580 9 Ae3-1-Sj3.sp3-1-Sh3 -bend 0.04 74.580 9 H-1-Sj3.sp3-1-Ae3 - -# 150 degree Sugar JunctionSugar Sugar -bend 0.04 150.000 9 Ss3-1-Sj3.sp3-1-Ss3 -bend 0.04 150.000 9 H-1-Sj3.sp3-1-H - -# 150 degree Sugar JunctionSugar end (CHECK/FIX ANGLE) -bend 0.04 150.000 9 Ss3-1-Sj3.sp3-1-Se3 -bend 0.04 150.000 9 Ss3-1-Sj3.sp3-1-Sh3 -bend 0.04 150.000 9 H-1-Sj3.sp3-1-Se3 -bend 0.04 150.000 9 H-1-Sj3.sp3-1-Sh3 - -# 115.8 degree JunctionSugar Phosphate-link JunctionSugar -bend 0.04 115.800 9 Sj3-1-Pl3.sp3-1-Sj3 - -# 127 degree Sugar Hairpin Sugar (CHECK/FIX ANGLE) -bend 0.04 127.000 9 Se3-1-Hp3.sp3-1-Se3 -bend 0.04 127.000 9 Se3-1-Hp3.sp3-1-Sh3 -bend 0.04 127.000 9 Sh3-1-Hp3.sp3-1-Sh3 -bend 0.04 127.000 9 H-1-Hp3.sp3-1-Se3 -bend 0.04 127.000 9 H-1-Hp3.sp3-1-Sh3 -bend 0.04 127.000 9 H-1-Hp3.sp3-1-H - -# parameters for pattern match routines - -pattern PAM5:Ax-Ax-Ss_low_ktheta 1.0 -pattern PAM5:Ax-Ax-Ss_low_theta0 85.000 - -pattern PAM5:Ax-Ax-Ss_high_ktheta 1.0 -pattern PAM5:Ax-Ax-Ss_high_theta0 95.000 - - -# For the PAM5-Stack pattern, two base pair planes are defined, each by -# a pair of basis vectors from an Ax to an Ss pseudo-atom. Since the -# double helix can be viewed from either end (180 degree rotational -# symmetry), each Ss is similar to the one diagonally opposite it, -# across the minor groove. Between the two stacked base pairs, the -# minor groove rotates, so that one pair of similar Ss pseudo-atoms -# will always be farther apart than the other. The farther apart pair -# we will call P, with the closer pair called Q. - -# One base pair is called A, the other B. Each plane contains a set -# of numbered virtual interaction sites, so vDa1 is the first site in -# plane A. The location of each site is defined as a linear -# combination of the two basis vectors for that plane, with the basis -# vectors labeled P and Q, corrosponding to the Ss at the tip of that -# vector (the Ax is the tail for both). - -pattern PAM5-Stack:vDa1-p 0.011 -pattern PAM5-Stack:vDa1-q 0.012 - -pattern PAM5-Stack:vDb1-p 0.111 -pattern PAM5-Stack:vDb1-q 0.112 - -pattern PAM5-Stack:vDa2-p 0.021 -pattern PAM5-Stack:vDa2-q 0.022 - -pattern PAM5-Stack:vDb2-p 0.121 -pattern PAM5-Stack:vDb2-q 0.122 - -pattern PAM5-Stack:vDa3-p 0.031 -pattern PAM5-Stack:vDa3-q 0.032 - -pattern PAM5-Stack:vDb3-p 0.131 -pattern PAM5-Stack:vDb3-q 0.132 - -pattern PAM5-Stack:vDa4-p 0.041 -pattern PAM5-Stack:vDa4-q 0.042 - -pattern PAM5-Stack:vDb4-p 0.141 -pattern PAM5-Stack:vDb4-q 0.142 - -pattern PAM5-Stack:vDa5-p 0.051 -pattern PAM5-Stack:vDa5-q 0.052 - -pattern PAM5-Stack:vDb5-p 0.151 -pattern PAM5-Stack:vDb5-q 0.152 - -pattern PAM5-Stack:vDa6-p 0.061 -pattern PAM5-Stack:vDa6-q 0.062 - -pattern PAM5-Stack:vDb6-p 0.161 -pattern PAM5-Stack:vDb6-q 0.162 - -pattern PAM5-Stack:vDa7-p 0.071 -pattern PAM5-Stack:vDa7-q 0.072 - -pattern PAM5-Stack:vDb7-p 0.171 -pattern PAM5-Stack:vDb7-q 0.172 - -pattern PAM5-Stack:vDa8-p 0.081 -pattern PAM5-Stack:vDa8-q 0.082 - -pattern PAM5-Stack:vDb8-p 0.181 -pattern PAM5-Stack:vDb8-q 0.182 - -pattern PAM5-Stack:vDn-pq 0.250 - -# ks r0 de beta inflectionR qual quad bondName - -stretch 1.00 300.00 1.0000 -1 -1 9 1 vDa1-1-vDb1 -stretch 1.00 300.00 1.0000 -1 -1 9 1 vDa2-1-vDb2 -stretch 1.00 300.00 1.0000 -1 -1 9 1 vDa3-1-vDb3 -stretch 1.00 300.00 1.0000 -1 -1 9 1 vDa4-1-vDb4 -stretch 1.00 300.00 1.0000 -1 -1 9 1 vDa5-1-vDb5 -stretch 1.00 300.00 1.0000 -1 -1 9 1 vDa6-1-vDb6 -stretch 1.00 300.00 1.0000 -1 -1 9 1 vDa7-1-vDb7 -stretch 1.00 300.00 1.0000 -1 -1 9 1 vDa8-1-vDb8 |