remarks remarks PARAM19.RCV remarks ========== remarks remarks Force field parameters for the prosthetic groups of the remarks photosynthetic reaction center of Rps. viridis remarks remarks (H. Treutlein et al., in: The photosynthetic bacterial remarks reaction center: Structure and dynamics, J.Breton, A.Vermeglio,Eds. remarks (Plenum Press, London 1987), p. 139. remarks remarks !! ALL PARAMETERS have been ESTIMATED from existing parameters remarks !! used for similar chemical structures inside proteins and hem groups remarks !! to reproduce the X-ray structure (3.0 A resolution, remarks !! J.Deisenhofer et al., Nature 318(1985)618 ) AS GOOD AS POSSIBLE. remarks remarks Parameters of the heme group are from John Kuriyan (26-Oct-1985). remarks The Heme group is for the liganded FE(II) state remarks with perfect D4H symmetry. The atom types used are for remarks PARAM19 and the structural parameters are taken from remarks Kitagawa, Abe and Ogoshi J.C.P. 69, (1978) pages 4526-4534 remarks remarks H. Treutlein (6-Sept-1989) set echo=false end ! Eb = Kb ( r - r0 ) **2 ! ! Kb r0 ! (Kcal/mol A**2) A ! bond FE OM 250.0 1.8! JUST A GUESS. bond FE NR 65.0 1.98! FROM NAGAI ET AL(1980) bond FE CM 258.0 1.90! FROM MB-CO X-RAY KURYAN ET AL. bond FE NP 65.0 1.96! FROM KITAGAWA ET AL. !bond LP OH2 450.0 0.080! FROM ST2 GEOMETRY bond H H 0.0 1.6329931 ! FROM ST2 GEOMETRY (for SHAKE ) !bond HT OT 450.0 0.9572 ! FROM TIPS3P GEOMETRY !bond HT HT 0.0 1.5139 ! FROM TIPS3P GEOMETRY (for SHAKE ) bond CPA CPB 450.0 1.44 ! FOLLOWING bondS ARE FROM KITAGAWA ET AL. bond CPB CPB 450.0 1.36 bond CPA NP 471.0 1.38 bond CPB CH2E 405.0 1.52 bond CPB CH3E 405.0 1.52 bond CPB CR1E 450.0 1.38 bond CPA CPM 450.0 1.37 bond CC CF 450.0 1.40 bond CC CH2E 405.0 1.52 ! HISTIDINE PARAMETERS FROM MBCO STRUCT. bond CF NB 450.0 1.40 bond NB CP 450.0 1.30 bond CP NA 450.0 1.35 bond NB FE 65.0 2.20 bond CC NA 471.0 1.40 bond NA H 405.0 0.98 ! Et = Kt ( theta - theta0 )**2 ! ! Kt theta0 ! (Kcal/mol A**2) deg. ! angle C NP FE 50.0 128.0! FORCE CONSTANT FROM PARMFIX9 angle CR1E NR FE 30.0 124.8! FORCE CONSTANT FROM PARMFIX9 angle CH1E CH2E CC 35.0 112.5 angle CH2E CC NA 20.0 117.5 angle CH2E CC CF 70.0 121.5 angle CPA NP CPA 70.0 104.0 angle CPA CPB CPB 70.0 106.4 angle CPA CPB CR1E 70.0 126.8 angle CPA CPB CH3E 65.0 126.8 angle CPA CPB CH2E 65.0 126.8 angle CPA CPM CPA 90.0 125.2 angle CPB CPB CR1E 70.0 126.8 angle CPB CPB CH3E 65.0 126.8 angle CPB CPB CH2E 65.0 126.8 angle CPB CR1E CH2E 70.0 121.5 angle CPB CH2E CH2E 70.0 113.0 angle CPB CPA CPM 70.0 124.0 angle CC CF NB 90.0 102.0 angle CC NA H 30.0 127.5 angle CF NB CP 65.0 110.0 angle CP NA CC 60.0 105.0 angle CP NA H 35.0 127.5 angle FE CM OM 35.0 180.0! F.C. FROM JONES (1972) JCP 57 2050 angle FE NP CPA 50.0 128.0 angle FE NB CP 30.0 130.0 angle FE NB CF 30.0 120.0 angle FE OM OM 0.0 180.0! DUMMY PARAMETER FOR PATCH AND ANALYSIS. angle H OH2 H 55.0 109.47122 ! TETRAHEDRAL FOR ST2'S !angle H OH2 LP 55.0 109.47122 ! TETRAHEDRAL FOR ST2'S !angle HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY angle NP FE NP 50.0 90.0 !angle NP FE NR 5.0 115.0 ! for myoglobin angle NP FE NR 5.0 90.0 ! for cytochrome angle NP FE CM 50.0 90.0! F.C. FROM JONES (1972) JCP 57 2050 angle NP FE OM 5.0 180.0! JUST A GUESS FROM EXISTING FE CM DATA angle NP CPA CPM 65.0 124.4 angle NP CPA CPB 65.0 111.6 angle NB CP NA 70.0 111.0 angle NB FE NP 50. 90.0 ! HIS/HEME/LIG LINKAGE PARAMS FOLLOW angle NB FE CM 50. 180.0 ! F.C. FROM JONES (1972) JCP 57 2050 angle NA CC CF 65.0 110.5 angle NR FE CM 5.0 180.0 angle NR FE OM 5.0 180.0! JUST A GUESS FROM EXISTING FE CM DATA !angle LP OH2 LP 55.0 109.47122 ! TETRAHEDRAL FOR ST2'S ! Ed = Kd ( 1.0 + cos( n*phi + d ) ! ! Kd n d , ! (kcal/mol A**2) deg. ! ! where d can be 0.0 or 180.0 ! 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 CH2E CC X 0.0 3 0.0! NEW HISTIDINE (WHY ZERO??) dihe X CPA CPM X 10.0 2 180.0 dihe X CPB CR1E X 1.0 2 180.0! JUST A GUESS J.K. dihe X CPB CH2E X 1.0 3 0.0! ! Ei = Ki ( omega - omega0 )**2 (for periodicity=0) ! ! Ki periodicity omega0 ! (Kcal/mol A**2) deg. ! impr NP X X NP 25.0 0 180.0 ! FOR PORPHYRIN NITROGEN PLANARIT impr CPM X X CPA 90.0 0 0.0 impr CPB X X CH2E 90.0 0 0.0 impr CPB X X CH3E 90.0 0 0.0 impr CPB X X CR1E 90.0 0 0.0 impr CC X X CH2E 90.0 0 0.0 ! NEW HIS PARAM impr NA X X H 45.0 0 0.0 impr CC X X NB 25.0 0 0.0 ! HIS OUT OF PLANE imprS impr NA X X CF 25.0 0 0.0 impr CP X X CC 25.0 0 0.0 impr CF X X CP 25.0 0 0.0 impr NB X X NA 25.0 0 0.0 impr FE X X NP 20.0 0 0.0! FROM PARMFIX9 ! Lennard-Jones parameters ! ------1-4------- ! epsilon sigma epsilon sigma ! (Kcal/mol) (A) (Kcal/mol) (A) ! NONBonded CC 0.1200 3.7418 0.1 3.3854 !HISTIDINE CG NONBonded CPA 0.1200 3.7418 0.1 3.3854 !HEME ST2 carbon NONBonded CPB 0.1200 3.7418 0.1 3.3854 !HEME ST2 carbon NONBonded CPM 0.1200 3.7418 0.1 3.3854 !HEME MESO carbon NONBonded CP 0.1200 3.7418 0.1 3.3854 !HIS RING carbon NONBonded CF 0.1200 3.7418 0.1 3.3854 !HIS RING carbon NONBonded CT 0.0262 4.4367 0.1 3.3854 ! explicit H carbon NONBonded CM 0.0262 4.4367 0.1 3.3854 !for carbon monoxide NONBonded FE 0.001 1.1582 0.001 1.1582 !NONBonded HT 0.0498 1.4254 0.0498 1.4254! TIPS3 water hydrogen NONBonded NA 0.2384 2.8509 0.2384 2.8509 NONBonded NB 0.2384 2.8509 0.2384 2.8509 !NONBonded OT 0.1591 2.8509 0.1591 2.8509! TIPS3 water oxigeN bond CH2E CPM 225.0 1.54! bond length from x-ray bond CH2E OS 292.0 1.38! inference from CH3E - OS bond CPA C 450.0 1.36! bond length from x-ray bond CPA CH1E 405.0 1.52! inference from CPB - CH2E bond CPA CH2E 405.0 1.53! bond length from x-ray bond CPA CH3E 405.0 1.54! bond length from x-ray bond CPB C 450.0 1.36! bond length from x-ray bond CPB CH1E 405.0 1.52! inference from CPB - CH2E bond CR1E CH3E 225.0 1.53! bond length from x-ray bond MG NP 65.0 2.00! inference from FE - NP and x-ray bond NH1 CPA 471.0 1.38! from CPA - NP bond NR MG 65.0 2.23! inference from FE - NR AND X-RAY bond S CH1E 450.0 1.79! bond length from x-ray bond S FE 450.0 2.12! bond length from x-ray bond OC FE 250.0 2.09! just a guess and x-ray bond CH3E N 422.0 1.45! from CH1(2)E - N and x-ray bond ON N 400.0 1.22! from x-ray bond CPM CPM 225.0 1.53! from CH3E - CH3E bond CPA O 292.0 1.23! x-ray and C-O bond CPB OS 292.0 1.34! x-ray bond CR1E O 292.0 1.23! x-ray !bond NR MG 65.0 1.98! inference from FE - NR angle CH1E C CH2E 70.0 120.0 angle CH1E C CH3E 70.0 120.0 angle CH1E C CPA 65.0 110.0 angle CH1E C CR1E 65.0 130.0 angle CH3E C CH2E 70.0 120.0 angle CPA C CPA 65.0 125.0 angle CPA C CR1E 65.0 123.5 angle CPB C CH1E 65.0 103.5! angle from x-ray angle CPB C CH3E 65.0 120.0! standart geometry angle CPB C O 65.0 130.0! angle from x-ray angle CR1E C CH3E 70.0 120.0 angle OC C OS 70.0 121.0! !angle CH1E C CPA 65.0 117.4! FROM X-RAY, MEAN OF TWO POSSIBLE VALUES !angle CH1E C CPA 65.0 105.0 !angle CPB C CH2E 65.0 112.9! angle from x-ray angle C CH1E C 65.0 107.0! angle from x-ray angle C CH1E CPM 65.0 111.0! angle from x-ray angle CH2E CH1E CH2E 45.0 112.5 angle CPA CH1E C 65.0 105.0! angle from x-ray angle CPA CH1E CH1E 65.0 105.0! angle from x-ray angle CPA CH1E CH2E 65.0 118.0! angle from x-ray angle CPA CH1E CH3E 65.0 112.0! angle from x-ray angle CPB CH1E CH3E 65.0 112.9! angle from x-ray angle S CH1E CH3E 65.0 110.0! angle from x-ray angle S CH1E CPB 65.0 110.5! angle from x-ray angle OS CH2E CH1E 65.0 111.5! angle CPA CH2E CH2E 65.0 112.5! angle CH2E CH2E CPM 65.0 111.0! angle CH2E CH2E CR1E 70.0 120.0 angle OS CH2E CPM 65.0 112.0 angle C CH2E CPM 65.0 105.0! angle CH1E CPA CPM 70.0 124.5! angle from x-ray ? angle NH1 CPA CPM 65.0 124.4! from NP - CPA - CPM angle NH1 CPA CPB 65.0 111.6! from NP - CPA - CPB angle NH1 CPA C 65.0 126.5! angle NP CPA CH1E 65.0 110.0! angle from x-ray angle CH1E CPA C 70.0 125.0! angle from x-ray angle CPM CPA CH3E 65.0 124.5! angle CPM CPA CH2E 65.0 122.5! angle CH3E CPA CH2E 65.0 112.6! angle CH3E CPA CH3E 65.0 112.6! angle NP CPA C 65.0 126.5! angle CPB CPA C 65.0 120.0! angle C CPA CPM 70.0 124.5 angle CPA CPB C 70.0 117.5! angle from x-ray angle CPA CPB CH1E 70.0 117.5! angle from x-ray angle CPB CPB C 70.0 134.0! angle from x-ray angle CPB CPB CH1E 70.0 134.0! angle from x-ray angle CH2E CPM CPA 65.0 131.0! angle C CR1E CH3E 90.0 125.0 angle S FE NP 65.0 90.0! angle from x-ray !angle NR MG NP 5.0 115.0! inference from NR - FE - NP angle NP MG NP 50.0 90.0! inference from NP - FE - NP angle NR MG NP 5.0 90.0! inference from NR FE NP and symetry angle CPA NH1 CPA 70.0 104.0! from CPA - NP - CPA angle CPA NH1 H 30.0 128.0! from C - NH1 - H and geometry angle MG NP CPA 50.0 128.0! inference from FE - NP - CPA angle CR1E NR MG 30.0 124.8! inference from CR1E - NR - MG angle C OS CH2E 65.0 113.5! angle CH2E S CH1E 65.0 101.3! angle from x-ray angle CH2E S FE 65.0 128.8! angle from x-ray angle CH3E S FE 65.0 123.2! angle from x-ray angle OC C OH1 85.0 122.2! from x-ray and OC C OC and O C OH1 angle C OC FE 5.0 87.5! x-ray and guess angle CH3E N CH3E 60.0 102.0! X-RAY angle CH3E N ON 60.0 110.0! X-RAY angle ON N CH2E 60.0 110.0! X-RAY angle C C OS 65.0 119.0! from C C OH1/O angle CPM CPM CPM 65.0 120.0! x-ray angle CPM CPA CPM 65.0 120.0! x-ray angle CPM CPM CPA 65.0 120.0! x-ray angle CPB CPA O 65.0 120.0! X-RAY angle CPB CPA CPB 65.0 120.0! X-RAY angle CPA CPB OS 65.0 120.0! X-RAY angle CPB CPB OS 65.0 120.0! X-RAY angle CPB OS CH3E 65.0 120.0! X-RAY angle CPB CH2E CPM 65.0 112.0! X-RAY angle O CR1E NH1 80.0 111.6! X-RAY angle CR1E NH1 CH1E 65.0 109.5! X-RAY AND CH1E-NH3-CH2E angle CPB CR1E CR1E 90.0 119.0! FROM C-CR1E-CR1E dihe CPB CPB C CH3E 1.0 2 180.0 dihe CH2E C C CH3E 1.0 2 180.0 dihe CH3E C C O 1.0 2 180.0 dihe C C C C 1.0 2 180.0 dihe C C C O 1.0 2 180.0 dihe C C C CH2E 1.0 2 180.0 dihe C CR1E CR1E CR1E 1.0 2 180.0 dihe CR1E CR1E CR1E CR1E 1.0 2 180.0 dihe C CH2E CR1E C 1.0 2 180.0 dihe CH2E CH2E CR1E C 1.0 2 180.0 dihe CH2E S FE NP 0.05 4 0.0 dihe X OS CH2E X 0.5 3 0.0 dihe X CH2E CPM X 1.0 3 0.0 dihe CPM CPA CH2E CH2E 1.0 3 0.0 dihe CH2E CH2E CPM CPA 1.0 3 0.0 dihe CPA C CPA NH1 1.0 2 180.0 dihe CPA C CPA NP 1.0 2 180.0 !dihe CPB CPB C CH2E 1.0 3 0.0 dihe CPB CPB CH1E CH3E 1.0 3 0.0 !dihe CH2E S C CPB 1.0 3 0.0 dihe CH2E S CH1E CPB 1.0 3 0.0 !dihe C CH2E CPM CPA 0.0 2 0.0 !dihe C OS CH2E CPM !dihe C OS CH2E CH1E 0.0 2 0.0 !dihe OS CH2E CPM CPA dihe X CPA NP X 8.2 2 180.0 !from X-C-N-X for TOPRC.MOD !!!! dihe CPA NH1 CPA CPM 8.2 2 180.0 !from X-C-N-X dihe CPA NH1 CPA C 8.2 2 180.0 !from X-C-N-X dihe CPA CPA CPB C 2.5 2 180.0 !from C-C dihe CPA CPB CPA C 2.5 2 180.0 !from C-C dihe X CPM CPM X 1.6 3 0.0 !CH1E-CH1E dihe X CPA CPB X 2.5 2 180.0 !C-C dihe X CPB CPB X 2.5 2 180.0 !C-C dihe CPA CPB OS CH3E 1.8 2 180.0 !C-OS x-ray dihe X CR1E NH1 X 0.3 3 0.0!FROM X-CH1E-NH1-X dihe CPB CR1E CR1E CR1E 1.0 2 180.0!FROM C-... (S.O.) impr CPB X X C 50.0 0 0.0 impr CPA X X NP 50.0 0 0.0 impr CPA C CPB NH1 50.0 0 0.0 impr CH1E X X C 50.0 0 0.0 impr MG CPA CPA NP 50.0 0 0.0 impr CPB CPA C CPB 50.0 0 0.0! 180.0 ! ??????????? impr C X X CPA 50.0 0 0.0 impr C CPA NP CPA 50.0 0 180.0 impr CPM CPA NP CPA 50.0 0 180.0 impr CPA CPM CH2E CH3E 50.0 0 0.0 impr CPA CPA CH1E CH1E 50.0 0 180.0 impr CH1E CPM C C 50.0 0 0.0 impr CH1E C CPA C 50.0 0 0.0 impr CH1E C C C 50.0 0 35.264 impr CPB CPB CPA CH1E 50.0 0 0.0 impr CH3E N ON CH3E 55.0 0 -110.0! X-RAY impr C C C OS 100.0 0 0.0 impr CPB X X CPB 25.0 0 0.0 !FROM C X X C impr CPA X X CPA 100.0 0 0.0 !FROM C X X C impr CPA CPB CPB O 100.0 0 0.0 !FROM C X X O impr CPB CPB CPA OS 100.0 0 0.0 !FROM C X X O/OC !impr CPB CPB CPA C 50.0 0 0.0 !impr CPA CPM CPB NP 50.0 0 0.0 !impr C O CH3E CPB 0.0 0 180.0 ! ??????????? !impr C NP CH1E CPA !impr C NP CPB CPA !impr CPA C CPB NP !impr C CPA CH1E CPA !impr CH1E OC OS C 50.0 0 0.0! 180.0 ! ??????????? NONBonded MG 0.2000 2.8509 0.2000 2.8509 ! G U E S S NONBonded ON 0.1591 2.8509 0.1591 2.8509 ! from O NONBonded EL 0.0250 0.7000 0.0250 0.7000 set echo=true end