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|
#
# 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 213 0 0 P5d Ah5 DNA-Pseudo-Axis-Handle 1.0 0.0 0.0 1 100 0 0
element 219 0 0 P5V vAh5 DNA-Pseudo-Axis-Handle-v 0.0 0.0 0.0 1 100 0 0
element 220 0 0 P5V vDa1 virtual-DNA-planeA-1 0.0 0.0 0.0 1 100 0 1
element 221 0 0 P5V vDa1p virtual-DNA-planeA-1p 0.0 0.0 0.0 1 100 0 1
element 222 0 0 P5V vDa2 virtual-DNA-planeA-2 0.0 0.0 0.0 1 100 0 1
element 223 0 0 P5V vDa2p virtual-DNA-planeA-2p 0.0 0.0 0.0 1 100 0 1
element 224 0 0 P5V vDa3 virtual-DNA-planeA-3 0.0 0.0 0.0 1 100 0 1
element 225 0 0 P5V vDa4 virtual-DNA-planeA-4 0.0 0.0 0.0 1 100 0 1
element 226 0 0 P5V vDa5 virtual-DNA-planeA-5 0.0 0.0 0.0 1 100 0 1
element 230 0 0 P5V vDb1 virtual-DNA-planeB-1 0.0 0.0 0.0 1 100 0 1
element 231 0 0 P5V vDb1p virtual-DNA-planeB-1p 0.0 0.0 0.0 1 100 0 1
element 232 0 0 P5V vDb2 virtual-DNA-planeB-2 0.0 0.0 0.0 1 100 0 1
element 233 0 0 P5V vDb2p virtual-DNA-planeB-2p 0.0 0.0 0.0 1 100 0 1
element 234 0 0 P5V vDb3 virtual-DNA-planeB-3 0.0 0.0 0.0 1 100 0 1
element 235 0 0 P5V vDb4 virtual-DNA-planeB-4 0.0 0.0 0.0 1 100 0 1
element 236 0 0 P5V vDb5 virtual-DNA-planeB-5 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.
# For Yukawa potentials, the numbers on vdw lines are irrelevant, only
# their existence matters, defining the set of interacting pseudo
# atoms.
#
# rvdW evdW start end name
vdw 700.0 10.0 100.0 7.2 Pl5-v-Pl5
vdw 700.0 10.0 100.0 7.2 Ss3-v-Ss3
vdw 700.0 10.0 100.0 7.2 Ss3-v-Sj3
vdw 700.0 10.0 100.0 7.2 Ss3-v-Se3
vdw 700.0 10.0 100.0 7.2 Sj3-v-Sj3
vdw 700.0 10.0 100.0 7.2 Sj3-v-Se3
vdw 700.0 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 4.00 400.00 1.0000 -1 -1 9 1 Pl5-1-Sj5
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 0.00 180.00 1.0000 -1 -1 9 1 H-1-Ax5
stretch 0.00 200.00 1.0000 -1 -1 9 1 H-1-Ss5
stretch 0.00 200.00 1.0000 -1 -1 9 1 H-1-Gv5
stretch 0.00 200.00 1.0000 -1 -1 9 1 H-1-Pl5
stretch 0.00 200.00 1.0000 -1 -1 9 1 H-1-Hp5
######## From among the "PAM5 Parameters"
stretch 10.00 923.40 1.0000 -1 -1 9 1 Gr5-1-Ss5
stretch 0.00 519.00 1.0000 -1 -1 9 1 Gv5-1-Gr5
stretch 0.00 519.00 1.0000 -1 -1 9 1 Gr5-1-Gr5
###########################################################
######## PAM5 Parameters ######################################
# ks r0 de beta inflectionR qual quad bondName
stretch 50.00 1075.00 1.0000 -1 -1 9 6 Ss5-1-Ss5
stretch 50.00 923.40 1.0000 -1 -1 9 1 Gv5-1-Ss5
# this stretch is to the Pl on the 5' side of the Gv
stretch 1.00 1092.90 1.0000 -1 -1 9 1 Gv5-1-Pl5
# this stretch is to the Pl on the 3' side of the Gv
stretch 0.0 1092.9 1.0000 -1 -1 9 1 Gv5-2-Pl5
stretch 0.5 650.00 1.0000 -1 -1 9 1 Pl5-1-Pl5
stretch 0.00 519.00 1.0000 -1 -1 9 1 Gv5-1-Gv5
# These are the stretch terms for the two different Pl-Ss
# interactions. 5 and 3 represent the 5' and 3' ends of the strand.
pattern PAM5:5-Pl-Ss-3_r0 509.0
pattern PAM5:5-Pl-Ss-3_ks 50.0
pattern PAM5:5-Ss-Pl-3_r0 420.9
pattern PAM5:5-Ss-Pl-3_ks 50.0
# ktheta theta0 qual bondName
# bend 0.05442 88.000 9 Pl5-1-Ss5-1-Pl5
bend 0.020 61.000 9 Ss5-1-Pl5-1-Ss5
# bend to Pl on the 3' side of the Gv (the 5' bend is suppressed)
bend 0.007 180.000 9 Gv5-1-Ss5-1-Pl5
# 0.07684 aJ/rad^2 => 0.5 N/m equivalent stretching stiffness @ 61 degrees
# 0.05442 aJ/rad^2 => 0.5 N/m equivalent stretching stiffness 2 88 degrees
# should convert back to a modified Pl5-Pl5 stretch
# mean Gv-Pl in 1NVN = 10.19 most in the range 9.4 - 11.1
# This is the interaction between the two bridging Pl's in a
# crossover. Its labeled as a double bond (its not) to distinguish
# it from the Pl5-1-Pl5 case above (which also is not a real bond).
# Note that quadratic = 6 here, which tells GROMACS to not consider
# this as a chemical bond for purposes of exclusion of non-bonded
# interactions. Otherwise, we'd end up excluding two diagonal Pl-Pl
# interactions which we'd like to include.
stretch 100.0 600.0 1.0000 -1 -1 9 6 Pl5-2-Pl5
#### Non-bonded exclusions ####
# If non-zero, exclude non-bonded interactions within the same
# duplex. Also adds an exclusion between bridging phosphates in a
# crossover, so changing this requires changing the Pl5-2-Pl5 stretch
# term as well.
pattern enableExclusions 0
###############################################################
###########################################################
# this is overridden by separate directional parameters below, but we
# still need a max value for bond stretch indicators
stretch 4.00 510.00 1.0000 -1 -1 9 1 Ss5-1-Pl5
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
# 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
# these two bends are not used by current code.
#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
################(( Pattern-stretches, Non-bonded exclusions flag copied from here ))################
# 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:basis-x_o 0.4996
pattern PAM5:basis-x_g 0.75075
pattern PAM5:basis-y_m 0.53745
# upper ends lower ends
# Ks(N/m) r0(pm) X1 (nm) Y1 (nm) X2 (nm) Y2 (nm)
strut PAM5-1 1.69474 381.6 0.17941 0.53496 -0.22256 0.35814
strut PAM5-1p 1.69474 381.6 -0.22256 -0.35814 0.17941 -0.53496
strut PAM5-2 0.94669 416.3 0.33045 -0.24420 0.46175 0.16547
strut PAM5-2p 0.94669 416.3 0.46175 -0.16547 0.33045 0.24420
strut PAM5-3 1.04685 834.1 -0.05386 0.42674 -0.05386 -0.42674
strut PAM5-4 0.57124 339.8 -0.20685 0.12986 -0.20685 -0.12986
strut PAM5-5 0.38792 324.6 -0.47384 0.09686 -0.47384 -0.09686
###############((( Stretching constants moved from here )))######################
# Switching function to smoothly reduce Yukawa potential to zero.
# Between RSwitch and RCutoff (both in nm), the non-bonded potential
# function is multiplied by a function which smoothly reduces from 1.0
# (for 0 < r < RSwitch) to 0.0 (for RCutoff < r). The switching
# function is disabled if RSwitch > RCutoff.
ne1 YukawaRSwitch 2.0
ne1 YukawaRCutoff 3.0
# If true, yukawa(RCutoff) is subtracted from the potential (before
# applying the switching function. This reduces the work of the
# switching function, but modifies the total energy of the system.
ne1 YukawaShift True
# Net charge of individual counterions in solution. 1 for Na, 2 for
# Mg. If you are using a mixture of counterions, you can average the
# charges and molarities. Note that the formula is the sum of
# (molarity * charge^2). You can adjust the single molarity and
# charge terms available here to duplicate the results of any sum of
# such terms.
ne1 YukawaCounterionCharge 2.0
# Concentration of counterions in solution.
ne1 YukawaCounterionMolarity 0.02
# Temperature of the solution
ne1 YukawaTemperatureKelvin 298.0
# Dielectric constant of the solution, not including the counterions.
# Water is 78.5
ne1 YukawaDielectric 78.5
# The potential is multiplied by this fudge factor.
ne1 YukawaConstantMultiple 1.0
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