# # 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