remarks file toppar/protein.param remarks protein parameters with Lennard-Jones van der Waals parameters remarks for crystallographic structure determination ! ! Please cite the following reference when using these parameters: ! Engh, R.A. and Huber, R. (1991). Accurate Bond and ! Angle Parameters for X-ray Protein-Structure Refinement, ! Acta Cryst. A47, 392-400. ! ! set echo=false end checkversion 1.2 bond C5W CW 1827.161 1.433 ! 0.018 bond CW CW 2048.443 1.409 ! 0.017 bond C CH1E 1342.404 1.525 ! 0.021 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 C CH2G 1827.161 1.516 ! 0.010 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 bond C N 2312.500 1.341 ! 0.016 bond C NC2 1827.161 1.326 ! 0.018 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 bond C NH2 1342.404 1.328 ! 0.021 bond C5 NR 2048.443 1.371 ! 0.017 bond C O 1480.000 1.231 ! 0.020 bond C OC 1639.889 1.249 ! 0.019 bond CY2 OH1 1342.404 1.376 ! 0.021 bond C OH1 1223.141 1.304 ! 0.022 bond CH1E CH1E 812.071 1.540 ! 0.027 bond CH1E CH2E 1480.000 1.530 ! 0.020 bond CH1E CH3E 543.618 1.521 ! 0.033 bond CH1E N 2631.111 1.466 ! 0.015 bond CH1E NH1 1639.889 1.458 ! 0.019 bond CH1E NH3 1342.404 1.491 ! 0.021 bond CH1E OH1 2312.500 1.433 ! 0.016 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 bond CH2E CH3E 389.218 1.513 ! 0.039 bond CH2P N 3020.408 1.473 ! 0.014 bond CH2P NH3 3020.408 1.473 ! 0.014 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 bond CH2E NH3 657.778 1.489 ! 0.030 bond CH3E NH3 657.778 1.489 ! 0.030 taken from CH2E parameter PDA 6/98 bond CH2G NH3 657.778 1.489 ! 0.030* bond CH2E OH1 1480.000 1.417 ! 0.020 bond CH2E S 1480.000 1.822 ! 0.020 bond CH2E SE 500.000 1.930 ! PDA & data from Mike Carson (UAB) 6/99 bond CH2E SM 512.111 1.803 ! 0.034 bond CH2E SH1E 543.618 1.808 ! 0.033 bond CH3E SE 500.000 1.930 ! PDA & data from Mike Carson (UAB) 6/99 bond CH3E SM 170.066 1.791 ! 0.059 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 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 bond CR1E NR 657.778 1.382 ! 0.030 bond S S 2410.110 2.030 ! 0.008 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 !* angle C5W CW CW 1349.600 107.200 !1.2 angle CW C5W CH2E 991.543 126.800 !1.4 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 angle CW CW NH1 1149.956 107.400 !1.3 angle CH1E C N 863.744 116.900 !1.5 angle CH1E C NH1 485.856 116.200 !2.0 angle CH1E C O 672.465 120.800 !1.7 angle CH1E C OC 310.948 117.000 !2.5 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 angle CH2E C N 440.686 118.200 !2.1 angle CH2G C N 440.686 118.200 !2.1 * 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 * angle CH2E C NH2 863.744 116.400 !1.5 angle CH2E C5 NR 863.744 121.600 !1.5 angle CH2E C O 485.856 120.800 !2.0 angle CH2G C O 440.686 120.800 !2.1 angle CH2E C OC 367.377 118.400 !2.3 angle CH2G C OC 367.377 118.400 !2.3 * 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 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 angle CR1E C5 NR 1943.424 109.200 !0.7 HISE, taken as 1.0 angle CR1E CY2 OH1 215.936 119.900 !3.0 angle N C O 991.543 122.000 !1.4 angle NC2 C NC2 599.823 119.700 !1.8 angle NC2 C NH1 538.345 120.000 !1.9 angle NH1 C O 759.150 123.000 !1.6 angle NH2 C O 1943.424 122.600 !1.0 angle OC C OC 337.400 122.900 !2.4 angle C CH1E CH1E 401.534 109.100 !2.2 angle C CH1E CH2E 538.345 110.100 !1.9 angle C CH1E CH3E 863.744 110.500 !1.5 angle C CH1E N 310.948 111.800 !2.5 angle C CH1E NH1 247.886 111.200 !2.8 angle C CH1E NH3 247.886 111.200 !2.8 * angle CH1E CH1E CH2E 672.465 110.400 !1.7 angle CH1E CH1E CH3E 672.465 110.500 !1.7 angle CH1E CH1E NH1 672.465 111.500 !1.7 angle CH1E CH1E NH3 672.465 111.500 !1.7 * angle CH1E CH1E OH1 863.744 109.600 !1.5 angle CH2E CH1E CH3E 215.936 110.700 !3.0 angle CH2E CH1E N 1606.136 103.000 !1.1 angle CH2E CH1E NH1 672.465 110.500 !1.7 angle CH2E CH1E NH3 672.465 110.500 !1.7 * angle CH3E CH1E CH3E 401.534 110.800 !2.2 angle CH3E CH1E NH1 863.744 110.400 !1.5 angle CH3E CH1E NH3 672.465 110.500 !1.7 * angle CH3E CH1E OH1 485.856 109.300 !2.0 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 angle C CH2E CH2E 672.465 112.600 !1.7 angle C CH2G NH1 231.085 112.500 !2.9 angle C CH2G NH3 231.085 112.500 !2.9 * angle CH1E CH2E CH1E 158.647 116.300 !3.5 angle CH1E CH2E CH2P 538.345 104.500 !1.9 angle CH1E CH2E CH2E 485.856 114.100 !2.0 angle CH1E CH2E CH3E 440.686 113.800 !2.1 angle CH1E CH2E OH1 485.856 111.100 !2.0 angle CH1E CH2E S 367.377 114.400 !2.3 angle CH1E CH2E SH1E 367.377 114.400 !2.3 * angle CH2E CH2E CH2E 367.377 111.300 !2.3 angle CH2E CH2P CH2P 189.788 106.100 !3.2 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 angle CH2E CH2E NH1 401.534 112.000 !2.2 angle CH2E CH2E NH3 189.788 111.900 !3.2 angle CH2E CH2E SE 215.936 112.700 ! guess based on methionine PDA 9/16/97 angle CH2E CH2E SM 215.936 112.700 !3.0 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 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 angle C5 CR1E NR 367.377 109.500 !2.3 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 angle NH1 CRHH NH1 1943.424 108.400 !1.0 angle NH1 CRH NR 1149.956 111.700 !1.3 HisE, applied also to HisD angle C N CH1E 77.737 122.600 !5.0 angle C N CH2P 115.611 125.000 !4.1 angle HC NH3 CH2P 500. 125.000 !4.1 !added ATB 5/19/93 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 angle C NH1 CH1E 599.823 121.700 !1.8 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 * 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 angle CRHH NH1 CR1H 1943.424 109.000 !1.0 angle CRH NH1 CR1E 1149.956 106.900 !1.3 angle C5 NR CRH 1943.424 105.600 !1.0 HisE angle CR1E NR CRH 215.936 107.000 !3.0, HisD, weak statistics angle CH2E SE CH3E 400.000 98.900 ! PDA & data from Mike Carson (UAB) 6/99 angle CH2E SM CH3E 401.534 100.900 !2.2 angle CH2E S S 599.823 103.800 !1.8 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 CH2E NH3 CH3E 35.0 109.5 !* taken from HC parameter PDA 6/98 angle CH2G NH3 HC 35.0 109.5 !* angle HC NH3 HC 40.0 109.5 !* angle CH3E NH3 CH3E 40.0 109.5 !* taken from HC parameter PDA 6/98 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 !* ! SEE ABOVE REGARDING DIHEDRALS { Weis 5/11/92 scaled up 3x for consistency with bond and angle parameters.} { Note: didn't change commented lines. } dihe CH1E C N CH1E 1250.0 2 180.0! reduced -> to allow cis PRO dihe CH2E C N CH1E 1250.0 2 180.0 dihe CH2G C N CH1E 1250.0 2 180.0 !dihe CR1E C C CR1E 100.0 2 180.0 dihe CR1E CW CW CR1E 300.0 2 180.0 dihe CR1E CW CW CR1W 300.0 2 180.0 !dihe CR1E C C C 100.0 2 180.0 dihe CR1W CW CW C5W 300.0 2 180.0 !dihe CR1E C C NH1 100.0 2 180.0 dihe CR1E CW CW NH1 300.0 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 30.0 2 180.0 !dihe X C CT X 0.0 3 0.0 dihe X C N X 24.6 2 180.0 dihe X C NC2 X 24.6 2 180.0 dihe X C NH1 X 1250.0 1 0.0 dihe X C NH2 X 24.6 2 180.0 !dihe X C OH1 X 1.8 2 180.0 dihe X CY2 OH1 X 5.4 2 180.0 dihe X CH1E CH1E X 4.8 3 0.0 dihe X CH1E CH2E X 4.8 3 0.0 dihe X CH1E N X 0.9 3 0.0 dihe X CH1E NH1 X 0.9 3 0.0 dihe X CH1E NH2 X 5.4 3 0.0 dihe X CH1E NH3 X 1.8 3 0.0 dihe X CH1E OH1 X 1.5 3 0.0 dihe X CH2E CH2E X 4.8 3 0.0 dihe X CH2E CH2P X 4.8 3 0.0 dihe X CH2P CH2P X 4.8 3 0.0 dihe X CH2E N X 0.9 3 0.0 dihe X CH2P N X 0.9 3 0.0 dihe X CH2P NH3 X 0.9 3 0.0 dihe X CH2E NH1 X 0.9 3 0.0 dihe X CH2G NH1 X 0.9 3 0.0 dihe X CH2E NH2 X 1.8 3 0.0 dihe X CH2E NH3 X 1.8 3 0.0 dihe X CH2G NH3 X 1.8 3 0.0 dihe X CH2E OH1 X 1.5 3 0.0 dihe X CH2E S X 3.6 2 0.0 dihe X CH2E SE X 3.6 2 0.0 ! guess from MET, PDA 9/16/97 dihe X CH2E SM X 3.6 2 0.0 !dihe X CT CT X 1.6 3 0.0 !dihe X CT N X 0.3 3 0.0 !dihe X CT NC2 X 0.3 3 0.0 !dihe X CT NH1 X 0.3 3 0.0 !dihe X CT NH2 X 0.6 3 0.0 !dihe X CT NH3 X 0.6 3 0.0 !dihe X CT OH1 X 0.5 3 0.0 !dihe X CT S X 1.2 2 0.0 !dihe X FE NR X 0.05 4 0.0 !dihe X FE CM X 0.05 4 0.0 !dihe X FE OM X 0.00 4 0.0 dihe X S S X 12.0 2 0.0 dihe CH2E NH1 C NC2 300.0 2 180. ! SEE ABOVE REGARDING IMPROPERS { Weis 5/11/92 scaled up 3x for consistency with bond and angle parameters.} { Note: didn't change commented lines. } impr C C CR1E CH2E 750.0 0 0.0 impr C CR1E C CH2E 750.0 0 0.0 impr C5W CR1E CW CH2E 750.0 0 0.0 impr C CR1E CR1E CH2E 750.0 0 0.0 impr CF CR1E CR1E CH2E 750.0 0 0.0 impr CY CR1E CR1E CH2E 750.0 0 0.0 impr C CR1E NH1 CH2E 750.0 0 0.0 impr C5 NH1 CR1E CH2E 750.0 0 0.0 impr C5 NH1 CR1H CH2E 750.0 0 0.0 impr C5 NH1 CRHH CH2E 750.0 0 0.0 impr C CR1E CR1E OH1 750.0 0 0.0 impr CY2 CR1E CR1E OH1 750.0 0 0.0 impr C H H NH2 135.0 0 0.0 impr C OC OC CH1E 300.0 0 0.0 impr C OC OC CH2E 300.0 0 0.0 impr C X X C 75.0 0 0.0 impr CY X X CY2 75.0 0 0.0 impr C5W X X CW 75.0 0 0.0 impr C X X CH2E 270.0 0 0.0 impr C5 X X CH2E 270.0 0 0.0 impr C X X CH3E 270.0 0 0.0 impr C X X CR1E 750.0 0 0.0 impr C5 X X CRH 750.0 0 0.0 impr CF X X CR1E 750.0 0 0.0 impr CW X X CR1E 750.0 0 0.0 impr CW X X CR1W 750.0 0 0.0 impr C5 X X CRHH 750.0 0 0.0 impr C X X H 225.0 0 0.0 impr C X X HA 225.0 0 0.0 impr C X X NH1 300.0 0 0.0 impr CW X X NH1 300.0 0 0.0 impr C5W X X NH1 300.0 0 0.0 impr C5 X X NH1 300.0 0 0.0 impr C X X O 300.0 0 0.0 impr C X X OC 300.0 0 0.0 impr C X X OH1 450.0 0 0.0 impr CH1E X X CH1E 300.0 0 35.26439 impr CH1E X X CH2E 300.0 0 35.26439 impr CH1E X X CH3E 300.0 0 35.26439 impr CR1E X X CR1E 750.0 0 0.0 impr CR1E X X CRH 750.0 0 0.0 impr CR1W X X CR1E 750.0 0 0.0 impr CR1H X X CRHH 750.0 0 0.0 impr CR1H X X NH1 750.0 0 0.0 impr CR1E X X NH1 750.0 0 0.0 !impr FE X X NP 20.0 0 0.0 impr H X X O 135.0 0 0.0 !impr N CH1E CH2E C 45.0 0 0.0 impr N CH1E CH2P C 135.0 0 0.0 impr N X X CH2E 135.0 0 0.0 impr N X X CT 135.0 0 0.0 impr NC2 X X CT 135.0 0 0.0 impr NC2 X X HC 135.0 0 0.0 impr NH1 X X CH1E 135.0 0 0.0 impr NH1 X X CH2E 135.0 0 0.0 impr NH1 X X CH3E 135.0 0 0.0 impr NH1 X X CT 135.0 0 0.0 impr NH1 X X H 135.0 0 0.0 impr NH1 X X NH1 75.0 0 0.0 impr NH1 X X NR 75.0 0 0.0 impr NH2 X X H 135.0 0 0.0 impr NR X X C5 75.0 0 0.0 impr NR X X CR1E 750.0 0 0.0 impr NR X X CT 75.0 0 0.0 impr NR X X CH3E 75.0 0 0.0 impr HC NC2 C NH1 135.0 0 0.0 ! ARG hydrogens PDA 4/98 {* nonbonding parameter section *} {* ============================ *} nbonds { This statement specifies the } atom cdie shift eps=1.0 e14fac=0.4 { nonbonded interaction energy } cutnb=7.5 ctonnb=6.0 ctofnb=6.5 { options. Note the reduced } nbxmod=5 vswitch tolerance=0.5 { nonbonding cutoff to save } end { some CPU time } ! eps sigma eps(1:4) sigma(1:4) ! (kcal/mol) (A) ! --------------------------------------- NONBonded H 0.0498 1.4254 0.0498 1.4254 NONBonded HA 0.0450 2.6157 0.0450 2.6157 !- charged group. NONBonded HC 0.0498 1.0691 0.0498 1.0691 ! Reduced vdw radius ! NONBonded C 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon NONBonded C5 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon NONBonded C5W 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon NONBonded CF 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon NONBonded CW 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon NONBonded CY 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon NONBonded CY2 0.1200 3.7418 0.1000 3.3854 ! carbonyl carbon NONBonded CH1E 0.0486 4.2140 0.1000 3.3854 ! \ NONBonded CH2E 0.1142 3.9823 0.1000 3.3854 ! extended carbons NONBonded CH2G 0.1142 3.9823 0.1000 3.3854 ! extended carbons NONBonded CH2P 0.1142 3.9823 0.1000 3.3854 ! extended carbons NONBonded CH3E 0.1811 3.8576 0.1000 3.3854 ! / NONBonded CR1E 0.1200 3.7418 0.1000 3.3854 ! ring carbons NONBonded CR1H 0.1200 3.7418 0.1000 3.3854 ! ring carbons NONBonded CR1W 0.1200 3.7418 0.1000 3.3854 ! ring carbons NONBonded CRHH 0.1200 3.7418 0.1000 3.3854 ! ring carbons NONBonded CRH 0.1200 3.7418 0.1000 3.3854 ! ring carbons ! NONBonded N 0.2384 2.8509 0.2384 2.8509 NONBonded NC2 0.2384 2.8509 0.2384 2.8509 NONBonded NH1 0.2384 2.8509 0.2384 2.8509 NONBonded NH2 0.2384 2.8509 0.2384 2.8509 NONBonded NH3 0.2384 2.8509 0.2384 2.8509 NONBonded NP 0.2384 2.8509 0.2384 2.8509 NONBonded NR 0.2384 2.8509 0.2384 2.8509 ! NONBonded O 0.1591 2.8509 0.1591 2.8509 NONBonded OC 0.6469 2.8509 0.6469 2.8509 NONBonded OH1 0.1591 2.8509 0.1591 2.8509 ! NONBonded S 0.0430 3.3676 0.0430 3.3676 NONBonded SM 0.0430 3.3676 0.0430 3.3676 NONBonded SH1E 0.0430 3.3676 0.0430 3.3676 NONBonded SE 0.0430 3.5100 0.0430 3.5100 ! guess PDA 9/16/97 ! set echo=true end