remark file parallhdg.pro version 4.05 date 16-Feb-1998 remark for file topallhdg.pro version 4.01 date 29-Jul-96 remark Geometric energy function parameters for distance geometry and remark simulated annealing. remark Author: Michael Nilges, EMBL Heidelberg remark last modified: 25-Feb-1998 set echo off message off end !***********************************************************************! ! Copyright (C) 1995,1996 by Michael Nilges. All rights reserved. ! ! Copying and redistribution of this files is authorized only if etiher ! ! (1) you make absolutely no changes to your copy, including name, or ! ! (2) if you do make changes, you name it something other than ! ! topallhdg.pro and topallhdg.x.xx.pro, and clearly mark the changes. ! ! The information in this software is subject to change without notice ! ! and should not be construed as a commitment by the EMBL or by the ! ! authors. Neither the EMBL, Yale University, nor the authors assume ! ! responsibility for the use or reliability of this software. ! ! We do hope, however, to get responses from users, especially when ! ! errors have been found. ! !***********************************************************************! ! Description: ! ! This parameter file was originally derived from the parameter files ! ! PARMALLH6 and PARHCSDX. It was designed specifically for the initial ! ! stages of calculating structures from NMR restraints. ! !***********************************************************************! ! PARHCSDX includes bond and angle parameters for non-hydrogen atoms ! ! derived from Cambridge Data Base model structures (R. A. Engh and R. ! ! Huber, Acta Cryst. Sect. A., 1991). Hydrogens were added with X-PLOR ! ! scripts for minimization and the PARAmeter LEARn statement. Dihedral, ! ! improper and non-bonded values are from previous PARALLHDG versions, ! ! and assigned to new atom types where appropriate. Due to the ! ! minimization procedure used in the derivation, there are very small ! ! deviations from the parameter values in PARHCSDX. ! ! Heavy atom types are exactly as in PARHCSDX, hydrogen types as in ! ! PARALLHDG. ! !***********************************************************************! ! History: ! version 4.05 (16-Feb-98) : allow different nonbonded parameter options ! version 4.04 (28-Jan-98) : added missing dihedral parameters ! version 4.03 (27-Mar-97) : added missing dihedral parameters ! version 4.02 (25-Sep-96) : all covalent parameters ! version 4.01 (29-Jul-96) : all covalent parameters ! version 4.00 (19-Jul-96) : all atom types from CSDX implemented ! version 3.00 (24-Oct-95) : mapped CSDX parmameters on parallhdg, ! no changes in topallhdg ! ! previous modifications: ! proline residue modified (MN) ! added hbond acceptor and donor definitions for analysis (MN) ! all references to internal coordinates (IC's) removed (MN) ! added stereospecific impropers for all pro-chiral centers (ATB, JK) ! modification of PARMALLH6 parameters to improve geometric consistency (JK) ! all dihedrals defining planarity converted to impropers (MN, PK) ! additional impropers at planar centers (MN) !***********************************************************************! BOND C CH1E 1000.000 {sd= 0.001} 1.525 BOND C CH2E 1000.000 {sd= 0.001} 1.516 BOND C CH2G 1000.000 {sd= 0.001} 1.516 BOND C N 1000.000 {sd= 0.001} 1.341 BOND C NC2 1000.000 {sd= 0.001} 1.326 BOND C NH1 1000.000 {sd= 0.001} 1.329 BOND C NH2 1000.000 {sd= 0.001} 1.328 BOND C O 1000.000 {sd= 0.001} 1.231 BOND C OC 1000.000 {sd= 0.001} 1.249 BOND C5 CH2E 1000.000 {sd= 0.001} 1.497 BOND C5 CR1E 1000.000 {sd= 0.001} 1.357 BOND C5 CR1H 1000.000 {sd= 0.001} 1.354 BOND C5 NH1 1000.000 {sd= 0.001} 1.378 BOND C5 NR 1000.000 {sd= 0.001} 1.373 BOND C5W CH2E 1000.000 {sd= 0.001} 1.498 BOND C5W CR1E 1000.000 {sd= 0.001} 1.365 BOND C5W CW 1000.000 {sd= 0.001} 1.433 BOND CF CH2E 1000.000 {sd= 0.001} 1.502 BOND CF CR1E 1000.000 {sd= 0.001} 1.385 BOND CH1E CH1E 1000.000 {sd= 0.001} 1.540 BOND CH1E CH2E 1000.000 {sd= 0.001} 1.530 BOND CH1E CH3E 1000.000 {sd= 0.001} 1.521 BOND CH1E HA 1000.000 {sd= 0.001} 1.080 BOND CH1E N 1000.000 {sd= 0.001} 1.466 BOND CH1E NH1 1000.000 {sd= 0.001} 1.458 BOND CH1E NH3 1000.000 {sd= 0.001} 1.486 BOND CH2E CH2E 1000.000 {sd= 0.001} 1.520 BOND CH2E CH2P 1000.000 {sd= 0.001} 1.490 BOND CH2E CH3E 1000.000 {sd= 0.001} 1.513 BOND CH2E CY 1000.000 {sd= 0.001} 1.512 BOND CH2E HA 1000.000 {sd= 0.001} 1.080 BOND CH2E NH1 1000.000 {sd= 0.001} 1.460 BOND CH2E NH3 1000.000 {sd= 0.001} 1.489 BOND CH2E OH1 1000.000 {sd= 0.001} 1.417 BOND CH2E S 1000.000 {sd= 0.001} 1.822 BOND CH2E SH1E 1000.000 {sd= 0.001} 1.808 BOND CH2E SM 1000.000 {sd= 0.001} 1.803 BOND CH2G HA 1000.000 {sd= 0.001} 1.080 BOND CH2G NH1 1000.000 {sd= 0.001} 1.451 BOND CH2G NH3 1000.000 {sd= 0.001} 1.489 BOND CH2P CH2P 1000.000 {sd= 0.001} 1.504 BOND CH2P HA 1000.000 {sd= 0.001} 1.080 BOND CH2P N 1000.000 {sd= 0.001} 1.473 BOND CH2P NH3 1000.000 {sd= 0.001} 1.474 BOND CH3E HA 1000.000 {sd= 0.001} 1.080 BOND CH3E SM 1000.000 {sd= 0.001} 1.791 BOND CR1E CR1E 1000.000 {sd= 0.001} 1.382 BOND CR1E CR1W 1000.000 {sd= 0.001} 1.400 BOND CR1E CW 1000.000 {sd= 0.001} 1.398 BOND CR1E CY 1000.000 {sd= 0.001} 1.389 BOND CR1E CY2 1000.000 {sd= 0.001} 1.379 BOND CR1E HA 1000.000 {sd= 0.001} 1.080 BOND CR1E NH1 1000.000 {sd= 0.001} 1.373 BOND CR1E NR 1000.000 {sd= 0.001} 1.391 BOND CR1H HA 1000.000 {sd= 0.001} 1.081 BOND CR1H NH1 1000.000 {sd= 0.001} 1.374 BOND CR1W CR1W 1000.000 {sd= 0.001} 1.368 BOND CR1W CW 1000.000 {sd= 0.001} 1.393 BOND CR1W HA 1000.000 {sd= 0.001} 1.080 BOND CRH HA 1000.000 {sd= 0.001} 1.080 BOND CRH NH1 1000.000 {sd= 0.001} 1.341 BOND CRH NR 1000.000 {sd= 0.001} 1.319 BOND CRHH HA 1000.000 {sd= 0.001} 1.080 BOND CRHH NH1 1000.000 {sd= 0.001} 1.321 BOND CW CW 1000.000 {sd= 0.001} 1.409 BOND CW NH1 1000.000 {sd= 0.001} 1.370 BOND CY2 OH1 1000.000 {sd= 0.001} 1.376 BOND H NH1 1000.000 {sd= 0.001} 0.980 BOND H NH2 1000.000 {sd= 0.001} 0.980 BOND H OH1 1000.000 {sd= 0.001} 0.960 BOND H SH1E 1000.000 {sd= 0.001} 0.960 BOND HC NC2 1000.000 {sd= 0.001} 1.000 BOND HC NH3 1000.000 {sd= 0.001} 1.040 BOND S S 1000.000 {sd= 0.001} 2.030 ANGLe C CH1E CH1E 500.00 {sd= 0.031} 109.0754 ANGLe C CH1E CH2E 500.00 {sd= 0.031} 110.1094 ANGLe C CH1E CH3E 500.00 {sd= 0.031} 110.4838 ANGLe C CH1E HA 500.00 {sd= 0.031} 108.9914 ANGLe C CH1E N 500.00 {sd= 0.031} 111.9082 ANGLe C CH1E NH1 500.00 {sd= 0.031} 111.1396 ANGLe C CH1E NH3 500.00 {sd= 0.031} 111.1703 ANGLe C CH2E CH1E 500.00 {sd= 0.031} 112.5947 ANGLe C CH2E CH2E 500.00 {sd= 0.031} 112.5943 ANGLe C CH2E HA 500.00 {sd= 0.031} 108.5877 ANGLe C CH2G HA 500.00 {sd= 0.031} 108.8528 ANGLe C CH2G NH1 500.00 {sd= 0.031} 112.4999 ANGLe C CH2G NH3 500.00 {sd= 0.031} 112.4990 ANGLe C N CH1E 500.00 {sd= 0.031} 122.7632 ANGLe C N CH2P 500.00 {sd= 0.031} 125.1134 ANGLe C NC2 HC 500.00 {sd= 0.031} 119.9992 ANGLe C NH1 CH1E 500.00 {sd= 0.031} 121.6541 ANGLe C NH1 CH2E 500.00 {sd= 0.031} 124.1226 ANGLe C NH1 CH2G 500.00 {sd= 0.031} 120.5859 ANGLe C NH1 H 500.00 {sd= 0.031} 119.2489 ANGLe C NH2 H 500.00 {sd= 0.031} 118.1853 ANGLe C5 CH2E CH1E 500.00 {sd= 0.031} 113.7931 ANGLe C5 CH2E HA 500.00 {sd= 0.031} 108.1195 ANGLe C5 CR1E HA 500.00 {sd= 0.031} 126.2616 ANGLe C5 CR1E NH1 500.00 {sd= 0.031} 106.5015 ANGLe C5 CR1E NR 500.00 {sd= 0.031} 109.4272 ANGLe C5 CR1H HA 500.00 {sd= 0.031} 126.4031 ANGLe C5 CR1H NH1 500.00 {sd= 0.031} 107.1610 ANGLe C5 NH1 CRH 500.00 {sd= 0.031} 108.0959 ANGLe C5 NH1 CRHH 500.00 {sd= 0.031} 109.4352 ANGLe C5 NH1 H 500.00 {sd= 0.031} 126.0497 ANGLe C5 NR CRH 500.00 {sd= 0.031} 105.7163 ANGLe C5W CH2E CH1E 500.00 {sd= 0.031} 113.5788 ANGLe C5W CH2E HA 500.00 {sd= 0.031} 108.1831 ANGLe C5W CR1E HA 500.00 {sd= 0.031} 124.5037 ANGLe C5W CR1E NH1 500.00 {sd= 0.031} 110.0962 ANGLe C5W CW CR1E 500.00 {sd= 0.031} 133.9320 ANGLe C5W CW CW 500.00 {sd= 0.031} 107.2333 ANGLe CF CH2E CH1E 500.00 {sd= 0.031} 113.7937 ANGLe CF CH2E HA 500.00 {sd= 0.031} 108.1268 ANGLe CF CR1E CR1E 500.00 {sd= 0.031} 120.7850 ANGLe CF CR1E HA 500.00 {sd= 0.031} 119.4540 ANGLe CH1E C N 500.00 {sd= 0.031} 116.9940 ANGLe CH1E C NH1 500.00 {sd= 0.031} 116.1998 ANGLe CH1E C O 500.00 {sd= 0.031} 120.8258 ANGLe CH1E C OC 500.00 {sd= 0.031} 118.0611 ANGLe CH1E CH1E CH2E 500.00 {sd= 0.031} 110.3824 ANGLe CH1E CH1E CH3E 500.00 {sd= 0.031} 110.4882 ANGLe CH1E CH1E HA 500.00 {sd= 0.031} 108.2775 ANGLe CH1E CH1E NH1 500.00 {sd= 0.031} 111.4875 ANGLe CH1E CH1E NH3 500.00 {sd= 0.031} 111.4875 ANGLe CH1E CH2E CH1E 500.00 {sd= 0.031} 116.0385 ANGLe CH1E CH2E CH2E 500.00 {sd= 0.031} 114.0589 ANGLe CH1E CH2E CH2P 500.00 {sd= 0.031} 104.3952 ANGLe CH1E CH2E CH3E 500.00 {sd= 0.031} 113.7404 ANGLe CH1E CH2E CY 500.00 {sd= 0.031} 113.8748 ANGLe CH1E CH2E HA 500.00 {sd= 0.031} 109.2833 ANGLe CH1E CH2E OH1 500.00 {sd= 0.031} 111.0593 ANGLe CH1E CH2E S 500.00 {sd= 0.031} 114.3551 ANGLe CH1E CH2E SH1E 500.00 {sd= 0.031} 114.3558 ANGLe CH1E CH3E HA 500.00 {sd= 0.031} 109.4726 ANGLe CH1E N CH2P 500.00 {sd= 0.031} 112.1234 ANGLe CH1E NH1 H 500.00 {sd= 0.031} 119.2367 ANGLe CH1E NH3 CH2P 500.00 {sd= 0.031} 110.6738 ANGLe CH1E NH3 HC 500.00 {sd= 0.031} 104.9708 ANGLe CH2E C NH2 500.00 {sd= 0.031} 116.4617 ANGLe CH2E C O 500.00 {sd= 0.031} 120.9106 ANGLe CH2E C OC 500.00 {sd= 0.031} 118.4969 ANGLe CH2E C5 CR1E 500.00 {sd= 0.031} 129.6325 ANGLe CH2E C5 CR1H 500.00 {sd= 0.031} 131.2043 ANGLe CH2E C5 NH1 500.00 {sd= 0.031} 123.4237 ANGLe CH2E C5 NR 500.00 {sd= 0.031} 121.5772 ANGLe CH2E C5W CR1E 500.00 {sd= 0.031} 126.9191 ANGLe CH2E C5W CW 500.00 {sd= 0.031} 126.8167 ANGLe CH2E CF CR1E 500.00 {sd= 0.031} 120.6527 ANGLe CH2E CH1E CH3E 500.00 {sd= 0.031} 110.6376 ANGLe CH2E CH1E HA 500.00 {sd= 0.031} 109.2487 ANGLe CH2E CH1E N 500.00 {sd= 0.031} 103.0552 ANGLe CH2E CH1E NH1 500.00 {sd= 0.031} 110.4763 ANGLe CH2E CH1E NH3 500.00 {sd= 0.031} 108.4924 ANGLe CH2E CH2E CH2E 500.00 {sd= 0.031} 111.3121 ANGLe CH2E CH2E HA 500.00 {sd= 0.031} 108.7236 ANGLe CH2E CH2E NH1 500.00 {sd= 0.031} 111.9978 ANGLe CH2E CH2E NH3 500.00 {sd= 0.031} 111.8939 ANGLe CH2E CH2E SM 500.00 {sd= 0.031} 112.6822 ANGLe CH2E CH2P CH2P 500.00 {sd= 0.031} 106.1000 ANGLe CH2E CH2P HA 500.00 {sd= 0.031} 109.9548 ANGLe CH2E CH3E HA 500.00 {sd= 0.031} 109.4694 ANGLe CH2E CY CR1E 500.00 {sd= 0.031} 120.9304 ANGLe CH2E NH1 H 500.00 {sd= 0.031} 118.0987 ANGLe CH2E NH3 HC 500.00 {sd= 0.031} 109.4693 ANGLe CH2E OH1 H 500.00 {sd= 0.031} 109.4969 ANGLe CH2E S S 500.00 {sd= 0.031} 103.7998 ANGLe CH2E SH1E H 500.00 {sd= 0.031} 107.9769 ANGLe CH2E SM CH3E 500.00 {sd= 0.031} 100.8987 ANGLe CH2G C N 500.00 {sd= 0.031} 117.7918 ANGLe CH2G C NH1 500.00 {sd= 0.031} 116.3225 ANGLe CH2G C O 500.00 {sd= 0.031} 120.6203 ANGLe CH2G C OC 500.00 {sd= 0.031} 118.4971 ANGLe CH2G NH1 H 500.00 {sd= 0.031} 119.7297 ANGLe CH2G NH3 HC 500.00 {sd= 0.031} 109.4688 ANGLe CH2P CH2E HA 500.00 {sd= 0.031} 111.1127 ANGLe CH2P CH2P HA 500.00 {sd= 0.031} 110.3818 ANGLe CH2P CH2P N 500.00 {sd= 0.031} 103.2695 ANGLe CH2P CH2P NH3 500.00 {sd= 0.031} 103.6880 ANGLe CH2P NH3 HC 500.00 {sd= 0.031} 123.8148 ANGLe CH3E CH1E CH3E 500.00 {sd= 0.031} 110.7707 ANGLe CH3E CH1E HA 500.00 {sd= 0.031} 108.1279 ANGLe CH3E CH1E NH1 500.00 {sd= 0.031} 110.3844 ANGLe CH3E CH1E NH3 500.00 {sd= 0.031} 110.4751 ANGLe CH3E CH2E HA 500.00 {sd= 0.031} 108.0408 ANGLe CH3E CH2E OH1 500.00 {sd= 0.031} 108.0961 ANGLe CR1E C5 NH1 500.00 {sd= 0.031} 105.6758 ANGLe CR1E C5 NR 500.00 {sd= 0.031} 109.3402 ANGLe CR1E C5W CW 500.00 {sd= 0.031} 106.2641 ANGLe CR1E CF CR1E 500.00 {sd= 0.031} 118.6946 ANGLe CR1E CR1E CR1E 500.00 {sd= 0.031} 119.9118 ANGLe CR1E CR1E CR1W 500.00 {sd= 0.031} 121.1513 ANGLe CR1E CR1E CW 500.00 {sd= 0.031} 118.6734 ANGLe CR1E CR1E CY 500.00 {sd= 0.031} 121.1348 ANGLe CR1E CR1E CY2 500.00 {sd= 0.031} 119.6224 ANGLe CR1E CR1E HA 500.00 {sd= 0.031} 119.9433 ANGLe CR1E CR1W CR1W 500.00 {sd= 0.031} 121.4832 ANGLe CR1E CR1W HA 500.00 {sd= 0.031} 118.7598 ANGLe CR1E CW CW 500.00 {sd= 0.031} 118.8347 ANGLe CR1E CY CR1E 500.00 {sd= 0.031} 118.1392 ANGLe CR1E CY2 CR1E 500.00 {sd= 0.031} 120.3463 ANGLe CR1E CY2 OH1 500.00 {sd= 0.031} 119.8269 ANGLe CR1E NH1 CRH 500.00 {sd= 0.031} 106.8630 ANGLe CR1E NH1 CW 500.00 {sd= 0.031} 108.9983 ANGLe CR1E NH1 H 500.00 {sd= 0.031} 125.8235 ANGLe CR1E NR CRH 500.00 {sd= 0.031} 105.7678 ANGLe CR1H C5 NH1 500.00 {sd= 0.031} 106.0900 ANGLe CR1H NH1 CRHH 500.00 {sd= 0.031} 108.9901 ANGLe CR1H NH1 H 500.00 {sd= 0.031} 125.5054 ANGLe CR1W CR1E HA 500.00 {sd= 0.031} 119.1706 ANGLe CR1W CR1W CW 500.00 {sd= 0.031} 117.4515 ANGLe CR1W CR1W HA 500.00 {sd= 0.031} 120.2616 ANGLe CR1W CW CW 500.00 {sd= 0.031} 122.4059 ANGLe CR1W CW NH1 500.00 {sd= 0.031} 130.1860 ANGLe CRH NH1 H 500.00 {sd= 0.031} 126.0322 ANGLe CRHH NH1 H 500.00 {sd= 0.031} 125.1896 ANGLe CW CR1E HA 500.00 {sd= 0.031} 121.0317 ANGLe CW CR1W HA 500.00 {sd= 0.031} 121.7822 ANGLe CW CW NH1 500.00 {sd= 0.031} 107.4081 ANGLe CW NH1 H 500.00 {sd= 0.031} 125.9221 ANGLe CY CH2E HA 500.00 {sd= 0.031} 108.0910 ANGLe CY CR1E HA 500.00 {sd= 0.031} 119.1931 ANGLe CY2 CR1E HA 500.00 {sd= 0.031} 120.3261 ANGLe CY2 OH1 H 500.00 {sd= 0.031} 109.4984 ANGLe H NH2 H 500.00 {sd= 0.031} 123.6294 ANGLe HA CH1E N 500.00 {sd= 0.031} 111.0977 ANGLe HA CH1E NH1 500.00 {sd= 0.031} 108.0508 ANGLe HA CH1E NH3 500.00 {sd= 0.031} 108.5074 ANGLe HA CH2E HA 500.00 {sd= 0.031} 109.4074 ANGLe HA CH2E NH1 500.00 {sd= 0.031} 108.9030 ANGLe HA CH2E NH3 500.00 {sd= 0.031} 108.9390 ANGLe HA CH2E OH1 500.00 {sd= 0.031} 108.6930 ANGLe HA CH2E S 500.00 {sd= 0.031} 107.9228 ANGLe HA CH2E SH1E 500.00 {sd= 0.031} 107.9185 ANGLe HA CH2E SM 500.00 {sd= 0.031} 108.6768 ANGLe HA CH2G HA 500.00 {sd= 0.031} 108.8718 ANGLe HA CH2G NH1 500.00 {sd= 0.031} 108.8510 ANGLe HA CH2G NH3 500.00 {sd= 0.031} 108.8586 ANGLe HA CH2P HA 500.00 {sd= 0.031} 110.4563 ANGLe HA CH2P N 500.00 {sd= 0.031} 110.8278 ANGLe HA CH2P NH3 500.00 {sd= 0.031} 110.7246 ANGLe HA CH3E HA 500.00 {sd= 0.031} 109.4703 ANGLe HA CH3E SM 500.00 {sd= 0.031} 109.4700 ANGLe HA CR1E NH1 500.00 {sd= 0.031} 125.8803 ANGLe HA CR1E NR 500.00 {sd= 0.031} 125.1878 ANGLe HA CR1H NH1 500.00 {sd= 0.031} 126.4359 ANGLe HA CRH NH1 500.00 {sd= 0.031} 124.3534 ANGLe HA CRH NR 500.00 {sd= 0.031} 124.3404 ANGLe HA CRHH NH1 500.00 {sd= 0.031} 125.8381 ANGLe HC NC2 HC 500.00 {sd= 0.031} 120.0016 ANGLe HC NH3 HC 500.00 {sd= 0.031} 108.1992 ANGLe N C O 500.00 {sd= 0.031} 122.0016 ANGLe NC2 C NC2 500.00 {sd= 0.031} 119.7933 ANGLe NC2 C NH1 500.00 {sd= 0.031} 120.1034 ANGLe NH1 C O 500.00 {sd= 0.031} 122.9907 ANGLe NH1 CRH NR 500.00 {sd= 0.031} 111.3061 ANGLe NH1 CRHH NH1 500.00 {sd= 0.031} 108.3237 ANGLe NH2 C O 500.00 {sd= 0.031} 122.6277 ANGLe OC C OC 500.00 {sd= 0.031} 123.3548 IMPRoper C CH1E HA HA 500.00 {sd= 0.031} 0 -70.4072 IMPRoper C CH1E N CH1E 500.00 {sd= 0.031} 0 -179.9829 IMPRoper C CH1E NH1 CH1E 500.00 {sd= 0.031} 0 0.0130 IMPRoper C CH1E NH1 CH2G 500.00 {sd= 0.031} 0 -0.0382 IMPRoper C CH1E OC OC 500.00 {sd= 0.031} 0 0.0210 IMPRoper C CH2E HA HA 500.00 {sd= 0.031} 0 -70.4459 IMPRoper C CH2E O NH2 500.00 {sd= 0.031} 0 0.0124 IMPRoper C CH2E OC OC 500.00 {sd= 0.031} 0 -0.0137 IMPRoper C CH2G N CH1E 500.00 {sd= 0.031} 0 -179.9669 IMPRoper C CH2G NH1 CH1E 500.00 {sd= 0.031} 0 0.0484 IMPRoper C CH2G NH1 CH2G 500.00 {sd= 0.031} 0 -0.0248 IMPRoper C CH2G OC OC 500.00 {sd= 0.031} 0 0.0223 IMPRoper C NC2 H NH1 500.00 {sd= 0.031} 0 -0.0121 IMPRoper C NH1 HA HA 500.00 {sd= 0.031} 0 -70.8745 IMPRoper C NH1 NC2 NC2 500.00 {sd= 0.031} 0 -0.0088 IMPRoper C NH3 HA HA 500.00 {sd= 0.031} 0 70.6479 IMPRoper C O N CH1E 500.00 {sd= 0.031} 0 -0.0235 IMPRoper C O NH1 CH1E 500.00 {sd= 0.031} 0 -179.9689 IMPRoper C O NH1 CH2G 500.00 {sd= 0.031} 0 -180.0127 IMPRoper C5 CH1E HA HA 500.00 {sd= 0.031} 0 -69.9815 IMPRoper C5 CH2E NH1 CR1E 500.00 {sd= 0.031} 0 -0.0386 IMPRoper C5 CH2E NH1 CR1H 500.00 {sd= 0.031} 0 -0.0237 IMPRoper C5 CH2E NR CR1E 500.00 {sd= 0.031} 0 0.0178 IMPRoper C5 CR1E NH1 CRH 500.00 {sd= 0.031} 0 0.0072 IMPRoper C5 CR1E NR CRH 500.00 {sd= 0.031} 0 -0.0138 IMPRoper C5 CR1H NH1 CRHH 500.00 {sd= 0.031} 0 -0.0209 IMPRoper C5 NH1 CRH NR 500.00 {sd= 0.031} 0 -0.0652 IMPRoper C5 NH1 CRHH NH1 500.00 {sd= 0.031} 0 -0.0660 IMPRoper C5 NR CRH NH1 500.00 {sd= 0.031} 0 0.0250 IMPRoper C5W CH1E HA HA 500.00 {sd= 0.031} 0 -70.0142 IMPRoper C5W CW CR1E CR1E 500.00 {sd= 0.031} 0 -179.9506 IMPRoper C5W CW CW CR1W 500.00 {sd= 0.031} 0 179.9618 IMPRoper CF CH1E HA HA 500.00 {sd= 0.031} 0 -70.0169 IMPRoper CF CR1E CR1E CR1E 500.00 {sd= 0.031} 0 0.0069 IMPRoper CF CR1E CR1E HA 500.00 {sd= 0.031} 0 179.9729 IMPRoper CH1E C CH2P N 500.00 {sd= 0.031} 0 0.0332 IMPRoper CH1E C H NH1 500.00 {sd= 0.031} 0 179.9918 IMPRoper CH1E C N CH1E 500.00 {sd= 0.031} 0 179.9873 IMPRoper CH1E C N CH2P 500.00 {sd= 0.031} 0 0.0025 IMPRoper CH1E C NH1 CH1E 500.00 {sd= 0.031} 0 -180.0067 IMPRoper CH1E C NH1 CH2G 500.00 {sd= 0.031} 0 -180.0018 IMPRoper CH1E C NH1 H 500.00 {sd= 0.031} 0 0.0023 IMPRoper CH1E C NH1 HA 500.00 {sd= 0.031} 0 66.2535 IMPRoper CH1E C NH3 HA 500.00 {sd= 0.031} 0 66.3265 IMPRoper CH1E CH1E HA HA 500.00 {sd= 0.031} 0 -69.6639 IMPRoper CH1E N C CH2G 500.00 {sd= 0.031} 0 179.9856 IMPRoper CH1E N C O 500.00 {sd= 0.031} 0 0.0111 IMPRoper CH1E NH1 C CH2G 500.00 {sd= 0.031} 0 -179.9916 IMPRoper CH1E NH1 C O 500.00 {sd= 0.031} 0 -0.0057 IMPRoper CH2E C N HA 500.00 {sd= 0.031} 0 67.7957 IMPRoper CH2E C NH1 HA 500.00 {sd= 0.031} 0 66.1640 IMPRoper CH2E C NH2 H 500.00 {sd= 0.031} 0 0.0000 IMPRoper CH2E C NH3 HA 500.00 {sd= 0.031} 0 66.3265 IMPRoper CH2E C5W CW CW 500.00 {sd= 0.031} 0 179.9679 IMPRoper CH2E CF CR1E CR1E 500.00 {sd= 0.031} 0 -179.9993 IMPRoper CH2E CH1E HA HA 500.00 {sd= 0.031} 0 -70.0781 IMPRoper CH2E CH2E HA HA 500.00 {sd= 0.031} 0 -70.7825 IMPRoper CH2E CH3E CH1E HA 500.00 {sd= 0.031} 0 -65.2137 IMPRoper CH2E CY CR1E CR1E 500.00 {sd= 0.031} 0 -179.9903 IMPRoper CH2G C CH2P N 500.00 {sd= 0.031} 0 -0.0151 IMPRoper CH2G C H NH1 500.00 {sd= 0.031} 0 180.0020 IMPRoper CH2G C N CH2P 500.00 {sd= 0.031} 0 -0.0116 IMPRoper CH2G C NH1 CH2G 500.00 {sd= 0.031} 0 179.9899 IMPRoper CH2G C NH1 H 500.00 {sd= 0.031} 0 0.0161 IMPRoper CH2G NH1 C O 500.00 {sd= 0.031} 0 -0.0048 IMPRoper CH2P CH1E HA HA 500.00 {sd= 0.031} 0 -71.9385 IMPRoper CH2P CH1E HC HC 500.00 {sd= 0.031} 0 -70.7727 IMPRoper CH2P CH2E HA HA 500.00 {sd= 0.031} 0 -71.8986 IMPRoper CH3E C NH1 HA 500.00 {sd= 0.031} 0 65.9907 IMPRoper CH3E C NH3 HA 500.00 {sd= 0.031} 0 65.6779 IMPRoper CH3E CH1E HA HA 500.00 {sd= 0.031} 0 -70.1069 IMPRoper CH3E CH3E CH1E HA 500.00 {sd= 0.031} 0 -65.0462 IMPRoper CH3E CH3E CH2E HA 500.00 {sd= 0.031} 0 -65.1424 IMPRoper CH3E OH1 CH1E HA 500.00 {sd= 0.031} 0 66.1521 IMPRoper CR1E C5 NH1 CRH 500.00 {sd= 0.031} 0 0.0557 IMPRoper CR1E C5 NR CRH 500.00 {sd= 0.031} 0 -0.0198 IMPRoper CR1E C5W CW CR1E 500.00 {sd= 0.031} 0 179.9645 IMPRoper CR1E CF CR1E CR1E 500.00 {sd= 0.031} 0 -0.0034 IMPRoper CR1E CF CR1E HA 500.00 {sd= 0.031} 0 -179.9624 IMPRoper CR1E CR1E CR1E CR1E 500.00 {sd= 0.031} 0 -0.0034 IMPRoper CR1E CR1E CR1E HA 500.00 {sd= 0.031} 0 179.9935 IMPRoper CR1E CR1E CR1W CR1W 500.00 {sd= 0.031} 0 -0.0413 IMPRoper CR1E CR1E CR1W HA 500.00 {sd= 0.031} 0 -179.9535 IMPRoper CR1E CR1E CW CW 500.00 {sd= 0.031} 0 -0.0109 IMPRoper CR1E CR1E CY CR1E 500.00 {sd= 0.031} 0 0.0135 IMPRoper CR1E CR1E CY2 CR1E 500.00 {sd= 0.031} 0 0.0133 IMPRoper CR1E CR1E CY2 OH1 500.00 {sd= 0.031} 0 -179.9788 IMPRoper CR1E CR1W CR1W CW 500.00 {sd= 0.031} 0 0.0360 IMPRoper CR1E CR1W CR1W HA 500.00 {sd= 0.031} 0 179.9725 IMPRoper CR1E CW CW CR1W 500.00 {sd= 0.031} 0 0.0072 IMPRoper CR1E CW CW NH1 500.00 {sd= 0.031} 0 -179.9720 IMPRoper CR1E CY CR1E HA 500.00 {sd= 0.031} 0 -179.9985 IMPRoper CR1E CY2 CR1E HA 500.00 {sd= 0.031} 0 179.9891 IMPRoper CR1E NH1 C5 HA 500.00 {sd= 0.031} 0 -0.0175 IMPRoper CR1E NH1 CRH NR 500.00 {sd= 0.031} 0 -0.0206 IMPRoper CR1E NH1 CW CR1W 500.00 {sd= 0.031} 0 -179.9685 IMPRoper CR1E NR C5 HA 500.00 {sd= 0.031} 0 -0.0096 IMPRoper CR1E NR CRH NH1 500.00 {sd= 0.031} 0 0.0490 IMPRoper CR1H C5 NH1 CRHH 500.00 {sd= 0.031} 0 0.0496 IMPRoper CR1H NH1 C5 HA 500.00 {sd= 0.031} 0 0.0047 IMPRoper CR1H NH1 CRHH NH1 500.00 {sd= 0.031} 0 0.0534 IMPRoper CR1W CR1E CR1E CW 500.00 {sd= 0.031} 0 0.0275 IMPRoper CR1W CR1E CR1E HA 500.00 {sd= 0.031} 0 -179.9902 IMPRoper CR1W CR1W CR1E HA 500.00 {sd= 0.031} 0 179.9587 IMPRoper CR1W CR1W CW CW 500.00 {sd= 0.031} 0 -0.0194 IMPRoper CR1W CR1W CW NH1 500.00 {sd= 0.031} 0 179.9546 IMPRoper CRH NH1 NR HA 500.00 {sd= 0.031} 0 0.0429 IMPRoper CRH NR NH1 HA 500.00 {sd= 0.031} 0 -0.0123 IMPRoper CRHH NH1 NH1 HA 500.00 {sd= 0.031} 0 0.0414 IMPRoper CW CW NH1 H 500.00 {sd= 0.031} 0 179.9788 IMPRoper CW NH1 CR1E HA 500.00 {sd= 0.031} 0 -179.9528 IMPRoper CY CH1E HA HA 500.00 {sd= 0.031} 0 -70.0662 IMPRoper CY CR1E CR1E CY2 500.00 {sd= 0.031} 0 -0.0270 IMPRoper CY CR1E CR1E HA 500.00 {sd= 0.031} 0 -179.9841 IMPRoper CY2 CR1E CR1E HA 500.00 {sd= 0.031} 0 179.9517 IMPRoper H C CH2E NH1 500.00 {sd= 0.031} 0 0.0051 IMPRoper H C5 CRH NH1 500.00 {sd= 0.031} 0 0.0263 IMPRoper H C5 CRHH NH1 500.00 {sd= 0.031} 0 0.0282 IMPRoper H H C NH2 500.00 {sd= 0.031} 0 0.0032 IMPRoper HA CH1E HA HA 500.00 {sd= 0.031} 0 -66.5692 IMPRoper HA CH2E HA HA 500.00 {sd= 0.031} 0 -66.5934 IMPRoper HA HA CH1E OH1 500.00 {sd= 0.031} 0 -69.8494 IMPRoper HA HA CH1E S 500.00 {sd= 0.031} 0 -72.0980 IMPRoper HA HA CH1E SH1E 500.00 {sd= 0.031} 0 -72.0234 IMPRoper HA HA CH2E NH1 500.00 {sd= 0.031} 0 -70.1253 IMPRoper HA HA CH2E NH3 500.00 {sd= 0.031} 0 -70.4126 IMPRoper HA HA CH2E SM 500.00 {sd= 0.031} 0 -72.4655 IMPRoper HA HA CH2P N 500.00 {sd= 0.031} 0 -72.1561 IMPRoper HA HA CH2P NH3 500.00 {sd= 0.031} 0 -71.9018 IMPRoper HA HA SM HA 500.00 {sd= 0.031} 0 -65.1411 IMPRoper HC CH1E HC HC 500.00 {sd= 0.031} 0 -66.4313 IMPRoper HC CH2E HC HC 500.00 {sd= 0.031} 0 -66.4262 IMPRoper HC CH2G HC HC 500.00 {sd= 0.031} 0 -66.4073 IMPRoper HC HC C NC2 500.00 {sd= 0.031} 0 -0.0094 IMPRoper HC NC2 C NH1 500.00 {sd= 0.031} 0 0.0000 IMPRoper NH1 C5 CR1E NR 500.00 {sd= 0.031} 0 -0.0249 IMPRoper NH1 C5 CR1H NH1 500.00 {sd= 0.031} 0 -0.0178 IMPRoper NH1 CR1E C5 NR 500.00 {sd= 0.031} 0 0.0078 DIHEdral C CH2E CH2E CH1E 5.00 {sd= 0.031} 3 0.0000 DIHEdral CH1E CH1E CH2E CH3E 5.00 {sd= 0.031} 3 0.0000 DIHEdral CH1E CH2E CH2E CH2E 5.00 {sd= 0.031} 3 0.0000 DIHEdral CH1E CH2E CH2E SM 5.00 {sd= 0.031} 3 0.0000 DIHEdral CH1E CH2E CY CR1E 5.00 {sd= 0.031} 3 0.0000 DIHEdral CH2E CH1E CH1E NH1 5.00 {sd= 0.031} 3 0.0000 DIHEdral CH2E CH2E CH2E CH2E 5.00 {sd= 0.031} 3 0.0000 DIHEdral CH2E CH2E CH2E NH1 5.00 {sd= 0.031} 3 0.0000 DIHEdral CH2E CH2E NH1 C 5.00 {sd= 0.031} 3 0.0000 DIHEdral CH2E CH2E SM CH3E 5.00 {sd= 0.031} 3 0.0000 DIHEdral CH3E CH1E CH1E NH1 5.00 {sd= 0.031} 3 0.0000 DIHEdral CH3E CH1E CH2E CH1E 5.00 {sd= 0.031} 3 0.0000 DIHEdral CR1E C5W CH2E CH1E 5.00 {sd= 0.031} 3 0.0000 DIHEdral CR1E CF CH2E CH1E 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH1 C5 CH2E CH1E 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH1 CH1E CH2E C 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH1 CH1E CH2E C5 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH1 CH1E CH2E C5W 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH1 CH1E CH2E CF 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH1 CH1E CH2E CH1E 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH1 CH1E CH2E CH2E 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH1 CH1E CH2E CY 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH1 CH1E CH2E OH1 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH1 CH1E CH2E S 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH1 CH1E CH2E SH1E 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH3 CH1E CH2E C 5.00 {sd= 0.031} 3 0.0000 {Nter} DIHEdral NH3 CH1E CH2E C5 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH3 CH1E CH2E C5W 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH3 CH1E CH2E CF 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH3 CH1E CH2E CH1E 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH3 CH1E CH2E CH2E 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH3 CH1E CH2E CY 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH3 CH1E CH2E OH1 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH3 CH1E CH2E S 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH3 CH1E CH2E SH1E 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH3 CH1E CH1E CH3E 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH3 CH1E CH1E CH2E 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH3 CH1E CH1E OH1 5.00 {sd= 0.031} 3 0.0000 DIHEdral NH3 CH2E CH2E CH2E 5.00 {sd= 0.031} 3 0.0000 {Lys} DIHEdral NR C5 CH2E CH1E 5.00 {sd= 0.031} 3 0.0000 DIHEdral O C CH2E CH1E 5.00 {sd= 0.031} 3 0.0000 DIHEdral OC C CH2E CH1E 5.00 {sd= 0.031} 3 0.0000 DIHEdral O C CH2E CH2E 5.00 {sd= 0.031} 3 0.0000 DIHEdral OC C CH2E CH2E 5.00 {sd= 0.031} 3 0.0000 if ($par_nonbonded eq "PROLSQ") then {* nonbonding parameter section *} {* ============================ *} !! ! This uses a new form of the REPEL function: ! fVDW(R) = RCON *( Rmin ^ IREX - R ^ IREX ) ^ REXP ! ! PROLSQ uses a function of the form: ! fVDW(R) = (1 / 0.5) ^ 4 * ( Rmin ^ 4 - R ^ 4 ) ! ! The epsilon values are arbitrary since the repel function does not depend ! on epsilon. The sigma values come from converting the Van der Waals ! radii of the PROLSQ program into sigma values using the formula: ! Rmin = sigma * 2 ^ (1/6) ! Note: Prolsq decrements Van der Waals radii for non-bonded contacts ! that involve torsion angles (1:4 contacts) by .30 A, and ! hydrogen bonds (X...Y) by .2 A (X-H...Y) by .9. The former ! decrement is accomplished in CNS by using the ! 1-4 nonbonded terms. The latter decrement is accomplished by ! decreasing the van der Waals radius of hydrogens by 0.8 ! and that of O and N by 0.1 A. ! { suggested values: NBONds CUTNB=7.0 WMIN=1.5 REPEl = 1.0 REXPonent = 4 IREXponent = 1 RCONst = 16.0 TOLErance = 0.5 NBXMOD = 5 ctonnb=5.5 ctofnb=6.0 {* for consistency only, not needed for repel *} END } evaluate ($repel_radius = 1.0) evaluate ($repel_rcons = 20) evaluate ($repel_rexpo = 4) evaluate ($repel_irexp = 1) ! type van der Waals radius correction applied for hbond evaluate ($VR_C= 3.7) evaluate ($VR_N= 3.0) {-0.1} evaluate ($VR_O= 2.9) {-0.1} evaluate ($VR_S= 3.6) evaluate ($VR_FE= 2.4) evaluate ($VR_H= 1.6) {from 2.4 MN} evaluate ($VR_HH= 1.6) {-0.8} evaluate ($VR_P= 3.8) evaluate ($VR_I= 4.3) evaluate ($VR_C_SP2= 3.4) { convert radii into sigmas } evaluate ($VR_C = $VR_C / 2^(1/6)) evaluate ($VR_N = $VR_N / 2^(1/6)) evaluate ($VR_O = $VR_O / 2^(1/6)) evaluate ($VR_S = $VR_S / 2^(1/6)) evaluate ($VR_FE = $VR_FE / 2^(1/6)) evaluate ($VR_H = $VR_H / 2^(1/6)) evaluate ($VR_HH = $VR_HH / 2^(1/6)) evaluate ($VR_P = $VR_P / 2^(1/6)) evaluate ($VR_I = $VR_I / 2^(1/6)) evaluate ($VR_C_SP2=$VR_C_SP2/ 2^(1/6)) { compute 1-4 sigmas } evaluate ($VR14_C = $VR_C -0.3/ 2^(1/6)) evaluate ($VR14_N = $VR_N -0.3/ 2^(1/6)) evaluate ($VR14_O = $VR_O -0.3/ 2^(1/6)) evaluate ($VR14_S = $VR_S -0.3/ 2^(1/6)) evaluate ($VR14_FE = $VR_FE -0.3/ 2^(1/6)) evaluate ($VR14_H = $VR_H -0.3/ 2^(1/6)) evaluate ($VR14_HH = $VR_HH -0.3/ 2^(1/6)) evaluate ($VR14_P = $VR_P -0.3/ 2^(1/6)) evaluate ($VR14_I = $VR_I -0.3/ 2^(1/6)) evaluate ($VR14_C_SP2=$VR_C_SP2-0.3/ 2^(1/6)) evaluate ($VE=0.1) ! ! sigma= vdw radius / 2 ^ (1/6) ! ! eps sigma eps(1:4) sigma(1:4) ! (kcal/mol) (A) (kcal/mol) (A) ! -------------------------------------------------- NONBonded H $VE $VR_HH $VE $VR14_HH NONBonded HA $VE $VR_H $VE $VR14_H ! aliphatic hydrogen NONBonded HC $VE $VR_HH $VE $VR14_HH ! h attached to charg. ! NONBonded C $VE $VR_C_SP2 $VE $VR14_C_SP2 ! carbonyl carbon NONBonded C5 $VE $VR_C $VE $VR14_C ! carbonyl carbon NONBonded C5W $VE $VR_C $VE $VR14_C ! carbonyl carbon NONBonded CF $VE $VR_C $VE $VR14_C ! carbonyl carbon NONBonded CW $VE $VR_C $VE $VR14_C ! carbonyl carbon NONBonded CY $VE $VR_C $VE $VR14_C ! carbonyl carbon NONBonded CY2 $VE $VR_C $VE $VR14_C ! carbonyl carbon NONBonded CH1E $VE $VR_C $VE $VR14_C ! \ NONBonded CH2E $VE $VR_C $VE $VR14_C ! extended carbons NONBonded CH2G $VE $VR_C $VE $VR14_C ! extended carbons NONBonded CH2P $VE $VR_C $VE $VR14_C ! extended carbons NONBonded CH3E $VE $VR_C $VE $VR14_C ! / NONBonded CR1E $VE $VR_C $VE $VR14_C ! ring carbons NONBonded CR1H $VE $VR_C $VE $VR14_C ! ring carbons NONBonded CR1W $VE $VR_C $VE $VR14_C ! ring carbons NONBonded CRHH $VE $VR_C $VE $VR14_C ! ring carbons NONBonded CRH $VE $VR_C $VE $VR14_C ! ring carbons ! NONBonded N $VE $VR_N $VE $VR14_N NONBonded NC2 $VE $VR_N $VE $VR14_N NONBonded NH1 $VE $VR_N $VE $VR14_N NONBonded NH2 $VE $VR_N $VE $VR14_N NONBonded NH3 $VE $VR_N $VE $VR14_N NONBonded NP $VE $VR_N $VE $VR14_N NONBonded NR $VE $VR_N $VE $VR14_N ! NONBonded O $VE $VR_O $VE $VR14_O NONBonded OC $VE $VR_O $VE $VR14_O NONBonded OH1 $VE $VR_O $VE $VR14_O ! NONBonded S $VE $VR_S $VE $VR14_S NONBonded SM $VE $VR_S $VE $VR14_S NONBonded SH1E $VE $VR_S $VE $VR14_S elseif ($par_nonbonded eq "PARMALLH6") then { suggested values for refinement in vacuo NBONds CUTNB=10 WMIN=1.5 REPEl = 0.0 rdie vswitch TOLErance = 0.5 NBXMOD = 5 ctonnb=5.5 ctofnb=9.0 END HBOND AEXP=4 REXP=6 HAEX=4 AAEX=2 ACCEPTORS CUTHB=4.5 CTOFHB=4.0 CTONHB=3.5 CUTHA=90.0 CTOFHA=70.0 CTONHA=50.0 end or { suggested values: NBONds CUTNB=7.0 WMIN=1.5 REPEl = 0.8 REXPonent = 2 IREXponent = 2 RCONst = 5.0 TOLErance = 0.5 NBXMOD = 5 ctonnb=5.5 ctofnb=6.0 {* for consistency only, not needed for repel *} END } } evaluate ($repel_radius = 0.8) evaluate ($repel_rcons = 5.0) evaluate ($repel_rexpo = 2) evaluate ($repel_irexp = 2) NONBonded C 0.0903 3.2072 0.0903 3.2072 NONBonded CR1E 0.0903 3.2072 0.0903 3.2072 NONBonded CF 0.0903 3.2072 0.0903 3.2072 NONBonded CY 0.0903 3.2072 0.0903 3.2072 NONBonded CY2 0.0903 3.2072 0.0903 3.2072 NONBonded CR1W 0.0903 3.2072 0.0903 3.2072 NONBonded CW 0.0903 3.2072 0.0903 3.2072 NONBonded C5W 0.0903 3.2072 0.0903 3.2072 NONBonded CN 0.0903 3.2072 0.0903 3.2072 NONBonded C5 0.0903 3.2072 0.0903 3.2072 NONBonded CH1E 0.0903 3.2072 0.0903 3.2072 NONBonded CH2E 0.0903 3.2072 0.0903 3.2072 NONBonded CH3E 0.0903 3.2072 0.0903 3.2072 NONBonded CH2G 0.0903 3.2072 0.0903 3.2072 NONBonded CH2P 0.0903 3.2072 0.0903 3.2072 NONBonded CRH 0.0903 3.2072 0.0903 3.2072 NONBonded CR1H 0.0903 3.2072 0.0903 3.2072 NONBonded CRHH 0.0903 3.2072 0.0903 3.2072 NONBonded H 0.0498 1.4254 0.0498 1.4254 NONBonded HA 0.0045 2.6157 0.0045 2.6157 NONBonded HC 0.0498 1.4254 0.0498 1.4254 NONBonded N 0.1592 2.7618 0.1592 2.7618 NONBonded NR 0.1592 2.7618 0.1592 2.7618 NONBonded NH1 0.1592 2.7618 0.1592 2.7618 NONBonded NH2 0.1592 2.7618 0.1592 2.7618 NONBonded NH3 0.1592 2.7618 0.1592 2.7618 NONBonded NC2 0.1592 2.7618 0.1592 2.7618 NONBonded O 0.2342 2.6406 0.2342 2.6406 NONBonded OC 1.0244 2.6406 1.0244 2.6406 NONBonded OH1 0.2342 2.6406 0.2342 2.6406 NONBonded S 0.0239 3.3854 0.0239 3.3854 NONBonded SM 0.0239 3.3854 0.0239 3.3854 NONBonded SH1E 0.0239 3.3854 0.0239 3.3854 !! HBOND AEXP=4 REXP=6 HAEX=4 AAEX=2 ACCEPTORS !! CUTHB=4.5 CTOFHB=4.0 CTONHB=3.5 CUTHA=90.0 CTOFHA=70.0 CTONHA=50.0 ! AEXP 4 REXP 6 HAEX 4 AAEX 2 ! Emin Rmin ! (Kcal/mol) (A) hbond N*+* N% -3.00 3.0! VALUES FROM VINOGRADOV AND LINELL FOR hbond N*+* O* -3.50 2.9! TYPICAL LENGTHS AND DEPTHS. hbond OH* N% -4.00 2.85 hbond OH* O* -4.25 2.75 hbond SH1E N% -3.00 3.0 !! added, ATB hbond SH1E O* -3.50 2.9 !! added, ATB elseif ($par_nonbonded eq "OPLSX") then ! these are close to the original OPLS parameters without introducing ! new atom types. The commented out lines are for atom types that ! are unique in OPLS but would require additional atom types in ! allhdg. Michael Nilges. { suggested values for refinement in H2O NBONds CUTNB=12 WMIN=1.5 REPEl = 0.0 cdie shift TOLErance = 0.5 NBXMOD = 5 ctonnb=5.5 ctofnb=11.0 END } evaluate ($repel_radius = 0.0) NONBonded C 0.105 3.750 0.013 3.750 {OPLS C}! ! NONBonded C 0.110 3.750 0.014 3.750 {OPLS CAJ}! NONBonded CY2 0.105 3.750 0.013 3.750 {OPLS C} NONBonded CF 0.110 3.750 0.014 3.750 {OPLS CA} NONBonded CY 0.110 3.750 0.014 3.750 {OPLS CA} NONBonded CW 0.145 3.750 0.018 3.750 {OPLS CB} ! NONBonded CW 0.130 3.750 0.016 3.750 {OPLS CN} NONBonded CR1E 0.110 3.750 0.014 3.750 {OPLS CD}! ! NONBonded CR1E 0.130 3.750 0.016 3.750 {OPLS CG}! NONBonded CR1H 0.145 3.750 0.018 3.750 {OPLS CGJ} NONBonded CR1W 0.110 3.750 0.014 3.750 {OPLS CD}! NONBonded CH1E 0.080 3.800 0.010 3.800 {OPLS CH} ! NONBonded CH1E 0.080 3.850 0.010 3.850 {OPLS CHJ} NONBonded CRHH 0.145 3.750 0.018 3.750 {OPLS CP} NONBonded C5W 0.145 3.750 0.018 3.750 {OPLS CS} NONBonded CH2G 0.118 3.800 0.015 3.800 {OPLS C2} NONBonded CH2P 0.118 3.905 0.015 3.905 {OPLS C2J} ! NONBonded CH2P 0.118 3.800 0.015 3.800 {OPLS C2} NONBonded CH2E 0.118 3.905 0.015 3.905 {OPLS C2J} ! NONBonded CH3E 0.118 3.905 0.015 3.905 {OPLS C3} NONBonded CH3E 0.160 3.910 0.020 3.910 {OPLS C3J} ! NONBonded CH3E 0.175 3.905 0.022 3.905 {OPLS C3K} ! NONBonded CH3E 0.170 3.800 0.021 3.800 {OPLS C3L} NONBonded C5 0.145 3.750 0.145 3.750 {OPLS CC} NONBonded CRH 0.145 3.750 0.145 3.750 {OPLS 43} NONBonded H 0.05 0.50 0.004 0.50 NONBonded HA 0.05 0.50 0.004 0.50 NONBonded HC 0.05 0.50 0.004 0.50 NONBonded N 0.170 3.250 0.021 3.250 NONBonded NR 0.170 3.250 0.021 3.250 NONBonded NH1 0.170 3.250 0.021 3.250 NONBonded NH2 0.170 3.250 0.021 3.250 NONBonded NH3 0.170 3.250 0.021 3.250 NONBonded NC2 0.170 3.250 0.021 3.250 NONBonded O 0.210 2.960 0.021 2.960 NONBonded OC 0.210 2.960 0.021 2.960 NONBonded OH1 0.170 3.070 0.021 3.070 NONBonded S 0.250 3.550 0.031 3.550 NONBonded SM 0.250 3.550 0.031 3.550 NONBonded SH1E 0.250 3.550 0.031 3.550 else {standard PARALLHDG parameters} { suggested values: NBONds CUTNB=7.0 WMIN=1.5 REPEl = 0.78 REXPonent = 2 IREXponent = 2 RCONst = 5.0 TOLErance = 0.5 NBXMOD = 5 ctonnb=5.5 ctofnb=6.0 {* for consistency only, not needed for repel *} END } evaluate ($repel_radius = 0.78) evaluate ($repel_rcons = 5.0) evaluate ($repel_rexpo = 2) evaluate ($repel_irexp = 2) NONBonded C 0.0903 3.3409 0.0903 3.3409 NONBonded CR1E 0.1200 3.3409 0.1200 3.3409 NONBonded CF 0.1200 3.3409 0.1200 3.3409 NONBonded CY 0.1200 3.3409 0.1200 3.3409 NONBonded CY2 0.1200 3.3409 0.1200 3.3409 NONBonded CR1W 0.1200 3.3409 0.1200 3.3409 NONBonded CW 0.1450 3.3409 0.1450 3.3409 NONBonded C5W 0.1450 3.3409 0.1450 3.3409 NONBonded CN 0.1450 3.3409 0.1450 3.3409 NONBonded C5 0.1200 3.3409 0.1200 3.3409 NONBonded CH1E 0.0903 3.3409 0.0903 3.3409 NONBonded CH2E 0.0903 3.3409 0.0903 3.3409 NONBonded CH3E 0.0903 3.3409 0.0903 3.3409 NONBonded CH2G 0.0903 3.3409 0.0903 3.3409 NONBonded CH2P 0.1450 3.3409 0.1450 3.3409 NONBonded CRH 0.1200 3.3409 0.1200 3.3409 NONBonded CR1H 0.1200 3.3409 0.1200 3.3409 NONBonded CRHH 0.1200 3.3409 0.1200 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 NR 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 NC2 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 OH1 0.2342 2.7755 0.2342 2.7755 NONBonded S 0.0239 3.7458 0.0239 3.7458 NONBonded SM 0.0239 3.7458 0.0239 3.7458 NONBonded SH1E 0.0239 3.7458 0.0239 3.7458 NBFIx H NR 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 OH1 44.200 1.000 44.200 1.000 NBFIx HC NR 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 OH1 44.200 1.000 44.200 1.000 end if set echo on message on end