remark file parallhdg.pro version 3.00 remark geometric energy function parameters for distance geometry and remark simulated annealing. set message off echo off end ! ! Authors: Michael Nilges, Yale University, EMBL ! John Kuszewski, Yale University ! This parameter file was originally derived from the CHARMM parameter. ! PARMALLH6. ! ! The values of the force constants are somewhat arbitrary. The aim ! is to make ALL of them stiff compared to the weight on the NOE ! term. The force constant for the angles is adjusted such that the ! 1-3 distance is approximately as well maintained as the 1-2 distance. ! ! All angles around tetrahedral carbons (type CT) have been set ! to the ideal methane value, 109.5 degrees, by JK. ! this has been modified. see below. ! ! MN 1992 ! the non-bonded parameters have been modified such that they ! give approximately the large DISMAN radii with repel=0.9, ! and somewhat smaller than the small DISMAN radii (or the DISGEO radii) with ! repel= 0.75. At repel=0.8, the DISGEO radii are reproduced, apart from ! N. Suggested value is 0.78. ! ! MN 24-10-95 (version 2.00) ! the ideal values from the CSDX file have been mapped onto the PARALLHDG file ! in the following way: ! 1 A protein structure was minimized with PARCSDX (bonds and angles only) ! 2 New parameters were derived from this structure with PARAMETER LEARN ! 3 The protein structure was iteratively refined (bonds, angles, impropers) ! and new parameters generated with PARAMETER LEARN ! without NOEs and non-bonded, the final rms difference was 0.012 for angles. BOND C C 1000.000 1.380 BOND C CA 1000.000 1.379 BOND C CT 1000.000 1.523 BOND C HA 1000.000 1.080 BOND C N 1000.000 1.341 BOND C NC2 1000.000 1.326 BOND C NH1 1000.000 1.329 BOND C NH2 1000.000 1.328 BOND C NP 1000.000 1.305 BOND C NR 1000.000 1.305 BOND C O 1000.000 1.231 BOND C OC 1000.000 1.249 BOND C OH 1000.000 1.376 BOND CA CA 1000.000 1.385 BOND CA CB 1000.000 1.397 BOND CA CN 1000.000 1.388 BOND CA CT 1000.000 1.508 BOND CA HA 1000.000 1.080 BOND CB CN 1000.000 1.404 BOND CB CX 1000.000 1.443 BOND CC CT 1000.000 1.497 BOND CC CV 1000.000 1.358 BOND CC NA 1000.000 1.371 BOND CN NA 1000.000 1.361 BOND CP CP 1000.000 1.509 BOND CP CT 1000.000 1.495 BOND CP HA 1000.000 1.080 BOND CP N 1000.000 1.470 BOND CP NH3 1000.000 1.470 BOND CR HA 1000.000 1.080 BOND CR NA 1000.000 1.313 BOND CR NB 1000.000 1.323 BOND CT CT 1000.000 1.526 BOND CT CX 1000.000 1.498 BOND CT HA 1000.000 1.080 BOND CT N 1000.000 1.469 BOND CT NC2 1000.000 1.490 BOND CT NH1 1000.000 1.459 BOND CT NH2 1000.000 1.490 BOND CT NH3 1000.000 1.490 BOND CT OH 1000.000 1.419 BOND CT S 1000.000 1.800 BOND CV HA 1000.000 1.080 BOND CV NB 1000.000 1.383 BOND CW CX 1000.000 1.368 BOND CW HA 1000.000 1.080 BOND CW NA 1000.000 1.367 BOND H NA 1000.000 0.980 BOND H NH1 1000.000 0.980 BOND H NH2 1000.000 0.980 BOND H OH 1000.000 0.960 BOND H S 1000.000 0.960 BOND HC NC2 1000.000 1.000 BOND HC NH1 1000.000 0.980 BOND HC NH3 1000.000 1.040 BOND S S 1000.000 2.020 BOND YH YH 1000.000 1.800 ANGLe C C C 500.00 126.5000 ANGLe C C CT 500.00 122.3000 ANGLe C C HA 500.00 120.0000 ANGLe C C NH1 500.00 108.6000 ANGLe C C NP 500.00 109.5000 ANGLe C C NR 500.00 109.5000 ANGLe C C OH 500.00 122.3000 ANGLe C CA CA 500.00 119.7990 ANGLe C CA HA 500.00 120.1011 ANGLe C CT CT 500.00 110.0085 ANGLe C CT HA 500.00 109.0271 ANGLe C CT N 500.00 111.7470 ANGLe C CT NH1 500.00 110.5175 ANGLe C CT NH2 500.00 109.5000 ANGLe C CT NH3 500.00 110.4372 ANGLe C N CP 500.00 125.1177 ANGLe C N CT 500.00 122.6724 ANGLe C NC2 CT 500.00 107.5000 ANGLe C NC2 HC 500.00 119.9950 ANGLe C NH1 C 500.00 119.1000 ANGLe C NH1 CT 500.00 121.7065 ANGLe C NH1 H 500.00 119.0748 ANGLe C NH2 H 500.00 118.1727 ANGLe C NH3 CP 500.00 125.0000 ANGLe C NP C 500.00 106.0000 ANGLe C NR C 500.00 106.0000 ANGLe C OH H 500.00 109.5141 ANGLe CA C CA 500.00 120.3911 ANGLe CA C OH 500.00 119.8045 ANGLe CA CA CA 500.00 120.1097 ANGLe CA CA CB 500.00 119.4689 ANGLe CA CA CN 500.00 118.1144 ANGLe CA CA CT 500.00 120.1504 ANGLe CA CA HA 500.00 119.9656 ANGLe CA CB CN 500.00 118.4677 ANGLe CA CB CX 500.00 134.2066 ANGLe CA CN CB 500.00 122.3220 ANGLe CA CN NA 500.00 131.0384 ANGLe CA CT CT 500.00 113.0808 ANGLe CA CT HA 500.00 108.7281 ANGLe CB CA HA 500.00 120.2677 ANGLe CB CN NA 500.00 106.6397 ANGLe CB CX CT 500.00 126.8086 ANGLe CB CX CW 500.00 106.3595 ANGLe CC CT CT 500.00 112.9974 ANGLe CC CT HA 500.00 108.7477 ANGLe CC CV HA 500.00 126.1153 ANGLe CC CV NB 500.00 107.7663 ANGLe CC NA CR 500.00 111.0179 ANGLe CC NA H 500.00 124.4819 ANGLe CN CA HA 500.00 120.9422 ANGLe CN CB CX 500.00 107.3257 ANGLe CN NA CW 500.00 110.8641 ANGLe CN NA H 500.00 124.5629 ANGLe CP CP CT 500.00 107.4824 ANGLe CP CP HA 500.00 110.1721 ANGLe CP CP N 500.00 104.2149 ANGLe CP CP NH3 500.00 103.2000 ANGLe CP CT CT 500.00 105.3466 ANGLe CP CT HA 500.00 110.2676 ANGLe CP N CT 500.00 112.2099 ANGLe CP NH3 CT 500.00 112.0000 ANGLe CP NH3 HC 500.00 109.4882 ANGLe CR NA H 500.00 124.5003 ANGLe CR NB CV 500.00 108.2574 ANGLe CT C N 500.00 116.9287 ANGLe CT C NH1 500.00 116.2037 ANGLe CT C NH2 500.00 116.4810 ANGLe CT C O 500.00 120.8080 ANGLe CT C OC 500.00 118.4693 ANGLe CT C OH 500.00 117.5000 ANGLe CT CC CV 500.00 131.7850 ANGLe CT CC NA 500.00 123.3052 ANGLe CT CP HA 500.00 109.8579 ANGLe CT CT CT 500.00 111.2078 ANGLe CT CT CX 500.00 112.8482 ANGLe CT CT HA 500.00 109.0239 ANGLe CT CT N 500.00 103.8131 ANGLe CT CT NC2 500.00 109.5000 ANGLe CT CT NH1 500.00 110.0496 ANGLe CT CT NH2 500.00 104.0000 ANGLe CT CT NH3 500.00 111.3108 ANGLe CT CT OH 500.00 110.4500 ANGLe CT CT S 500.00 112.6705 ANGLe CT CX CW 500.00 126.8319 ANGLe CT N CT 500.00 119.0000 ANGLe CT NC2 HC 500.00 107.5000 ANGLe CT NH1 H 500.00 119.2187 ANGLe CT NH2 H 500.00 120.0000 ANGLe CT NH3 HC 500.00 109.4882 ANGLe CT OH H 500.00 109.5106 ANGLe CT S CT 500.00 100.8884 ANGLe CT S H 500.00 108.0013 ANGLe CT S S 500.00 104.2000 ANGLe CV CC NA 500.00 104.9098 ANGLe CW NA H 500.00 124.5730 ANGLe CX CT HA 500.00 108.7736 ANGLe CX CW HA 500.00 125.5967 ANGLe CX CW NA 500.00 108.8111 ANGLe H NH1 H 500.00 107.5000 ANGLe H NH2 H 500.00 123.6545 ANGLe HA C NH1 500.00 120.0000 ANGLe HA C NH2 500.00 120.0000 ANGLe HA C NR 500.00 120.0000 ANGLe HA C O 500.00 120.0000 ANGLe HA CP HA 500.00 110.2129 ANGLe HA CP N 500.00 110.4797 ANGLe HA CP NH3 500.00 109.5000 ANGLe HA CR NA 500.00 125.9744 ANGLe HA CR NB 500.00 125.9770 ANGLe HA CT HA 500.00 109.2835 ANGLe HA CT N 500.00 110.5395 ANGLe HA CT NC2 500.00 109.5000 ANGLe HA CT NH1 500.00 108.9002 ANGLe HA CT NH3 500.00 109.0679 ANGLe HA CT OH 500.00 109.2219 ANGLe HA CT S 500.00 109.1100 ANGLe HA CV NB 500.00 126.1184 ANGLe HA CW NA 500.00 125.5922 ANGLe HC NC2 HC 500.00 120.0100 ANGLe HC NH3 HC 500.00 109.4543 ANGLe N C O 500.00 122.1170 ANGLe NA CR NB 500.00 108.0486 ANGLe NC2 C NC2 500.00 119.7892 ANGLe NC2 C NH1 500.00 120.1054 ANGLe NH1 C NR 500.00 117.0000 ANGLe NH1 C O 500.00 122.9960 ANGLe NH2 C O 500.00 122.6605 ANGLe O C OH 500.00 124.5000 ANGLe OC C OC 500.00 123.0614 DIHEdral CA CA CT CT 0.00 3 0.0000 DIHEdral CT CT CX CW 0.00 3 0.0000 DIHEdral NA CC CT CT 0.00 3 0.0000 DIHEdral X C CT X 0.00 3 0.0000 DIHEdral X CT CT X 0.00 3 0.0000 DIHEdral X CT NH1 X 0.00 3 0.0000 DIHEdral X CT S X 0.00 3 0.0000 IMPRoper C CA CA CA 500.00 0 0.0000 IMPRoper C CA CA HA 500.00 0 180.0000 IMPRoper C CT HA HA 500.00 0 -70.8740 IMPRoper C CT N CT 500.00 0 180.0000 IMPRoper C CT NH1 CT 500.00 0 180.0000 IMPRoper C NH1 HA HA 500.00 0 -70.8740 IMPRoper C NH3 HA HA 500.00 0 -70.8740 IMPRoper C O N CT 500.00 0 0.0000 IMPRoper C O NH1 CT 500.00 0 0.0000 IMPRoper C X X C 500.00 0 0.0000 IMPRoper C X X CT 500.00 0 0.0000 IMPRoper C X X H 500.00 0 0.0000 IMPRoper C X X HA 500.00 0 0.0000 IMPRoper C X X N 500.00 0 0.0000 IMPRoper C X X NC2 500.00 0 0.0000 IMPRoper C X X NH1 500.00 0 0.0000 IMPRoper C X X NH2 500.00 0 0.0000 IMPRoper C X X NR 500.00 0 0.0000 IMPRoper C X X O 500.00 0 0.0000 IMPRoper C X X OC 500.00 0 0.0000 IMPRoper C X X OH 500.00 0 0.0000 IMPRoper CA C CA CA 500.00 0 0.0000 IMPRoper CA C CA HA 500.00 0 180.0000 IMPRoper CA CA C HA 500.00 0 0.0000 IMPRoper CA CA C OH 500.00 0 180.0000 IMPRoper CA CA CA CA 500.00 0 0.0000 IMPRoper CA CA CA CB 500.00 0 0.0000 IMPRoper CA CA CA CN 500.00 0 0.0000 IMPRoper CA CA CA CT 500.00 0 180.0000 IMPRoper CA CA CA HA 500.00 0 180.0000 IMPRoper CA CA CB CA 500.00 0 0.0000 IMPRoper CA CA CB CN 500.00 0 0.0000 IMPRoper CA CA CB CX 500.00 0 180.0000 IMPRoper CA CA CB HA 500.00 0 0.0000 IMPRoper CA CA CN CA 500.00 0 0.0000 IMPRoper CA CA CN CB 500.00 0 0.0000 IMPRoper CA CA CN NA 500.00 0 180.0000 IMPRoper CA CB CN CA 500.00 0 0.0000 IMPRoper CA CB CN NA 500.00 0 180.0000 IMPRoper CA CB CX CW 500.00 0 180.0000 IMPRoper CA CN CA HA 500.00 0 0.0000 IMPRoper CA CN CB CX 500.00 0 180.0000 IMPRoper CA CN CX CB 500.00 0 0.0000 IMPRoper CA CN NA CW 500.00 0 180.0000 IMPRoper CA CT HA HA 500.00 0 -70.8740 IMPRoper CB CN NA CW 500.00 0 0.0000 IMPRoper CB CN NA H 500.00 0 180.0000 IMPRoper CB CX CW NA 500.00 0 0.0000 IMPRoper CC CT HA HA 500.00 0 -70.8740 IMPRoper CC CT NA CV 500.00 0 0.0000 IMPRoper CC CV NB CR 500.00 0 0.0000 IMPRoper CC NA CR NB 500.00 0 0.0000 IMPRoper CN CB CA NA 500.00 0 0.0000 IMPRoper CN CB CX CT 500.00 0 180.0000 IMPRoper CN CB CX CW 500.00 0 0.0000 IMPRoper CN NA CW CX 500.00 0 0.0000 IMPRoper CN NA CW HA 500.00 0 180.0000 IMPRoper CP C N CT 500.00 0 180.0000 IMPRoper CP CT CT N 500.00 0 25.0000 IMPRoper CP CT CT NH3 500.00 0 25.0000 IMPRoper CP CT HA HA 500.00 0 -70.8740 IMPRoper CP N C CT 500.00 0 0.0000 IMPRoper CR NA CC CV 500.00 0 0.0000 IMPRoper CR NA NB HA 500.00 0 0.0000 IMPRoper CT C CP N 500.00 0 0.0000 IMPRoper CT C H NH1 500.00 0 0.0000 IMPRoper CT C N CT 500.00 0 180.0000 IMPRoper CT C N HA 500.00 0 65.9770 IMPRoper CT C NH1 CT 500.00 0 180.0000 IMPRoper CT C NH1 H 500.00 0 0.0000 IMPRoper CT C NH1 HA 500.00 0 65.9770 IMPRoper CT C NH2 H 500.00 0 0.0000 IMPRoper CT C NH3 HA 500.00 0 65.9770 IMPRoper CT CB CW CX 500.00 0 0.0000 IMPRoper CT CT CT HA 500.00 0 -65.9770 IMPRoper CT CT HA HA 500.00 0 -70.8740 IMPRoper CT N C HA 500.00 0 65.9770 IMPRoper CT N C O 500.00 0 0.0000 IMPRoper CT NH1 C HA 500.00 0 65.9770 IMPRoper CT NH1 C O 500.00 0 0.0000 IMPRoper CT NH3 C HA 500.00 0 65.9770 IMPRoper CT OH CT HA 500.00 0 65.9770 IMPRoper CT X X N 500.00 0 0.0000 IMPRoper CT X X NC2 500.00 0 0.0000 IMPRoper CT X X NH1 500.00 0 0.0000 IMPRoper CT X X NH3 500.00 0 0.0000 IMPRoper CT X X NR 500.00 0 0.0000 IMPRoper CV NB CC HA 500.00 0 0.0000 IMPRoper CV NB CR NA 500.00 0 0.0000 IMPRoper CW CX NA HA 500.00 0 0.0000 IMPRoper CX CB CN NA 500.00 0 0.0000 IMPRoper CX CT HA HA 500.00 0 -70.8740 IMPRoper H CC CR NA 500.00 0 0.0000 IMPRoper H CN CW NA 500.00 0 0.0000 IMPRoper H X X NH1 500.00 0 0.0000 IMPRoper H X X NH2 500.00 0 0.0000 IMPRoper H X X O 500.00 0 0.0000 IMPRoper HA CT HA HA 500.00 0 -66.5140 IMPRoper HA HA CP N 500.00 0 -70.8740 IMPRoper HA HA CP NH3 500.00 0 -70.8740 IMPRoper HA HA CT NH1 500.00 0 -70.8740 IMPRoper HA HA CT NH3 500.00 0 -70.8740 IMPRoper HA HA CT OH 500.00 0 -71.8840 IMPRoper HA HA CT S 500.00 0 -73.2300 IMPRoper HA HA S HA 500.00 0 -66.0000 IMPRoper HC CT HC HC 500.00 0 -66.0000 IMPRoper CP CT HC HC 500.00 0 -66.0000 IMPRoper HC NC2 CT NH1 500.00 0 0.0000 IMPRoper HC X X NC2 500.00 0 0.0000 IMPRoper HC X X NH1 500.00 0 0.0000 IMPRoper HC X X NH3 500.00 0 0.0000 IMPRoper NA CC CV NB 500.00 0 0.0000 IMPRoper NH1 X X NH1 500.00 0 0.0000 IMPRoper NH1 X X NR 500.00 0 0.0000 ! eps sigma eps(1:4) sigma(1:4) NONBonded C 0.0903 3.3409 0.0903 3.3409 NONBonded CA 0.1200 3.3409 0.1200 3.3409 NONBonded CB 0.1450 3.3409 0.1450 3.3409 NONBonded CC 0.1450 3.3409 0.1450 3.3409 NONBonded CN 0.1450 3.3409 0.1450 3.3409 NONBonded CP 0.1450 3.3409 0.1450 3.3409 NONBonded CR 0.1200 3.3409 0.1200 3.3409 NONBonded CT 0.0903 3.3409 0.0903 3.3409 NONBonded CV 0.1200 3.3409 0.1200 3.3409 NONBonded CW 0.1200 3.3409 0.1200 3.3409 NONBonded CX 0.1450 3.3409 0.1450 3.3409 NONBonded H 0.0498 2.2272 0.0498 2.2272 NONBonded HA 0.0045 2.2272 0.0045 2.2272 NONBonded HC 0.0498 2.2272 0.0498 2.2272 NONBonded N 0.1592 3.0068 0.1592 3.0068 NONBonded NA 0.1592 3.0068 0.1592 3.0068 NONBonded NB 0.1592 3.0068 0.1592 3.0068 NONBonded NC2 0.1592 3.0068 0.1592 3.0068 NONBonded NH1 0.1592 3.0068 0.1592 3.0068 NONBonded NH2 0.1592 3.0068 0.1592 3.0068 NONBonded NH3 0.1592 3.0068 0.1592 3.0068 NONBonded O 0.2342 2.7755 0.2342 2.7755 NONBonded OC 1.0244 2.7755 1.0244 2.7755 NONBonded OH 0.2342 2.7755 0.2342 2.7755 NONBonded S 0.0239 3.7458 0.0239 3.7458 NONBonded YH 0.0045 1.0000 0.0045 1.0000 NBFIx H NB 44.200 1.000 44.200 1.000 NBFIx H O 44.200 1.000 44.200 1.000 NBFIx H OC 44.200 1.000 44.200 1.000 NBFIx H OH 44.200 1.000 44.200 1.000 NBFIx HC NB 44.200 1.000 44.200 1.000 NBFIx HC O 44.200 1.000 44.200 1.000 NBFIx HC OC 44.200 1.000 44.200 1.000 NBFIx HC OH 44.200 1.000 44.200 1.000 SET ECHO ON MESSAGE ON END