remarks file toppar/protein_rep.param remarks Parameter file including bond and angle parameters remarks derived from Cambridge Data Base model structures remarks (R. A. Engh and R. Huber, Acta Cryst. Sect. A., 1991). remarks Nonbonded parameters taken from PROLSQ using REPEL function. remarks Small dihedral angle energy constants set to zero. All other remarks dihedral and improper energy constants set to uniform values. remarks Water parameters are included. ! ! References: ! Engh, R.A. and Huber, R. (1991). Accurate Bond and ! Angle Parameters for X-ray Protein-Structure Refinement, ! Acta Cryst. A47, 392-400. ! ! Hendrickson W.A. and Konnert J.H. in "Computing in ! Crystallography" (ed. R. Diamond, S. Ramaseshan ! and K. Venkatesan) (Bangalore, Indian Institute of ! Science, 1980) 13.01-13.23 ! set echo=off message=off end REMARK These parameters use additional atom types (14 more than in REMARK param19x) and requires the corresponding topology file for REMARK psf file generation. ! The XPL19X comments are the original XPLOR param19x parameters. Under ! these lines are the corresponding new parameters. Where new atom ! types are defined, several bond or angle types correspond to a single ! XPL19X definition. The numerical values in comments represent the ! CSD determined sample standard deviation from which the force constants ! were derived by assuming the standard deviation represents expected ! deviations from potential minima at a temperature of 293 K. Although ! some forces have up to seven significant figures, they might be considered ! useful only to about one significant figure. ! Some values were not determined from the Cambridge Data Base (CSD) but were ! taken either from related geometry types or from X-PLOR parameters. These ! are marked with an asterisk and include hydrogen related parameters and some ! other rarely occurring geometries. ! Only bond and angle parameters were taken from the CSD. Dihedrals and ! improper dihedrals retain the original XPL19X target values and force ! constants. One result is that the bonds and angles are weighted ! approximately 3 and 7 times as heavily, respectively, compared to ! XPL19X parameters. This is not an error, but is a matter for consideration. ! In general, the relative weighting of different types of restraints ! is not standard, and depends primarily on the desired deviations from ! target values. We think that the relative weighting of bonds and angles ! is correctly represented in these parameters. The other parameters ! may be scaled according to any special criteria. ! IF any parameters are missing or inconsistent, contact me by E-MAIL ! at engh@nmrvex.biochem.mpg.de or engh@mpib-martinsried.mpg.dbp.de. If there ! is no reply, please use physical, tangible, slow, reliable mail to R. Engh, ! Max-Planck-Institut fuer Biochemie, D8033 Martinsried bei Muenchen, ! Fed. Rep. of Germany. !XPL19X BOND C C 450.0 1.38 bond C5W CW 1827.161 1.433 ! 0.018 bond CW CW 2048.443 1.409 ! 0.017 !XPL19X BOND C CH1E 405.0 1.52 bond C CH1E 1342.404 1.525 ! 0.021 !XPL19X BOND C CH2E 405.0 1.52 bond C5 CH2E 3020.408 1.497 ! 0.014 bond C5W CH2E 616.025 1.498 ! 0.031 bond CF CH2E 1119.093 1.502 ! 0.023 bond CY CH2E 1223.141 1.512 ! 0.022 bond C CH2E 947.200 1.516 ! 0.025 bond CN CH2E 1639.889 1.503 ! 0.019 bond C CH2G 1827.161 1.516 ! 0.010 !XPL19X BOND C CH3E 405.0 1.52 !XPL19X BOND C CR1E 450.0 1.38 bond C5W CR1E 947.200 1.365 ! 0.025 bond CW CR1E 2312.500 1.398 ! 0.016 bond CW CR1W 1342.404 1.394 ! 0.021 bond CF CR1E 1342.404 1.384 ! 0.021 bond CY CR1E 1342.404 1.389 ! 0.021 bond CY2 CR1E 1027.778 1.378 ! 0.024 bond C5 CR1H 4892.562 1.354 ! 0.011 bond C5 CR1E 4892.562 1.356 ! 0.011 !XPL19X BOND C CT 405.0 1.53 !XPL19X BOND C N 471.0 1.33 bond C N 2312.500 1.341 ! 0.016 !XPL19X BOND C NC2 400.0 1.33 bond C NC2 1827.161 1.326 ! 0.018 !XPL19X BOND C NH1 471.0 1.33 bond C5 NH1 4892.562 1.378 ! 0.011 bond CW NH1 4892.562 1.370 ! 0.011 bond C NH1 3020.408 1.329 ! 0.014 !XPL19X BOND C NH2 471.0 1.33 bond C NH2 1342.404 1.328 ! 0.021 !XPL19X BOND C NP 471.0 1.33 !XPL19X BOND C NR 471.0 1.33 bond C5 NR 2048.443 1.371 ! 0.017 !XPL19X BOND C O 580.0 1.23 bond C O 1480.000 1.231 ! 0.020 bond CN O 1119.093 1.208 ! 0.023 !XPL19X BOND C OC 580.0 1.23 bond C OC 1639.889 1.249 ! 0.019 !XPL19X BOND C OH1 450.0 1.38 bond CY2 OH1 1342.404 1.376 ! 0.021 bond C OH1 1223.141 1.304 ! 0.022 !XPL19X BOND CH1E CH1E 225.0 1.53 bond CH1E CH1E 812.071 1.540 ! 0.027 !XPL19X BOND CH1E CH2E 225.0 1.52 bond CH1E CH2E 1480.000 1.530 ! 0.020 !XPL19X BOND CH1E CH3E 225.0 1.52 bond CH1E CH3E 543.618 1.521 ! 0.033 !XPL19X BOND CH1E N 422.0 1.45 bond CH1E N 2631.111 1.466 ! 0.015 !XPL19X BOND CH1E NH1 422.0 1.45 bond CH1E NH1 1639.889 1.458 ! 0.019 !XPL19X BOND CH1E NH2 422.0 1.45 !XPL19X BOND CH1E NH3 422.0 1.45 bond CH1E NH3 1342.404 1.491 ! 0.021 !XPL19X BOND CH1E OH1 400.0 1.42 bond CH1E OH1 2312.500 1.433 ! 0.016 !XPL19X BOND CH2E CH2E 225.0 1.52 bond CH2E CH2E 657.778 1.520 ! 0.030 bond CH2P CH2E 236.800 1.492 ! 0.050 bond CH2P CH2P 512.111 1.503 ! 0.034 !XPL19X BOND CH2E CH3E 225.0 1.54 bond CH2E CH3E 389.218 1.513 ! 0.039 !XPL19X BOND CH2E CR1E 250.0 1.45 !XPL19X BOND CH2E N 422.0 1.45 bond CH2P N 3020.408 1.473 ! 0.014 bond CH2P NH3 3020.408 1.473 ! 0.014 !added 5/19/93 ATB !XPL19X BOND CH2E NH1 422.0 1.45 bond CH2G NH1 2312.500 1.451 ! 0.016 bond CH2E NH1 1827.161 1.460 ! 0.018 bond CH3E NH1 1827.161 1.460 ! copied for special residue !XPL19X BOND CH2E NH2 422.0 1.45 !XPL19X BOND CH2E NH3 422.0 1.45 bond CH2E NH3 657.778 1.489 ! 0.030 bond CH2G NH3 657.778 1.489 ! 0.030* !XPL19X BOND CH2E OH1 400.0 1.42 bond CH2E OH1 1480.000 1.417 ! 0.020 !XPL19X BOND CH2E S 450.0 1.81 bond CH2E S 1480.000 1.822 ! 0.020 bond CH2E SM 512.111 1.803 ! 0.034 !XPL19X BOND CH2E SH1E 450.0 1.81 bond CH2E SH1E 543.618 1.808 ! 0.033 !XPL19X BOND CH3E NH1 422.0 1.49 !XPL19X BOND CH3E NR 422.0 1.49 !XPL19X BOND CH3E S 450.0 1.77 bond CH3E SM 170.066 1.791 ! 0.059 !XPL19X BOND CM OM 1115.0 1.128 !XPL19X BOND CR1E CR1E 450.0 1.38 bond CR1E CR1E 657.778 1.382 ! 0.030 bond CR1E CR1W 947.200 1.400 ! 0.025 bond CR1W CR1W 1639.889 1.368 ! 0.019 !XPL19X BOND CR1E NH1 450.0 1.305 bond CR1E NH1 1342.404 1.374 ! 0.021 bond CRH NH1 1480.000 1.345 ! 0.020 bond CRHH NH1 5920.000 1.321 ! 0.010 bond CR1H NH1 4892.562 1.374 ! 0.011 !XPL19X BOND CR1E NR 450.0 1.305 bond CR1E NR 657.778 1.382 ! 0.030 !XPL19X BOND OC S 400.0 1.43 !XPL19X BOND OM OM 600.0 1.23 !XPL19X BOND S S 500.0 2.02 bond S S 2410.110 2.030 ! 0.008 !XPL19X BOND CR1E NR 450.0 1.305 bond CRH NR 3502.958 1.319 ! 0.013 bond H NH1 405.0 0.98 !* bond H NH2 405.0 0.98 !* bond H OH1 450.0 0.96 !* bond HA C 350.0 1.08 !* bond HA CT 300.0 1.08 !* bond HC NC2 405.0 1.00 !* bond HC NH1 405.0 0.98 !* bond HC NH3 405.0 1.04 !* BOND HT OT 450.0 0.9572 ! TIPS3P water geometry BOND HT HT 0.0 1.5139 ! TIPS3P water geometry !XPL19X ANGLE C C C 70.0 106.5 angle C5W CW CW 1349.600 107.200 !1.2 !XPL19X ANGLE C C CH2E 65.0 126.5 angle CW C5W CH2E 991.543 126.800 !1.4 !XPL19X ANGLE C C CR1E 70.0 122.5 angle C5W CW CR1E 1943.424 133.900 !1.0 angle CW CW CR1E 1943.424 118.800 !1.0 angle CW CW CR1W 1943.424 122.400 !1.0 angle CW C5W CR1E 759.150 106.300 !1.6 !XPL19X ANGLE C C NH1 65.0 109.0 angle CW CW NH1 1149.956 107.400 !1.3 !XPL19X ANGLE CH1E C N 20.0 117.5 angle CH1E C N 863.744 116.900 !1.5 !XPL19X ANGLE CH1E C NH1 20.0 117.5 angle CH1E C NH1 485.856 116.200 !2.0 !XPL19X ANGLE CH1E C O 85.0 121.5 angle CH1E C O 672.465 120.800 !1.7 !XPL19X ANGLE CH1E C OC 85.0 117.5 angle CH1E C OC 310.948 117.000 !2.5 !XPL19X ANGLE CH2E C CR1E 70.0 121.5 angle CH2E C5 CR1E 1149.956 129.100 !1.3 angle CH2E C5 CR1H 1149.956 131.200 !1.3 angle CH2E CF CR1E 672.465 120.700 !1.7 angle CH2E C5W CR1E 863.744 126.900 !1.5 angle CH2E CY CR1E 863.744 120.800 !1.5 !XPL19X ANGLE CH2E C N 20.0 117.5 angle CH2E C N 440.686 118.200 !2.1 angle CH2G C N 440.686 118.200 !2.1 * !XPL19X ANGLE CH2E C NH1 20.0 117.5 angle CH2E C5 NH1 863.744 122.700 !1.5 angle CH2E C NH1 440.686 116.500 !2.1 angle CH2G C NH1 440.686 116.400 !2.1 * !XPL19X ANGLE CH2E C NH2 20.0 117.5 angle CH2E C NH2 863.744 116.400 !1.5 !XPL19X ANGLE CH2E C NR 60.0 116.0 angle CH2E C5 NR 863.744 121.600 !1.5 !XPL19X ANGLE CH2E C O 85.0 121.6 angle CH2E C O 485.856 120.800 !2.0 angle CH2G C O 440.686 120.800 !2.1 !XPL19X ANGLE CH2E C OC 85.0 118.5 angle CH2E C OC 367.377 118.400 !2.3 angle CH2G C OC 367.377 118.400 !2.3 * !XPL19X ANGLE CR1E C CR1E 65.0 120.5 angle CR1E CY2 CR1E 485.856 120.300 !2.0 angle CR1E CY CR1E 863.744 118.100 !1.5 angle CR1E CF CR1E 863.744 118.600 !1.5 !XPL19X ANGLE CR1E C NH1 65.0 110.5 angle CR1W CW NH1 863.744 130.100 !1.5 angle CR1E C5 NH1 1943.424 105.200 !1.0 angle CR1H C5 NH1 1943.424 106.100 !1.0 !XPL19X ANGLE CR1E C NP 65.0 122.5 !XPL19X ANGLE CR1E C NR 65.0 122.5 angle CR1E C5 NR 1943.424 109.200 !0.7 HISE, taken as 1.0 !XPL19X ANGLE CR1E C OH1 65.0 119.0 angle CR1E CY2 OH1 215.936 119.900 !3.0 !XPL19X ANGLE N C O 85.0 121.0 angle N C O 991.543 122.000 !1.4 !XPL19X ANGLE NC2 C NC2 70.0 120.0 angle NC2 C NC2 599.823 119.700 !1.8 !XPL19X ANGLE NC2 C NH1 70.0 120.0 angle NC2 C NH1 538.345 120.000 !1.9 !XPL19X ANGLE NH1 C O 65.0 121.0 angle NH1 C O 759.150 123.000 !1.6 !XPL19X ANGLE NH2 C O 65.0 121.0 angle NH2 C O 1943.424 122.600 !1.0 !XPL19X ANGLE OC C OC 85.0 122.5 angle OC C OC 337.400 122.900 !2.4 !XPL19X ANGLE C CH1E CH1E 70.0 110.0 angle C CH1E CH1E 401.534 109.100 !2.2 !XPL19X ANGLE C CH1E CH2E 70.0 109.5 angle C CH1E CH2E 538.345 110.100 !1.9 !XPL19X ANGLE C CH1E CH3E 70.0 106.5 angle C CH1E CH3E 863.744 110.500 !1.5 !XPL19X ANGLE C CH1E N 45.0 111.6 angle C CH1E N 310.948 111.800 !2.5 !XPL19X ANGLE C CH1E NH1 45.0 111.6 angle C CH1E NH1 247.886 111.200 !2.8 angle C CH1E NH3 247.886 111.200 !2.8 * !XPL19X ANGLE CH1E CH1E CH2E 45.0 112.5 angle CH1E CH1E CH2E 672.465 110.400 !1.7 !XPL19X ANGLE CH1E CH1E CH3E 45.0 111.0 angle CH1E CH1E CH3E 672.465 110.500 !1.7 !XPL19X ANGLE CH1E CH1E NH1 50.0 110.0 angle CH1E CH1E NH1 672.465 111.500 !1.7 angle CH1E CH1E NH3 672.465 111.500 !1.7 * !XPL19X ANGLE CH1E CH1E OH1 50.0 104.5 angle CH1E CH1E OH1 863.744 109.600 !1.5 !XPL19X ANGLE CH2E CH1E CH3E 50.0 111.5 angle CH2E CH1E CH3E 215.936 110.700 !3.0 !XPL19X ANGLE CH2E CH1E N 65.0 104.0 angle CH2E CH1E N 1606.136 103.000 !1.1 !XPL19X ANGLE CH2E CH1E NH1 65.0 110.0 angle CH2E CH1E NH1 672.465 110.500 !1.7 angle CH2E CH1E NH3 672.465 110.500 !1.7 * !XPL19X ANGLE CH3E CH1E CH3E 50.0 111.0 angle CH3E CH1E CH3E 401.534 110.800 !2.2 !XPL19X ANGLE CH3E CH1E NH1 65.0 108.5 angle CH3E CH1E NH1 863.744 110.400 !1.5 !ANGLE CH3E CH1E NH2 65.0 109.5 !ANGLE CH3E CH1E NH3 65.0 109.5 angle CH3E CH1E NH3 672.465 110.500 !1.7 * !XPL19X ANGLE CH3E CH1E OH1 60.0 110.5 angle CH3E CH1E OH1 485.856 109.300 !2.0 !XPL19X ANGLE C CH2E CH1E 70.0 112.5 angle C CH2E CH1E 1943.424 112.600 !1.0 angle C5 CH2E CH1E 1943.424 113.800 !1.0 angle CF CH2E CH1E 1943.424 113.800 !1.0 angle C5W CH2E CH1E 538.345 113.600 !1.9 angle CY CH2E CH1E 599.823 113.900 !1.8 !XPL19X ANGLE C CH2E CH2E 70.0 113.0 angle C CH2E CH2E 672.465 112.600 !1.7 !XPL19X ANGLE C CH2E NH1 70.0 111.6 angle C CH2G NH1 231.085 112.500 !2.9 angle C CH2G NH3 231.085 112.500 !2.9 * !XPL19X ANGLE CH1E CH2E CH1E 45.0 117.0 angle CH1E CH2E CH1E 158.647 116.300 !3.5 !XPL19X ANGLE CH1E CH2E CH2E 45.0 112.5 angle CH1E CH2E CH2P 538.345 104.500 !1.9 angle CH1E CH2E CH2E 485.856 114.100 !2.0 !XPL19X ANGLE CH1E CH2E CH3E 45.0 113.0 angle CH1E CH2E CH3E 440.686 113.800 !2.1 !XPL19X ANGLE CH1E CH2E OH1 45.0 111.0 angle CH1E CH2E OH1 485.856 111.100 !2.0 !XPL19X ANGLE CH1E CH2E SH1E 50.0 112.5 angle CH1E CH2E S 367.377 114.400 !2.3 angle CH1E CH2E SH1E 367.377 114.400 !2.3 * !XPL19X ANGLE CH2E CH2E CH2E 45.0 110.0 angle CH2E CH2E CH2E 367.377 111.300 !2.3 angle CH2E CH2P CH2P 189.788 106.100 !3.2 !XPL19X ANGLE CH2E CH2E N 65.0 105.0 angle CH2P CH2P N 863.744 103.200 !1.5 angle CH2P CH2P NH3 863.744 103.200 !1.5 !added ATB 5/19/93 !XPL19X ANGLE CH2E CH2E NH1 65.0 111.0 angle CH2E CH2E NH1 401.534 112.000 !2.2 !XPL19X ANGLE CH2E CH2E NH3 65.0 110.5 angle CH2E CH2E NH3 189.788 111.900 !3.2 !XPL19X ANGLE CH2E CH2E S 50.0 112.5 angle CH2E CH2E SM 215.936 112.700 !3.0 !XPL19X ANGLE C CR1E CR1E 90.0 119.0 angle CY2 CR1E CR1E 599.823 119.600 !1.8 angle CW CR1E CR1E 1149.956 118.600 !1.3 angle CW CR1W CR1W 1149.956 117.500 !1.3 angle CF CR1E CR1E 672.465 120.700 !1.7 angle CY CR1E CR1E 863.744 121.200 !1.5 !XPL19X ANGLE C CR1E NH1 90.0 109.5 angle C5 CR1E NH1 1943.424 106.500 !1.0 angle C5 CR1H NH1 1943.424 107.200 !1.0 angle C5W CR1E NH1 1149.956 110.200 !1.3 !XPL19X ANGLE C CR1E NR 90.0 106.5 angle C5 CR1E NR 367.377 109.500 !2.3 !XPL19X ANGLE CR1E CR1E CR1E 90.0 120.5 angle CR1E CR1E CR1W 1149.956 121.100 !1.3 angle CR1W CR1W CR1E 1149.956 121.500 !1.3 angle CR1E CR1E CR1E 599.823 120.000 !1.8 !XPL19X ANGLE NH1 CR1E NH1 70.0 109.0 angle NH1 CRHH NH1 1943.424 108.400 !1.0 !XPL19X ANGLE NH1 CR1E NR 70.0 109.0 angle NH1 CRH NR 1149.956 111.700 !1.3 HisE, applied also to HisD !XPL19X ANGLE C N CH1E 80.0 120.0 angle C N CH1E 77.737 122.600 !5.0 !XPL19X ANGLE C N CH2E 80.0 120.0 angle C N CH2P 115.611 125.000 !4.1 angle HC NH3 CH2P 500. 125.000 !4.1 !added ATB 5/19/93 !XPL19X ANGLE CH1E N CH2E 60.0 110.0 angle CH1E N CH2P 991.543 112.000 !1.4 angle CH1E NH3 CH2P 991.543 112.000 !1.4 ! added ATB 5/19/93 !XPL19X ANGLE C NH1 CH1E 77.5 120.0 angle C NH1 CH1E 599.823 121.700 !1.8 !XPL19X ANGLE C NH1 CH2E 77.5 120.0 angle C NH1 CH2G 672.465 120.600 !1.7 angle C NH1 CH2E 863.744 124.200 !1.5 angle C NH1 CH3E 672.465 120.600 !1.7 * !XPL19X ANGLE C NH1 CR1E 60.0 108.0 angle C5 NH1 CRHH 672.465 109.300 !1.7 angle C5 NH1 CRH 672.465 109.000 !1.7 * angle CW NH1 CR1E 599.823 108.900 !1.8 !XPL19X ANGLE CR1E NH1 CR1E 65.0 110.0 angle CRHH NH1 CR1H 1943.424 109.000 !1.0 angle CRH NH1 CR1E 1149.956 106.900 !1.3 !XPL19X ANGLE C NR CR1E 70.0 109.5 angle C5 NR CRH 1943.424 105.600 !1.0 HisE !XPL19X ANGLE CR1E NR CR1E 65.0 110.0 angle CR1E NR CRH 215.936 107.000 !3.0, HisD, weak statistics !XPL19X ANGLE CH2E S CH3E 50.0 99.5 angle CH2E SM CH3E 401.534 100.900 !2.2 !XPL19X ANGLE CH2E S S 50.0 104.2 angle CH2E S S 599.823 103.800 !1.8 !XPL19X ANGLE C C HA 40.0 120.0 angle C NC2 HC 35.0 120.0 !* angle HC NC2 HC 40.0 120.0 !* angle C NH1 H 30.0 120.0 !* angle CW NH1 H 30.0 120.0 !* angle C5W NH1 H 30.0 120.0 !* angle C5 NH1 H 30.0 120.0 !* angle CH1E NH1 H 35.0 120.0 !* angle CRH NH1 H 35.0 120.0 !* angle CRHH NH1 H 35.0 120.0 !* angle CR1H NH1 H 35.0 120.0 !* angle CH2E NH1 H 35.0 120.0 !* angle CH2G NH1 H 35.0 120.0 !* angle CH3E NH1 H 35.0 120.0 !* angle CR1E NH1 H 35.0 120.0 !* angle C NH2 H 30.0 120.0 !* angle CH1E NH2 H 35.0 120.0 !* angle CH2E NH2 H 35.0 120.0 !* angle H NH2 H 40.0 125.0 !* angle CH1E NH3 HC 35.0 109.5 !* angle CH2E NH3 HC 35.0 109.5 !* angle CH2G NH3 HC 35.0 109.5 !* angle HC NH3 HC 40.0 109.5 !* angle C OH1 H 50.0 109.5 !* angle CY2 OH1 H 50.0 109.5 !* angle CH1E OH1 H 35.0 109.5 !* angle CH2E OH1 H 35.0 109.5 !* angle HT OT HT 55.0 104.52 ! tips3p water geometry evaluate ($kdih_const=1250.) { Weis 5/11/92 scaled up 3x for consistency with bond and angle parameters.} dihe CH1E C N CH1E $kdih_const 2 180.0 dihe CH2E C N CH1E $kdih_const 2 180.0 dihe CH2G C N CH1E $kdih_const 2 180.0 dihe CR1E CW CW CR1E $kdih_const 2 180.0 dihe CR1E CW CW CR1W $kdih_const 2 180.0 dihe CR1W CW CW C5W $kdih_const 2 180.0 dihe CR1E CW CW NH1 $kdih_const 2 180.0 dihe X C NH1 X $kdih_const 1 0.0 dihe CH2E NH1 C NC2 $kdih_const 2 180.0 dihe X C CH1E X 0.0 3 0.0 dihe X C CH2E X 0.0 3 0.0 dihe X C CH2G X 0.0 3 0.0 dihe X C5 CH2E X 0.0 3 0.0 dihe X C5W CH2E X 0.0 3 0.0 dihe X CF CH2E X 0.0 3 0.0 dihe X CY CH2E X 0.0 3 0.0 dihe X C CR1E X 0.0 2 180.0 dihe X C N X 0.0 2 180.0 dihe X C NC2 X 0.0 2 180.0 dihe X C NH2 X 0.0 2 180.0 dihe X CY2 OH1 X 0.0 2 180.0 dihe X CH1E CH1E X 0.0 3 0.0 dihe X CH1E CH2E X 0.0 3 0.0 dihe X CH1E N X 0.0 3 0.0 dihe X CH1E NH1 X 0.0 3 0.0 dihe X CH1E NH2 X 0.0 3 0.0 dihe X CH1E NH3 X 0.0 3 0.0 dihe X CH1E OH1 X 0.0 3 0.0 dihe X CH2E CH2E X 0.0 3 0.0 dihe X CH2E CH2P X 0.0 3 0.0 dihe X CH2P CH2P X 0.0 3 0.0 dihe X CH2E N X 0.0 3 0.0 dihe X CH2P N X 0.0 3 0.0 dihe X CH2P NH3 X 0.0 3 0.0 dihe X CH2E NH1 X 0.0 3 0.0 dihe X CH2G NH1 X 0.0 3 0.0 dihe X CH2E NH2 X 0.0 3 0.0 dihe X CH2E NH3 X 0.0 3 0.0 dihe X CH2G NH3 X 0.0 3 0.0 dihe X CH2E OH1 X 0.0 3 0.0 dihe X CH2E S X 0.0 2 0.0 dihe X CH2E SM X 0.0 2 0.0 dihe X S S X 0.0 2 0.0 evaluate ($impr_const=750.) { Weis 5/11/92 scaled up 3x for consistency with bond and angle parameters.} impr C C CR1E CH2E $impr_const 0 0.0 impr C CR1E C CH2E $impr_const 0 0.0 impr C5W CR1E CW CH2E $impr_const 0 0.0 impr C CR1E CR1E CH2E $impr_const 0 0.0 impr CF CR1E CR1E CH2E $impr_const 0 0.0 impr CY CR1E CR1E CH2E $impr_const 0 0.0 impr C CR1E NH1 CH2E $impr_const 0 0.0 impr C5 NH1 CR1E CH2E $impr_const 0 0.0 impr C5 NH1 CR1H CH2E $impr_const 0 0.0 impr C5 NH1 CRHH CH2E $impr_const 0 0.0 impr C CR1E CR1E OH1 $impr_const 0 0.0 impr CY2 CR1E CR1E OH1 $impr_const 0 0.0 impr C H H NH2 $impr_const 0 0.0 impr C OC OC CH1E $impr_const 0 0.0 impr C OC OC CH2E $impr_const 0 0.0 impr C X X C $impr_const 0 0.0 impr CY X X CY2 $impr_const 0 0.0 impr C5W X X CW $impr_const 0 0.0 impr C X X CH2E $impr_const 0 0.0 impr C5 X X CH2E $impr_const 0 0.0 impr C X X CH3E $impr_const 0 0.0 impr C X X CR1E $impr_const 0 0.0 impr C5 X X CRH $impr_const 0 0.0 impr CF X X CR1E $impr_const 0 0.0 impr CW X X CR1E $impr_const 0 0.0 impr CW X X CR1W $impr_const 0 0.0 impr C5 X X CRHH $impr_const 0 0.0 impr C X X H $impr_const 0 0.0 impr C X X HA $impr_const 0 0.0 impr C X X NH1 $impr_const 0 0.0 impr CW X X NH1 $impr_const 0 0.0 impr C5W X X NH1 $impr_const 0 0.0 impr C5 X X NH1 $impr_const 0 0.0 impr C X X O $impr_const 0 0.0 impr C X X OC $impr_const 0 0.0 impr C X X OH1 $impr_const 0 0.0 impr CH1E X X CH1E $impr_const 0 35.26439 impr CH1E X X CH2E $impr_const 0 35.26439 impr CH1E X X CH3E $impr_const 0 35.26439 impr CR1E X X CR1E $impr_const 0 0.0 impr CR1E X X CRH $impr_const 0 0.0 impr CR1W X X CR1E $impr_const 0 0.0 impr CR1H X X CRHH $impr_const 0 0.0 impr CR1H X X NH1 $impr_const 0 0.0 impr CR1E X X NH1 $impr_const 0 0.0 impr H X X O $impr_const 0 0.0 impr N CH1E CH2P C $impr_const 0 0.0 impr N X X CH2E $impr_const 0 0.0 impr N X X CT $impr_const 0 0.0 impr NC2 X X CT $impr_const 0 0.0 impr NC2 X X HC $impr_const 0 0.0 impr NH1 X X CH1E $impr_const 0 0.0 impr NH1 X X CH2E $impr_const 0 0.0 impr NH1 X X CH3E $impr_const 0 0.0 impr NH1 X X CT $impr_const 0 0.0 impr NH1 X X H $impr_const 0 0.0 impr NH1 X X NH1 $impr_const 0 0.0 impr NH1 X X NR $impr_const 0 0.0 impr NH2 X X H $impr_const 0 0.0 impr NR X X C5 $impr_const 0 0.0 impr NR X X CR1E $impr_const 0 0.0 impr NR X X CT $impr_const 0 0.0 impr NR X X CH3E $impr_const 0 0.0 {* nonbonding parameter section *} {* ============================ *} !! ! This uses a new form of the REPEL function: ! fVDW(R) = RCON *( Rmin ^ IREX - R ^ IREX ) ^ REXP ! ! PROLSQ uses a function of the form: ! fVDW(R) = (1 / 0.5) ^ 4 * ( Rmin ^ 4 - R ^ 4 ) ! ! The epsilon values are arbitrary since the repel function does not depend ! on epsilon. The sigma values come from converting the Van der Waals ! radii of the PROLSQ program into sigma values using the formula: ! Rmin = sigma * 2 ^ (1/6) ! Note: Prolsq decrements Van der Waals radii for non-bonded contacts ! that involve torsion angles (1:4 contacts) by .30 A, and ! hydrogen bonds (X...Y) by .2 A (X-H...Y) by .9. The former ! decrement is accomplished in X-PLOR(online) by using the ! 1-4 nonbonded terms. The latter decrement is accomplished by ! decreasing the van der Waals radius of hydrogens by 0.8 ! and that of O and N by 0.1 A. ! NBONds CUTNB=7.0 WMIN=1.5 REPEl = 1.0 REXPonent = 4 IREXponent = 1 RCONst = 16.0 TOLErance = 0.5 NBXMOD = 5 ctonnb=5.5 ctofnb=6.0 {* for consistency only, not needed for repel *} END ! type van der Waals radius correction applied for hbond evaluate ($vdw_radius_C= 3.7) evaluate ($vdw_radius_N= 3.0) {-0.1} evaluate ($vdw_radius_O= 2.9) {-0.1} evaluate ($vdw_radius_S= 3.6) evaluate ($vdw_radius_FE= 2.4) evaluate ($vdw_radius_H= 2.4) evaluate ($vdw_radius_HH= 1.6) {-0.8} evaluate ($vdw_radius_P= 3.8) evaluate ($vdw_radius_I= 4.3) evaluate ($vdw_radius_C_SP2= 3.4) { convert radii into sigmas } evaluate ($vdw_radius_C = $vdw_radius_C / 2^(1/6)) evaluate ($vdw_radius_N = $vdw_radius_N / 2^(1/6)) evaluate ($vdw_radius_O = $vdw_radius_O / 2^(1/6)) evaluate ($vdw_radius_S = $vdw_radius_S / 2^(1/6)) evaluate ($vdw_radius_FE = $vdw_radius_FE / 2^(1/6)) evaluate ($vdw_radius_H = $vdw_radius_H / 2^(1/6)) evaluate ($vdw_radius_HH = $vdw_radius_HH / 2^(1/6)) evaluate ($vdw_radius_P = $vdw_radius_P / 2^(1/6)) evaluate ($vdw_radius_I = $vdw_radius_I / 2^(1/6)) evaluate ($vdw_radius_C_SP2=$vdw_radius_C_SP2/ 2^(1/6)) { compute 1-4 sigmas } evaluate ($vdw_radius14_C = $vdw_radius_C -0.3/ 2^(1/6)) evaluate ($vdw_radius14_N = $vdw_radius_N -0.3/ 2^(1/6)) evaluate ($vdw_radius14_O = $vdw_radius_O -0.3/ 2^(1/6)) evaluate ($vdw_radius14_S = $vdw_radius_S -0.3/ 2^(1/6)) evaluate ($vdw_radius14_FE = $vdw_radius_FE -0.3/ 2^(1/6)) evaluate ($vdw_radius14_H = $vdw_radius_H -0.3/ 2^(1/6)) evaluate ($vdw_radius14_HH = $vdw_radius_HH -0.3/ 2^(1/6)) evaluate ($vdw_radius14_P = $vdw_radius_P -0.3/ 2^(1/6)) evaluate ($vdw_radius14_I = $vdw_radius_I -0.3/ 2^(1/6)) evaluate ($vdw_radius14_C_SP2=$vdw_radius_C_SP2-0.3/ 2^(1/6)) evaluate ($vdw_eps=0.1) ! ! sigma= vdw radius / 2 ^ (1/6) ! ! eps sigma eps(1:4) sigma(1:4) ! (kcal/mol) (A) (kcal/mol) (A) ! -------------------------------------------------- NONBonded H $vdw_eps $vdw_radius_HH $vdw_eps $vdw_radius14_HH NONBonded HA $vdw_eps $vdw_radius_H $vdw_eps $vdw_radius14_H ! aliphatic hydrogen NONBonded HC $vdw_eps $vdw_radius_HH $vdw_eps $vdw_radius14_HH ! h attached to charg. NONBonded HT $vdw_eps $vdw_radius_HH $vdw_eps $vdw_radius14_HH ! ! NONBonded C $vdw_eps $vdw_radius_C_SP2 $vdw_eps $vdw_radius14_C_SP2 ! carbonyl carbon NONBonded C5 $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! carbonyl carbon NONBonded C5W $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! carbonyl carbon NONBonded CF $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! carbonyl carbon NONBonded CW $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! carbonyl carbon NONBonded CY $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! carbonyl carbon NONBonded CY2 $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! carbonyl carbon NONBonded CH1E $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! \ NONBonded CH2E $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! extended carbons NONBonded CH2G $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! extended carbons NONBonded CH2P $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! extended carbons NONBonded CH3E $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! / NONBonded CR1E $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! ring carbons NONBonded CR1H $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! ring carbons NONBonded CR1W $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! ring carbons NONBonded CRHH $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! ring carbons NONBonded CRH $vdw_eps $vdw_radius_C $vdw_eps $vdw_radius14_C ! ring carbons ! NONBonded N $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N NONBonded NC2 $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N NONBonded NH1 $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N NONBonded NH2 $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N NONBonded NH3 $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N NONBonded NP $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N NONBonded NR $vdw_eps $vdw_radius_N $vdw_eps $vdw_radius14_N ! NONBonded O $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O NONBonded OC $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O NONBonded OH1 $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O NONBonded OT $vdw_eps $vdw_radius_O $vdw_eps $vdw_radius14_O ! NONBonded S $vdw_eps $vdw_radius_S $vdw_eps $vdw_radius14_S NONBonded SM $vdw_eps $vdw_radius_S $vdw_eps $vdw_radius14_S NONBonded SH1E $vdw_eps $vdw_radius_S $vdw_eps $vdw_radius14_S ! ! set echo=on message=on end