From b319ae5ae019492b596cae3f3376b60cfdc4465e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 22 Jun 2013 14:51:52 +0200 Subject: [PATCH] published COMPASS parameters collected by Paul Saxe --- .../biosym_frc_files/compass_published.frc | 1381 +++++++++++++++++ 1 file changed, 1381 insertions(+) create mode 100644 tools/msi2lmp/biosym_frc_files/compass_published.frc diff --git a/tools/msi2lmp/biosym_frc_files/compass_published.frc b/tools/msi2lmp/biosym_frc_files/compass_published.frc new file mode 100644 index 0000000000..6c2e681b5c --- /dev/null +++ b/tools/msi2lmp/biosym_frc_files/compass_published.frc @@ -0,0 +1,1381 @@ +!BIOSYM forcefield 1 + +#version compass_published.frc 1.1 30-Jun-09 +#version compass_published.frc 1.0 01-Jun-09 + +#define compass + +!Ver Ref Function Label +!---- --- --------------------------------- ------ + 1.0 1 atom_types compass + 1.0 1 equivalence compass + 1.0 1 quartic_bond compass + 1.0 1 quartic_angle compass + 1.0 1 bond-bond compass + 1.0 1 bond-bond_1_3 compass + 1.0 1 bond-angle compass + 1.0 1 torsion_3 compass + 1.0 1 end_bond-torsion_3 compass + 1.0 1 middle_bond-torsion_3 compass + 1.0 1 angle-torsion_3 compass + 1.0 1 wilson_out_of_plane compass + 1.0 1 angle-angle compass + 1.0 1 angle-angle-torsion_1 compass + 1.0 1 nonbond(9-6) compass + 1.0 1 bond_increments compass + 1.0 1 templates compass + +#atom_types compass + +> Atom type definitions for any variant of compass +> Masses from CRC 1973/74 pages B-250. + +!Ver Ref Type Mass Element Comment +!---- --- ---- ---------- ------- ----------------------------------------- + 1.0 5 ar 39.94400 Ar argon + 1.0 1 c3a 12.01115 C aromatic carbon + 1.0 5 c1o 12.01115 C carbon in CO + 1.0 5 c2= 12.01115 C carbon in CO2 and CS2 + 1.0 7 c3' 12.01115 C carbonyl carbon [one polar substituent] + 1.0 1 c4 12.01115 C generic sp3 carbon + 1.0 8 c41o 12.01115 C carbon, sp3, in methanol + 1.0 8 c43o 12.01115 C carbon, sp3 in secondary alcohols + 1.0 1 c43 12.01115 C sp3 carbon with three heavy atoms attached + 1.0 1 c44 12.01115 C sp3 carbon with four heavy atoms attached + 1.0 3 c4o 12.01115 C alpha carbon + 1.0 9 c4z 12.01115 C carbon, sp3, bonded to -N3 + 1.0 1 h1 1.00797 H nonpolar hydrogen + 1.0 5 h1h 1.00797 H hydrogen in H2 + 1.0 3 h1o 1.00797 H strongly polar hydrogen, bonded to O,F + 1.0 5 he 4.00300 He helium + 1.0 5 kr 83.80000 Kr krypton + 1.0 5 n1n 14.00670 N nitrogen in N2 + 1.0 5 n1o 14.00670 N nitrogen in NO + 1.0 5 n1z 14.00670 N nitrogen, terminal atom in -N3 + 1.0 4 n2= 14.00670 N nitrogen + 1.0 5 n2o 14.00670 N nitrogen in NO2 + 1.0 9 n2t 14.00670 N nitrogen, central atom in -N3 + 1.0 9 n2z 14.00670 N nitrogen, first atom in -N3 + 1.0 7 n3m 14.00670 N sp3 nitrogen in amides without hydrogen + 1.0 6 n3o 14.00670 N nitrogen in nitro group + 1.0 5 ne 20.18300 Ne neon + 1.0 5 o1= 15.99940 O oxygen in NO2 and SO2 [and carbonyl] + 1.0 5 o1=* 15.99940 O oxygen in CO2 + 1.0 6 o12 15.99940 O oxygen in nitro group (-NO2) + 1.0 5 o1c 15.99940 O oxygen in CO + 1.0 5 o1n 15.99940 O oxygen in NO + 1.0 5 o1o 15.99940 O oxygen in O2 + 1.0 2 o2 15.99940 O generic oxygen with two bonds attached + 1.0 3 o2e 15.99940 O ether oxygen + 1.0 3 o2h 15.99940 O hydroxyl oxygen + 1.0 6 o2n 15.99940 O oxygen in nitrates + 1.0 7 o2s 15.99940 O ester oxygen + 1.0 2 o2z 15.99940 O oxygen, in siloxanes and zeolites + 1.0 4 p4= 30.97380 P phosphorous + 1.0 5 s1= 32.06400 S sulfur in CS2 + 1.0 5 s2= 32.06400 S sulfur in SO2 + 1.0 2 si4 28.08600 Si generic silicon with four bonds attached + 1.0 2 si4c 28.08600 Si a subset of si4, non-hydrogen atom attached [siloxanes] + 1.0 5 xe 131.30000 Xe xenon + + +#equivalence compass + +! Equivalences +! ----------------------------------------- +!Ver Ref Type NonB Bond Angle Torsion OOP +!---- --- ---- ---- ---- ----- ------- ---- + 1.0 5 ar ar ar ar ar ar + 1.0 5 c1o c1o c1o c1o c1o c1o + 1.0 5 c2= c2= c2= c2= c2= c2= + 1.0 1 c3a c3a c3a c3a c3a c3a + 1.0 7 c3' c3' c3' c3' c3' c3' + 1.0 1 c4 c4 c4 c4 c4 c4 + 1.0 8 c41o c41o c4 c4 c4 c4 + 1.0 8 c43o c43o c4 c4 c4 c4 + 1.0 1 c43 c43 c4 c4 c4 c4 + 1.0 1 c44 c44 c4 c4 c4 c4 + 1.0 3 c4o c4o c4 c4 c4 c4 + 1.0 9 c4z c4z c4 c4 c4 c4 + 1.0 1 h1 h1 h1 h1 h1 h1 + 1.0 5 h1h h1h h1h h1 h1 h1 + 1.0 3 h1o h1o h1 h1 h1 h1 + 1.0 5 he he he he he he + 1.0 5 kr kr kr kr kr kr + 1.0 5 n1n n1n n1n n1n n1n n1n + 1.0 5 n1o n1o n1o n1o n1o n1o + 1.0 9 n1z n1z n1t n1t n1t n1t + 1.0 4 n2= n2= n2= n2= n2= n2= + 1.0 5 n2o n2o n2o n2o n2o n2o + 1.0 9 n2t n2t n2t n2t n2t n2t + 1.0 9 n2z n2z n2z n2z n2z n2z + 1.0 7 n3m n3m n3m n3m n3m n3m + 1.0 6 n3o n3o n3o n3o n3o n3o + 1.0 5 ne ne ne ne ne ne + 1.0 5 o1= o1= o1= o1= o1= o1= + 1.0 5 o1=* o1=* o1= o1= o1= o1= + 1.0 6 o12 o12 o1= o1= o1= o1= + 1.0 5 o1c o1c o1c o1c o1c o1c + 1.0 5 o1n o1n o1n o1n o1n o1n + 1.0 5 o1o o1o o1o o1o o1o o1o + 1.0 2 o2 o2 o2 o2 o2 o2 + 1.0 3 o2h o2h o2h o2 o2 o2 + 1.0 3 o2e o2e o2e o2 o2 o2 + 1.0 6 o2n o2n o2n o2n o2 o2 + 1.0 7 o2s o2s o2e o2 o2 o2 + 1.0 2 o2z o2z o2z o2z o2z o2z + 1.0 4 p4= p4= p4= p4= p4= p4= + 1.0 5 s1= s1= s1= s1= s1= s1= + 1.0 5 s2= s2= s2= s2= s2= s2= + 1.0 2 si4 si4 si4 si4 si4 si4 + 1.0 2 si4c si4c si4 si4 si4 si4 + 1.0 5 xe xe xe xe xe xe + + +#quartic_bond compass + +> E = K2 * (R - R0)^2 + K3 * (R - R0)^3 + K4 * (R - R0)^4 + +!Ver Ref I J R0 K2 K3 K4 +!---- --- ---- ---- ------- -------- --------- -------- + 1.0 1 c3a c3a 1.4170 470.8361 -627.6179 1327.6345 + 1.0 1 c3a c4 1.5010 321.9021 -521.8208 572.1628 + 1.0 1 c3a h1 1.0982 372.8251 -803.4526 894.3173 + 1.0 1 c4 c4 1.5300 299.6700 -501.7700 679.8100 + 1.0 1 c4 h1 1.1010 345.0000 -691.8900 844.6000 + 1.0 2 o2z si4 1.6400 350.1232 -517.3424 673.7067 + 1.0 3 c3a o2 1.3768 428.8798 -738.2350 1114.9655 + 1.0 3 c3a o2e 1.3768 428.8798 -738.2351 1114.9655 + 1.0 3 c3a o2h 1.3768 428.8798 -738.2351 1114.9655 + 1.0 3 c4 o2e 1.4200 400.3954 -835.1951 1313.0142 + 1.0 3 c4 o2h 1.4200 400.3954 -835.1951 1313.0142 + 1.0 3 h1 o2h 0.9494 540.3633 -1311.8663 2132.4446 + 1.0 4 c3a n2= 1.4000 350.0000 0.0000 0.0000 + 1.0 4 c3a p4= 1.7890 197.7020 -332.2510 325.7160 + 1.0 4 c4 n2= 1.4740 337.0600 -147.3700 213.6330 + 1.0 4 c4 p4= 1.8000 218.1400 -329.5110 290.3490 + 1.0 4 cl1p p4= 2.0000 158.7770 -239.1290 210.0840 + 1.0 4 f1p p4= 1.5650 340.0000 -882.3840 1197.9190 + 1.0 4 h1 n2= 1.0310 540.1120 -1500.2952 2431.0080 + 1.0 4 h1 p4= 1.4300 285.2040 -575.6850 677.8460 + 1.0 4 n2= p4= 1.5980 393.0060 -751.4050 767.4310 + 1.0 4 n3 p4= 1.6780 329.0000 -713.7950 902.9190 + 1.0 4 o2 p4= 1.6000 333.0980 -726.6230 924.6200 + 1.0 5 h1h h1h 0.7412 414.2185 -805.6549 914.1296 + 1.0 5 n1n n1n 1.0977 1651.3730 -4069.3178 5984.9629 + 1.0 5 o1o o1o 1.2074 846.7150 -2247.1760 3478.9900 + 1.0 5 c1o o1c 1.1283 1368.7676 -3157.0007 4247.5298 + 1.0 5 n1o o1n 1.1506 1147.8362 -3167.7349 5099.5811 + 1.0 5 o1= s2= 1.4308 730.8387 -1531.7910 1859.7753 + 1.0 5 c2= o1= 1.1600 1161.3421 -2564.5706 3932.8735 + 1.0 5 n2o o1= 1.1930 620.0000 -1808.6018 3077.5918 + 1.0 5 c2= s1= 1.5540 559.0065 -1348.6633 1248.8604 + 1.0 6 c3a n3o 1.4300 313.8329 -568.6087 600.9597 + 1.0 6 c4 n3o 1.4740 301.6051 -535.7028 555.0420 + 1.0 6 c4 o2n 1.4350 400.3954 -835.1951 1313.0142 + 1.0 6 h1 n3o 1.0400 439.9346 -943.7307 1180.9318 + 1.0 6 n3o o1= 1.2100 765.0664 -2070.2830 2793.3218 + 1.0 6 n3o o2n 1.4020 300.0000 -1000.0000 2000.0000 + 1.0 7 c3' o2e 1.3750 368.7309 -832.4784 1274.0231 + 1.0 7 c3' c4 1.5140 312.3719 -465.8290 473.8300 + 1.0 7 c3' o1= 1.2160 823.7948 -1878.7939 2303.5310 + 1.0 7 c3' c3a 1.4890 339.3574 -655.7236 670.2362 + 1.0 7 c3' n3m 1.3850 359.1591 -558.4730 1146.3810 + 1.0 7 c3a n3m 1.3950 344.0452 -652.1208 1022.2242 + 1.0 9 n1t n1t 1.1354 1337.7450 -2675.4900 3121.4049 + 1.0 9 n2z n2t 1.2343 720.3345 -1542.6689 1799.7804 + 1.0 9 n2t n1t 1.1354 1198.7450 -2675.4900 3121.4049 + 1.0 9 n2z c4 1.4814 324.4578 -648.9156 757.0681 + 1.0 9 n2z h1 1.0221 440.1623 -960.3246 1120.3787 + 1.0 10 c3a si4 1.8634 233.2433 -276.8692 161.6659 + 1.0 10 c4 si4 1.8995 189.6536 -279.4210 307.5135 + 1.0 10 h1 si4 1.4783 202.7798 -305.3603 280.2685 + 1.0 10 si4 si4 2.3384 114.2164 -140.4212 80.7084 + 1.0 10 c4 n3m 1.4000 350.0000 0.0000 0.0000 + + +#quartic_angle compass + +> Delta = Theta - Theta0 +> E = K2 * Delta^2 + K3 * Delta^3 + K4 * Delta^4 + +!Ver Ref I J K Theta0 K2 K3 K4 +!---- --- ---- ---- ---- -------- ------- -------- -------- + 1.0 1 c3a c3a c3a 118.9000 61.0226 -34.9931 0.0000 + 1.0 1 c3a c3a c4 120.0500 44.7148 -22.7352 0.0000 + 1.0 1 c3a c3a h1 117.9400 35.1558 -12.4682 0.0000 + 1.0 1 c3a c4 c3a 111.0000 44.3234 -9.4454 0.0000 + 1.0 1 c3a c4 c4 108.4000 43.9594 -8.3924 -9.3379 + 1.0 1 c3a c4 h1 111.0000 44.3234 -9.4454 0.0000 + 1.0 1 c4 c4 c4 112.6700 39.5160 -7.4430 -9.5583 + 1.0 1 c4 c4 h1 110.7700 41.4530 -10.6040 5.1290 + 1.0 1 h1 c4 h1 107.6600 39.6410 -12.9210 -2.4318 + 1.0 2 h1 o2z si4 122.8000 23.7764 -19.8152 9.6331 + 1.0 2 si4 o2z si4 159.0000 8.5000 -13.4188 -4.1785 + 1.0 2 c3a si4 o2z 114.9060 23.0218 -31.3993 24.9814 + 1.0 2 c4 si4 o2z 114.9060 23.0218 -31.3993 24.9814 + 1.0 2 h1 si4 o2z 107.4000 57.6643 -10.6506 4.6274 + 1.0 2 o2z si4 o2z 110.7000 70.3069 -6.9375 0.0000 + 1.0 3 c3a c3a o2 123.4200 73.6781 -21.6787 0.0000 + 1.0 3 c4 c4 o2 111.2700 54.5381 -8.3642 -13.0838 + 1.0 3 h1 c4 o2 108.7280 58.5446 -10.8088 -12.4006 + 1.0 3 c3a o2 c4 102.9695 38.9739 -6.2595 -8.1710 + 1.0 3 c3a o2 h1 108.1900 53.1250 -8.5016 0.0000 + 1.0 3 c4 o2 c4 104.5000 35.7454 -10.0067 -6.2729 + 1.0 3 c4 o2 h1 105.8000 52.7061 -12.1090 -9.8681 + 1.0 4 c3a c3a n2= 120.0000 60.0000 0.0000 0.0000 + 1.0 4 c3a c3a p4= 120.0010 47.8410 -15.2290 -10.9070 + 1.0 4 c4 c4 n2= 117.3170 55.2420 0.0000 0.0000 + 1.0 4 h1 c4 n2= 107.4990 62.7310 0.0000 0.0000 + 1.0 4 h1 c4 p4= 110.8860 33.8300 -7.0430 -7.2460 + 1.0 4 c4 n2= h1 117.2000 37.2620 0.0000 0.0000 + 1.0 4 h1 n2= h1 110.9100 31.0910 0.0000 0.0000 + 1.0 4 h1 n2= p4= 120.0000 26.0680 -8.2980 -5.9430 + 1.0 4 p4= n2= p4= 135.0000 23.8680 -8.7360 0.0000 + 1.0 4 c4 n3 p4= 120.0830 25.0010 -6.1170 -5.4570 + 1.0 4 h1 n3 p4= 120.0830 25.0010 -6.1170 -5.4570 + 1.0 4 c4 o2 p4= 118.2830 35.0010 -10.3600 -7.8700 + 1.0 4 h1 o2 p4= 117.0000 26.0310 -5.8280 -5.6200 + 1.0 4 c3a p4= c3a 110.2310 56.1850 -17.3160 -12.7280 + 1.0 4 c3a p4= h1 108.2310 36.1850 -6.4880 -7.6460 + 1.0 4 c3a p4= n2= 109.6000 63.0620 -19.7400 -14.3290 + 1.0 4 c3a p4= n3 108.1650 70.9770 -11.5480 -15.1090 + 1.0 4 c3a p4= o2 107.3650 71.9770 -10.9430 -15.2900 + 1.0 4 c4 p4= c4 102.5000 48.2320 -5.7980 -9.9660 + 1.0 4 c4 p4= h1 102.9000 52.0710 -6.4680 -10.7730 + 1.0 4 c4 p4= n2= 119.3000 47.3660 -14.6410 -10.7360 + 1.0 4 h1 p4= h1 101.4080 39.6950 -5.1340 -8.2270 + 1.0 4 h1 p4= n2= 110.0330 45.9780 -14.0520 -10.3990 + 1.0 4 h1 p4= n3 103.9780 68.2570 -9.2210 -14.1740 + 1.0 4 h1 p4= o2 103.9780 73.2570 -9.8970 -15.2120 + 1.0 4 n2= p4= n2= 125.0000 90.5230 -20.8010 -19.6020 + 1.0 4 n2= p4= n3 123.2150 89.9230 -32.6120 -21.0960 + 1.0 4 n2= p4= o2 112.2150 99.9230 -32.0930 -22.8210 + 1.0 4 n3 p4= n3 107.1000 85.7690 -5.7790 -17.4890 + 1.0 4 n3 p4= o2 108.3000 86.7690 -5.1750 -17.6710 + 1.0 4 o2 p4= o2 107.5000 86.7690 -4.5700 -17.8520 + 1.0 5 o1= c2= o1= 180.0000 57.1000 0.0000 0.0000 + 1.0 5 s1= c2= s1= 180.0000 48.0000 0.0000 0.0000 + 1.0 5 o1= n2o o1= 134.1000 150.0000 -82.1013 -40.0005 + 1.0 5 o1= s2= o1= 119.3000 115.2627 -35.6278 -26.1261 + 1.0 6 c3a c3a n3o 118.8000 29.2436 -8.8495 -6.6020 + 1.0 6 h1 c4 n3o 107.0000 54.9318 -9.1333 -11.5434 + 1.0 6 h1 c4 o2n 108.7280 58.5446 -10.8088 -12.4006 + 1.0 6 c3a n3o o1= 117.7000 63.9404 -18.4524 -14.3129 + 1.0 6 c4 n3o o1= 117.5000 64.5228 -18.4582 -14.4215 + 1.0 6 h1 n3o o1= 115.7000 53.8034 -14.1991 -11.8708 + 1.0 6 o1= n3o o1= 128.0000 95.1035 -47.4240 -27.9164 + 1.0 6 c4 o2n n3o 108.5000 55.7454 -10.0067 -6.2729 + 1.0 6 c4 c4 o2n 105.0000 54.5381 -8.3642 -13.0838 + 1.0 6 o2n n3o o1= 112.8000 85.5228 -18.4582 -14.4215 + 1.0 7 c3' o2 c4 109.0000 38.9739 -6.2595 -8.1710 + 1.0 7 c3' c4 h1 107.8594 38.0833 -17.5074 0.0000 + 1.0 7 c3' n3m c3' 121.9556 76.3105 -26.3166 -17.6944 + 1.0 7 c3a c3a c3' 116.0640 71.2598 -15.8273 2.0506 + 1.0 7 c3a c3' n3m 108.4400 84.8377 -19.9640 2.7405 + 1.0 7 c3a c3' o1= 125.5320 72.3167 -16.0650 2.0818 + 1.0 7 c3a c3a n3m 120.7640 73.2738 -27.4033 13.3920 + 1.0 7 c3a n3m c3' 120.0700 47.1131 -32.5592 13.1257 + 1.0 7 o1= c3' o2 118.9855 98.6813 -22.2485 10.3673 + 1.0 7 o1= c3' c4 119.3000 65.1016 -17.9766 0.0000 + 1.0 7 o2 c3' c4 100.3182 88.8631 -3.8323 -7.9802 + 1.0 7 n3m c3' o1= 121.5420 92.5720 -34.4800 -11.1871 + 1.0 9 n2z n2t n1t 171.6211 47.7899 0.0000 0.0000 + 1.0 9 n2t n2z h1 110.0345 55.7635 0.6618 0.0022 + 1.0 9 n2t n2z c4 113.5017 82.6294 0.9845 0.0033 + 1.0 9 n2z c4 h1 107.9744 52.7803 0.6615 0.0023 + 1.0 9 n2z c4 c4 110.9900 77.9387 0.9499 0.0033 + 1.0 10 c3a c3a si4 120.0000 30.4689 -23.5439 0.0000 + 1.0 10 c4 c4 si4 112.6700 39.5160 -7.4430 0.0000 + 1.0 10 h1 c4 si4 112.0355 28.7721 -13.9523 0.0000 + 1.0 10 c3a si4 h1 109.5932 41.9497 -42.3639 48.1442 + 1.0 10 c4 si4 c4 113.1855 36.2069 -20.3939 20.0172 + 1.0 10 c4 si4 h1 112.0977 36.4832 -12.8094 0.0000 + 1.0 10 h1 si4 h1 108.6051 32.5415 -8.3164 0.0000 + 1.0 10 c4 si4 si4 113.0000 19.4692 -34.3471 0.0000 + 1.0 10 h1 si4 si4 112.0893 22.5062 -11.5926 0.0000 + 1.0 10 si4 si4 si4 114.2676 24.9501 -19.5949 0.0000 + +#bond-bond compass + +> E = K(b,b') * (R - R0) * (R' - R0') + +!Ver Ref I J K K(b,b') +!---- --- ---- ---- ---- ------- + 1.0 1 c3a c3a c3a 68.2856 + 1.0 1 c3a c3a c4 12.0676 + 1.0 1 c3a c3a h1 1.0795 + 1.0 1 c3a c4 h1 2.9168 + 1.0 1 c4 c4 h1 3.3872 + 1.0 1 h1 c4 h1 5.3316 + 1.1 2 h1 c4 si4 6.3820 + 1.0 2 h1 o2z si4 6.3820 + 1.0 2 si4 o2z si4 41.1143 + 1.0 2 c4 si4 o2z 5.4896 + 1.0 2 h1 si4 o2z 11.6183 + 1.0 2 o2z si4 o2z 41.1143 + 1.0 3 c3a c3a o2 48.4754 + 1.0 3 h1 c3a o2 4.5800 + 1.0 3 c4 c4 o2 11.4318 + 1.0 3 h1 c4 o2 23.1979 + 1.0 3 o2 c4 o2 8.2983 + 1.0 3 c3a o2 h1 20.6577 + 1.0 3 c4 o2 c4 -7.1131 + 1.0 3 c4 o2 h1 -9.6879 + 1.0 4 c4 c4 n2= 22.7100 + 1.0 4 h1 c4 n2= 5.6640 + 1.0 4 h1 c4 p4= 1.0500 + 1.0 4 c4 n2= h1 12.5630 + 1.0 4 h1 n2= h1 1.4570 + 1.0 4 h1 n2= p4= -18.2870 + 1.0 4 p4= n2= p4= 20.0000 + 1.0 4 c4 p4= c4 6.2460 + 1.0 4 c4 p4= h1 3.8820 + 1.0 4 c4 p4= n2= 1.0720 + 1.0 4 h1 p4= h1 20.0000 + 1.0 4 h1 p4= n2= 12.5700 + 1.0 4 n2= p4= n2= 20.0000 + 1.0 5 o1= c2= o1= 275.4350 + 1.0 5 s1= c2= s1= 100.7369 + 1.0 5 o1= n2o o1= 20.0000 + 1.0 5 o1= s2= o1= 20.0000 + 1.0 6 c3a c3a n3o 21.0495 + 1.0 6 c4 c4 o2n 11.4318 + 1.0 6 h1 c4 n3o 3.3770 + 1.0 6 h1 c4 o2n 23.1979 + 1.0 6 c3a n3o o1= 93.7948 + 1.0 6 o2n n3o o1= 80.0000 + 1.0 6 c4 n3o o1= 48.1403 + 1.0 6 h1 n3o o1= 14.8226 + 1.0 6 o1= n3o o1= 265.7106 + 1.0 7 c3' o2 c3a 69.5999 + 1.0 7 c3' c4 h1 2.2522 + 1.0 7 c3' n3m c3' 25.9530 + 1.0 7 c3a c4 o2 0.0000 + 1.0 7 c3a o2 c3a 0.0000 + 1.0 7 c3' c3a c3a 37.8749 + 1.0 7 c3a c3' n3m 0.0000 + 1.0 7 c3a c3' o1= 116.9445 + 1.0 7 c3a c3a n3m 37.8749 + 1.0 7 c3a n3m c3' 0.0000 + 1.0 7 o1= c3' o2 210.1813 + 1.0 7 c4 c3' o1= 77.5201 + 1.0 7 c4 c3' o2 19.1069 + 1.0 7 n3m c3' o1= 138.4954 + 1.0 9 h1 n2z n2t 14.9026 + 1.0 9 n2z n2t n1t 204.9909 + 1.0 9 n2t n2z c4 84.2075 + 1.0 9 n2z c4 h1 18.4621 + 1.0 9 n2z c4 c4 36.9309 + 1.0 10 h1 c4 si4 1.6561 + 1.0 10 c3a c3a si4 21.3938 + 1.0 10 c3a si4 h1 3.9264 + 1.0 10 c4 si4 c4 3.7419 + 1.0 10 c4 si4 h1 3.9340 + 1.0 10 c4 si4 si4 2.3030 + 1.0 10 h1 si4 h1 4.6408 + 1.0 10 h1 si4 si4 3.5172 + 1.0 10 si4 si4 si4 6.0704 + + +#bond-bond_1_3 compass + +> E = K(b,b') * (R - R0) * (R' - R0') + +!Ver Ref I J K L K(b,b') +!--- --- ----- ----- ----- ----- -------- + 1.0 1 c3a c3a c3a c3a 53.0000 + 1.0 1 c3a c3a c3a c4 2.5085 + 1.0 1 c3a c3a c3a h1 -6.2741 + 1.0 1 c4 c3a c3a h1 0.8743 + 1.0 1 h1 c3a c3a h1 -1.7077 + 1.0 1 c3a c3a c4 h1 -3.4826 + 1.0 3 c3a c3a c3a o2 -2.2436 + 1.0 3 h1 c3a c3a o2 -2.0517 + 1.0 3 c3a c3a o2 h1 1.1590 + + +#bond-angle compass + +> E = K * (R - R0) * (Theta - Theta0) + +!Ver Ref I J K K(b,theta) K(b',theta) +!---- --- ---- ---- ---- ---------- ----------- + 1.0 1 c3a c3a c3a 28.8708 + 1.0 1 c3a c3a c4 31.0771 47.0579 + 1.0 1 c3a c3a h1 20.0033 24.2183 + 1.0 1 c3a c4 h1 26.4608 11.7717 + 1.0 1 c4 c4 c4 8.0160 + 1.0 1 c4 c4 h1 20.7540 11.4210 + 1.0 1 h1 c4 h1 18.1030 + 1.0 2 h1 o2z si4 18.0902 31.0726 + 1.0 2 si4 o2z si4 28.6686 + 1.0 2 c4 si4 o2z 6.4278 20.5669 + 1.0 2 h1 si4 o2z 6.4278 20.5669 + 1.0 2 o2z si4 o2z 23.4380 + 1.0 3 c3a c3a o2 58.4790 107.6806 + 1.0 3 c4 c4 o2 2.6868 20.4033 + 1.0 3 h1 c4 o2 4.6189 55.3270 + 1.0 3 c3a o2 h1 53.8614 23.9224 + 1.0 3 c4 o2 c4 -2.8112 + 1.0 3 c4 o2 h1 28.5800 18.9277 + 1.0 4 c4 c4 n2= 19.2440 59.4220 + 1.0 4 h1 c4 n2= 6.4070 46.3730 + 1.0 4 h1 c4 p4= 19.8120 16.9400 + 1.0 4 c4 n2= h1 18.4860 7.8370 + 1.0 4 h1 n2= h1 8.4900 + 1.0 4 h1 n2= p4= 40.0630 90.7910 + 1.0 4 c4 p4= c4 12.8050 + 1.0 4 c4 p4= h1 11.1260 -19.4700 + 1.0 4 c4 p4= n2= -7.1280 26.3530 + 1.0 4 h1 p4= n2= -24.3830 72.9250 + 1.0 5 o1= n2o o1= -50.0000 + 1.0 5 o1= s2= o1= 45.0585 + 1.0 6 c3a c3a n3o 30.5211 59.8025 + 1.0 6 c4 c4 o2n 2.6868 20.4033 + 1.0 6 h1 c4 n3o 12.2491 30.5314 + 1.0 6 h1 c4 o2n 4.6189 55.3270 + 1.0 6 c3a n3o o1= 40.3757 92.1955 + 1.0 6 c4 n3o o1= 27.2141 93.9927 + 1.0 6 h1 n3o o1= -8.6275 58.6036 + 1.0 6 o1= n3o o1= 95.6936 + 1.0 7 c3' o2 c4 21.5366 -16.6748 + 1.0 7 c3' c4 h1 15.5988 14.6287 + 1.0 7 c3' n3m c3' 20.0533 + 1.0 7 c3' c3a c3a 23.6977 45.8865 + 1.0 7 c3a c3a n3m 35.8865 53.6977 + 1.0 7 c3a c3' o1= 72.8758 76.1093 + 1.0 7 o1= c3' o2 79.4497 57.0987 + 1.0 7 c4 c3' o1= 31.8455 46.6613 + 1.0 7 c4 c3' o2 1.3435 4.6978 + 1.0 7 n3m c3' o1= 62.7124 52.4045 + 1.0 9 h1 n2z n2t 37.4419 141.1218 + 1.0 9 n2z n2t n1t 25.5611 1.2222 + 1.0 9 n2t n2z c4 195.9722 88.2679 + 1.0 9 n2z c4 h1 61.9652 3.3182 + 1.0 9 n2z c4 c4 67.8888 34.8803 + 1.0 10 c3a c3a si4 14.5831 23.7679 + 1.0 10 h1 c4 si4 16.6908 18.2764 + 1.0 10 c3a si4 h1 22.5947 8.7811 + 1.0 10 c4 si4 c4 18.5805 + 1.0 10 c4 si4 h1 13.3961 7.4104 + 1.0 10 c4 si4 si4 16.9455 11.4377 + 1.0 10 h1 si4 h1 9.3467 + 1.0 10 h1 si4 si4 5.6630 2.0706 + 1.0 10 si4 si4 si4 8.9899 + + +#torsion_3 compass + +> E = SUM(n=1,3) { V(n) * [ 1 - cos(n*Phi - Phi0(n)) ] } + +!Ver Ref I J K L V1 Phi0 V2 Phi0 V3 Phi0 +!---- --- ---- ---- ---- ---- ------- ------ ------- ------ ------- ------ + 1.0 1 c3a c3a c3a c3a 8.3667 0.0 1.2000 0.0 0.0000 0.0 + 1.0 1 c3a c3a c3a c4 0.0000 0.0 4.4072 0.0 0.0000 0.0 + 1.0 1 c3a c3a c3a h1 0.0000 0.0 3.9661 0.0 0.0000 0.0 + 1.0 1 c4 c3a c3a h1 0.0000 0.0 1.5590 0.0 0.0000 0.0 + 1.0 1 h1 c3a c3a h1 0.0000 0.0 2.3500 0.0 0.0000 0.0 + 1.0 1 c3a c3a c4 c3a -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 + 1.0 1 c3a c3a c4 c4 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 + 1.0 1 c3a c3a c4 h1 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 + 1.0 1 c3a c4 c4 h1 -0.0228 0.0 0.0280 0.0 -0.1863 0.0 + 1.0 1 c4 c4 c4 c4 0.0000 0.0 0.0514 0.0 -0.1430 0.0 + 1.0 1 c4 c4 c4 h1 0.0000 0.0 0.0316 0.0 -0.1681 0.0 + 1.0 1 h1 c4 c4 h1 -0.1432 0.0 0.0617 0.0 -0.1530 0.0 + 1.0 1 * c3a c3a * 0.0000 0.0 4.5000 0.0 0.0000 0.0 + 1.0 1 * c4 c4 * 0.0000 0.0 0.0000 0.0 -0.1530 0.0 + 1.0 2 h1 o2z si4 c4 0.0000 0.0 0.0000 0.0 -0.0500 0.0 + 1.0 2 h1 o2z si4 h1 0.0000 0.0 0.0000 0.0 -0.0500 0.0 + 1.0 2 h1 o2z si4 o2z 0.0000 0.0 0.0000 0.0 -0.0500 0.0 + 1.0 2 si4 o2z si4 c4 0.0000 0.0 0.0000 0.0 -0.0100 0.0 + 1.0 2 si4 o2z si4 h1 0.0000 0.0 0.0000 0.0 -0.0100 0.0 + 1.0 2 si4 o2z si4 o2z -0.2250 0.0 0.0000 0.0 -0.0100 0.0 + 1.0 2 * o2z si4 * 0.0000 0.0 0.0000 0.0 -0.0100 0.0 + 1.0 3 c3a c3a c3a o2 0.0000 0.0 4.8498 0.0 0.0000 0.0 + 1.0 3 h1 c3a c3a o2 0.0000 0.0 1.7234 0.0 0.0000 0.0 + 1.0 3 c3a c3a o2 c4 0.0000 0.0 1.5000 0.0 0.0000 0.0 + 1.0 3 c3a c3a o2 h1 -0.6900 0.0 0.5097 0.0 0.0095 0.0 + 1.0 3 c4 c4 c4 o2 0.7137 0.0 0.2660 0.0 -0.2545 0.0 + 1.0 3 h1 c4 c4 o2 -0.1435 0.0 0.2530 0.0 -0.0905 0.0 + 1.0 3 o2 c4 c4 o2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 + 1.0 3 c4 c4 o2 c4 -0.4000 0.0 -0.4028 0.0 -0.2450 0.0 + 1.0 3 c4 c4 o2 h1 -0.6732 0.0 -0.4778 0.0 -0.1670 0.0 + 1.0 3 h1 c4 o2 c3a 0.9513 0.0 0.1155 0.0 0.0720 0.0 + 1.0 3 h1 c4 o2 c4 0.5302 0.0 0.0000 0.0 -0.3966 0.0 + 1.0 3 h1 c4 o2 h1 0.1863 0.0 -0.4338 0.0 -0.2121 0.0 + 1.0 4 c3a c3a c3a p4= 0.0000 0.0 5.4770 0.0 0.0000 0.0 + 1.0 4 h1 c3a c3a p4= 0.0000 0.0 2.2700 0.0 0.0000 0.0 + 1.0 4 c3a c3a p4= h1 -0.2720 0.0 1.1900 0.0 0.0000 0.0 + 1.0 4 c3a c3a p4= n2= -0.2720 0.0 1.1900 0.0 0.0000 0.0 + 1.0 4 c4 c4 c4 n2= 0.0970 0.0 0.0720 0.0 -0.2580 0.0 + 1.0 4 h1 c4 c4 n2= -0.1510 0.0 0.0100 0.0 -0.1860 0.0 + 1.0 4 c4 c4 n2= h1 -5.0720 0.0 -0.4980 0.0 -0.4380 0.0 + 1.0 4 h1 c4 n2= h1 1.2660 0.0 -0.7740 0.0 0.0380 0.0 + 1.0 4 h1 c4 p4= c4 0.0000 0.0 0.0000 0.0 -0.0680 0.0 + 1.0 4 h1 c4 p4= h1 0.0000 0.0 0.0000 0.0 -0.0680 0.0 + 1.0 4 h1 c4 p4= n2= 0.0000 0.0 0.0000 0.0 -0.0680 0.0 + 1.0 4 h1 n2= p4= c3a 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 4 h1 n2= p4= c4 0.0000 0.0 0.0000 0.0 -0.3690 0.0 + 1.0 4 h1 n2= p4= h1 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 4 h1 n2= p4= o2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 4 p4= n2= p4= h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 4 p4= n2= p4= n2= 1.8000 0.0 0.5000 0.0 2.0000 0.0 + 1.0 4 h1 n3 p4= h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 4 h1 n3 p4= n2= 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 4 h1 n3 p4= o2 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 4 h1 o2 p4= h1 5.7080 0.0 2.1180 0.0 0.0000 0.0 + 1.0 4 h1 o2 p4= n2= 5.7080 0.0 2.1180 0.0 0.0000 0.0 + 1.0 4 h1 o2 p4= o2 5.7080 0.0 2.1180 0.0 0.0000 0.0 + 1.0 4 * o2 p4= * 5.7080 0.0 2.1180 0.0 0.0000 0.0 + 1.0 4 * c3a n2= * 0.0000 0.0 1.0000 0.0 0.0000 0.0 + 1.0 4 * c3a p4= * -0.2720 0.0 1.1900 0.0 0.0000 0.0 + 1.0 4 * c4 n2= * 0.0000 0.0 0.0000 0.0 -0.0200 0.0 + 1.0 4 * c4 p4= * 0.0000 0.0 0.0000 0.0 -0.0680 0.0 + 1.0 4 * n2= p4= * 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 4 * n3 p4= * 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 6 c3a c3a c3a n3o 0.0000 0.0 7.2124 0.0 0.0000 0.0 + 1.0 6 h1 c3a c3a n3o 0.0000 0.0 2.9126 0.0 0.0000 0.0 + 1.0 6 c3a c3a n3o o1= 0.0000 0.0 1.1600 0.0 0.0000 0.0 + 1.0 6 c4 c4 n3o o1= 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 6 h1 c4 n3o o1= 0.0000 0.0 0.0000 0.0 -0.3500 0.0 + 1.0 6 c4 c4 o2 n3o 0.0000 0.0 -0.4000 0.0 -0.2000 0.0 + 1.0 6 o1= n3o o2 c4 0.0000 0.0 2.0000 0.0 0.0000 0.0 + 1.0 7 c3' c3a c3a c3a 0.0000 0.0 4.6282 0.0 0.0000 0.0 + 1.0 7 c3' c3a c3a h1 0.0000 0.0 2.1670 0.0 0.0000 0.0 + 1.0 7 c3' n3m c3a c3a 0.0000 0.0 0.6500 0.0 0.0000 0.0 + 1.0 7 c3' n3m c3' o1 -0.4066 0.0 1.2513 0.0 -0.7507 0.0 + 1.0 7 c3' o2 c4 c4 0.1302 0.0 -0.3250 0.0 0.1134 0.0 + 1.0 7 c3' o2 c4 h1 0.9513 0.0 0.1155 0.0 0.0000 0.0 + 1.0 7 c3a c3a c3' o1= 0.0000 0.0 0.7800 0.0 0.0000 0.0 + 1.0 7 c3a c3a c3a n3m 0.0000 0.0 3.4040 0.0 0.0000 0.0 + 1.0 7 c3a n3m c3' o1= 0.0000 0.0 2.0521 0.0 0.0000 0.0 + 1.0 7 c4 o2 c3' c4 -2.5594 0.0 2.2013 0.0 0.0325 0.0 + 1.0 7 c4 o2 c3' o1= 0.8905 0.0 3.2644 0.0 0.2646 0.0 + 1.0 7 o1= c3' c4 h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 7 o2 c3' c4 h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 + 1.0 7 n3m c3a c3a h1 0.0000 0.0 3.4040 0.0 0.0000 0.0 + 1.0 9 h1 n2z n2t n1t 0.0000 0.0 0.0000 0.0 -0.2637 0.0 + 1.0 9 c4 n2z n2t n1t 0.0000 0.0 0.0000 0.0 -0.1823 0.0 + 1.0 9 n2t n2z c4 h1 0.0000 0.0 0.0000 0.0 -0.2181 0.0 + 1.0 9 n2t n2z c4 c4 0.0000 0.0 0.0000 0.0 -0.2021 0.0 + 1.0 9 n2z c4 c4 h1 0.0000 0.0 0.0000 0.0 -0.2259 0.0 + 1.0 10 c3a c3a c3a si4 0.0000 0.0 4.3270 0.0 0.0000 0.0 + 1.0 10 h1 c3a c3a si4 0.0000 0.0 1.5093 0.0 0.0000 0.0 + 1.0 10 c3a c3a si4 * 0.0000 0.0 0.0000 0.0 -0.0231 0.0 + 1.0 10 c4 c4 si4 si4 -0.3500 0.0 0.0000 0.0 -0.0657 0.0 + 1.0 10 * c4 si4 * 0.0000 0.0 0.0000 0.0 -0.0657 0.0 + 1.0 10 * si4 si4 * 0.0000 0.0 0.0000 0.0 -0.0657 0.0 + + +#end_bond-torsion_3 compass + +> E = (R - R0) * +> { F(1) * cos(phi) + F(2) * cos(2 * phi) + F(3) * cos(3 * phi) } + +! LEFT RIGHT +! ------------------------------- ------------------------------- +!Ver Ref I J K L F(1) F(2) F(3) F(1) F(2) F(3) +!---- --- ---- ---- ---- ---- ------- ------- ------- ------- ------- ------- + 1.0 1 c3a c3a c3a c3a -0.1185 6.3204 0.0000 + 1.0 1 c3a c3a c3a c4 0.0000 -0.6918 0.0000 0.0000 0.2421 0.0000 + 1.0 1 c3a c3a c3a h1 0.0000 -6.8958 0.0000 0.0000 -0.4669 0.0000 + 1.0 1 c4 c3a c3a h1 0.0000 -1.7970 0.0000 0.0000 -0.4879 0.0000 + 1.0 1 h1 c3a c3a h1 0.0000 -0.6890 0.0000 + 1.0 1 c3a c3a c4 c4 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 1.0 1 c3a c3a c4 h1 -0.5835 1.1220 0.3978 1.3997 0.7756 0.0000 + 1.0 1 c3a c4 c4 h1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 1.0 1 c4 c4 c4 c4 -0.0732 0.0000 0.0000 + 1.0 1 c4 c4 c4 h1 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 + 1.0 1 h1 c4 c4 h1 0.2130 0.3120 0.0777 + 1.0 3 c3a c3a c3a o2 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 + 1.0 3 h1 c3a c3a o2 0.0000 -1.5867 0.0000 0.0000 4.2641 0.0000 + 1.0 3 c3a c3a o2 h1 0.9000 -1.3456 1.1900 3.4132 0.5873 -0.1323 + 1.0 3 c4 c4 c4 o2 -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 + 1.0 3 h1 c4 c4 o2 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 + 1.0 3 o2 c4 c4 o2 1.0165 0.7553 -0.4609 + 1.0 3 c4 c4 o2 c4 -0.2456 1.0517 -0.7795 0.4741 1.2635 0.5576 + 1.0 3 c4 c4 o2 h1 -0.5800 0.9004 0.0000 0.0000 0.5343 0.9025 + 1.0 3 h1 c4 o2 c4 -0.6054 1.3339 0.9648 -0.1620 0.1564 -1.1408 + 1.0 3 h1 c4 o2 h1 -1.7554 1.3145 0.2263 0.2493 0.6803 0.0000 + 1.0 7 o1= c3' n3m c3' -0.7019 0.8305 -0.6874 0.1726 -0.4823 0.2666 + 1.0 7 c4 c4 o2 c3' -1.2164 -0.1715 -0.0964 0.2560 0.8133 -0.0728 + 1.0 7 h1 c4 o2 c3' 0.9589 0.9190 -0.6015 0.2282 2.2998 -0.4473 + 1.0 7 c4 c3' o2 c4 0.1928 1.3187 0.8599 0.0004 -1.0975 0.4831 + 1.0 7 o1= c3' o2 c4 -4.2421 10.1102 1.6824 0.0882 -2.4309 -0.7426 + 1.0 7 o1= c3' c4 h1 0.0536 0.0354 0.3853 2.9036 0.5307 0.1439 + 1.0 7 o2 c3' c4 h1 0.4160 -0.1140 0.7099 0.7800 1.3339 0.3268 + + +#middle_bond-torsion_3 compass + +> E = (R - R0) * +> { F(1) * cos(phi) + F(2) * cos(2 * phi) + F(3) * cos(3 * phi) } + +!Ver Ref I J K L F(1) F(2) F(3) +!---- --- ---- ---- ---- ---- -------- ------- ------- + 1.0 1 c3a c3a c3a c3a 27.5989 -2.3120 0.0000 + 1.0 1 c3a c3a c3a c4 0.0000 9.1792 0.0000 + 1.0 1 c3a c3a c3a h1 0.0000 -1.1521 0.0000 + 1.0 1 c4 c3a c3a h1 0.0000 3.9421 0.0000 + 1.0 1 h1 c3a c3a h1 0.0000 4.8228 0.0000 + 1.0 1 c3a c3a c4 c4 0.0000 0.0000 0.0000 + 1.0 1 c3a c3a c4 h1 -5.5679 1.4083 0.3010 + 1.0 1 c3a c4 c4 h1 0.0000 0.0000 0.0000 + 1.0 1 c4 c4 c4 c4 -17.7870 -7.1877 0.0000 + 1.0 1 c4 c4 c4 h1 -14.8790 -3.6581 -0.3138 + 1.0 1 h1 c4 c4 h1 -14.2610 -0.5322 -0.4864 + 1.0 3 c3a c3a c3a o2 0.0000 4.8255 0.0000 + 1.0 3 h1 c3a c3a o2 0.0000 5.5432 0.0000 + 1.0 3 c3a c3a o2 h1 1.1580 3.2697 3.5132 + 1.0 3 c4 c4 c4 o2 -21.8842 -7.6764 -0.6868 + 1.0 3 h1 c4 c4 o2 -16.7975 -1.2296 -0.2750 + 1.0 3 o2 c4 c4 o2 -17.2585 -3.6157 -0.8364 + 1.0 3 c4 c4 o2 c4 -5.9288 -2.7007 -0.3175 + 1.0 3 c4 c4 o2 h1 1.2472 0.0000 0.7485 + 1.0 3 h1 c4 o2 c4 -6.8007 -4.6546 -1.4101 + 1.0 3 h1 c4 o2 h1 0.0000 0.9241 -0.5889 + 1.0 4 c4 c4 c4 n2= 0.0000 0.0000 0.0000 + 1.0 4 h1 c4 c4 n2= -3.5150 -2.2980 -1.2770 + 1.0 4 c4 c4 n2= h1 -2.3800 2.5290 -0.7300 + 1.0 4 h1 c4 n2= h1 -0.4140 -2.8620 0.0070 + 1.0 4 p4= n2= p4= n2= 0.0000 0.0000 0.0000 + 1.0 7 c3' c3a c3a c3a 0.0000 3.8762 0.0000 + 1.0 7 o1= c3' n3m c3' -0.1118 -1.1990 0.6784 + 1.0 7 c4 c4 o2 c3' 9.9416 2.6421 2.2333 + 1.0 7 h1 c4 o2 c3' 7.7147 4.2557 -1.0118 + 1.0 7 o1= c3' c3a c3a 0.0000 2.4002 0.0000 + 1.0 7 c3a c3a c3a n3m 0.0000 5.2012 0.0000 + 1.0 7 c4 c3' o2 c4 1.3445 3.5515 -4.9202 + 1.0 7 o1= c3' o2 c4 0.4552 7.3091 0.2842 + 1.0 7 o1= c3' c4 h1 0.0000 0.0000 -1.0000 + 1.0 7 o2 c3' c4 h1 -13.7686 -2.5959 1.1934 + 1.0 7 h1 c3a c3a n3m 0.0000 5.2012 0.0000 + 1.0 10 c3a c3a c3a si4 0.0000 11.1576 0.0000 + 1.0 10 h1 c3a c3a si4 0.0000 6.2168 0.0000 + 1.0 10 c3a c3a si4 h1 0.0000 0.0000 -0.3146 + 1.0 10 h1 c4 si4 h1 0.0000 0.0000 -0.5906 + 1.0 10 h1 c4 si4 si4 0.0000 0.0000 -0.1909 + 1.0 10 c4 si4 si4 h1 0.0000 0.0000 -0.6941 + 1.0 10 h1 si4 si4 h1 0.0000 0.0000 -0.6302 + + +#angle-torsion_3 compass + +> E = (Theta - Theta0) * +> { F(1) * cos(phi) + F(2) * cos(2 * phi) + F(3) * cos(3 * phi) } + +! LEFT RIGHT +! ------------------------------- ------------------------------- +!Ver Ref I J K L F(1) F(2) F(3) F(1) F(2) F(3) +!---- --- ---- ---- ---- ---- ------- ------- ------- ------- ------- ------- + 1.0 1 c3a c3a c3a c3a 1.9767 1.0239 0.0000 + 1.0 1 c3a c3a c3a c4 0.0000 3.8987 0.0000 0.0000 -4.4683 0.0000 + 1.0 1 c3a c3a c3a h1 0.0000 2.5014 0.0000 0.0000 2.7147 0.0000 + 1.0 1 c4 c3a c3a h1 0.0000 -0.1242 0.0000 0.0000 3.4601 0.0000 + 1.0 1 h1 c3a c3a h1 0.0000 2.4501 0.0000 + 1.0 1 c3a c3a c4 c4 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 1.0 1 c3a c3a c4 h1 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 + 1.0 1 c3a c4 c4 h1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 1.0 1 c4 c4 c4 c4 0.3886 -0.3139 0.1389 + 1.0 1 c4 c4 c4 h1 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 + 1.0 1 h1 c4 c4 h1 -0.8085 0.5569 -0.2466 + 1.0 3 c3a c3a c3a o2 0.0000 10.0155 0.0000 0.0000 1.7404 0.0000 + 1.0 3 h1 c3a c3a o2 0.0000 1.8729 0.0000 0.0000 2.5706 0.0000 + 1.0 3 c3a c3a o2 h1 -5.1360 -1.0122 0.0000 4.6852 0.0230 -0.5980 + 1.0 3 c4 c4 c4 o2 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 + 1.0 3 h1 c4 c4 o2 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 + 1.0 3 o2 c4 c4 o2 0.5511 0.9737 -0.6673 + 1.0 3 c4 c4 o2 c4 -2.7466 1.4877 -0.8955 0.5676 0.9450 0.0703 + 1.0 3 c4 c4 o2 h1 -3.5903 2.5225 0.4888 0.8726 -0.3577 0.3888 + 1.0 3 h1 c4 o2 c4 -1.8234 1.6393 0.5144 -0.7777 0.4340 -0.6653 + 1.0 3 h1 c4 o2 h1 -3.4060 1.6396 0.0737 0.0000 -0.2810 -0.5944 + 1.0 4 c4 c4 c4 n2= -2.0980 1.8610 -1.6890 -0.1220 1.8930 -0.5670 + 1.0 4 h1 c4 c4 n2= -2.0980 1.8610 -1.6890 -0.1220 1.8930 -0.5670 + 1.0 4 c4 c4 n2= h1 -2.5230 2.8480 2.0590 -3.6920 4.0610 -1.5440 + 1.0 4 h1 c4 n2= h1 -1.8950 1.2210 -0.7460 0.1100 0.0650 0.1090 + 1.0 6 c3a c3a c3a n3o 0.0000 7.7594 0.0000 0.0000 0.0000 0.0000 + 1.0 6 h1 c3a c3a n3o 0.0000 -8.0369 0.0000 0.0000 0.0000 0.0000 + 1.0 6 c3a c3a n3o o1= 0.0000 0.0000 0.0000 0.0000 -3.4207 0.0000 + 1.0 6 h1 c4 n3o o1= 0.0000 -0.3086 0.0000 0.0000 1.0352 0.0000 + 1.0 6 o1= n3o o2 c4 -3.0000 0.0000 0.0000 0.0000 0.0000 0.0000 + 1.0 7 o1= c3' n3m c3' -1.5747 2.3997 -0.2851 -0.3038 -0.0548 -0.3188 + 1.0 7 c4 c4 o2 c3' -0.4620 1.4492 -0.6765 -0.0890 -0.9159 0.7229 + 1.0 7 h1 c4 o2 c3' -0.4990 2.8061 -0.0401 -0.3142 -0.8699 0.0971 + 1.0 7 c4 c3' o2 c4 0.9701 -2.5169 1.7195 0.8831 -0.8203 0.2405 + 1.0 7 o1= c3' o2 c4 5.9732 2.7261 1.9052 2.3573 1.0059 -0.0327 + 1.0 7 o1= c3' c4 h1 -2.0667 0.7308 -0.2083 14.4728 0.3339 0.0800 + 1.0 7 o2 c3' c4 h1 -0.0241 1.4427 0.1212 13.2959 0.8005 -0.0071 + 1.0 10 c3a c3a c3a si4 0.0000 -5.5448 0.0000 0.0000 4.3281 0.0000 + 1.0 10 h1 c3a c3a si4 0.0000 4.5914 0.0000 0.0000 1.1079 0.0000 + 1.0 10 c3a c3a si4 h1 0.0000 0.0000 -0.2779 0.0000 0.0000 -0.1932 + 1.0 10 h1 c4 si4 c4 0.0000 0.0000 0.3382 0.0000 0.0000 0.4272 + + +#wilson_out_of_plane compass + +> E = K * (Chi - Chi0)^2 + +!Ver Ref I J K L K Chi0 +!---- --- ---- ---- ---- ---- ------- ---- + 1.0 1 c3a c3a c3a c3a 7.1794 0.0 + 1.0 1 c3a c3a c3a c4 7.8153 0.0 + 1.0 1 c3a c3a c3a h1 4.8912 0.0 + 1.0 3 c3a c3a c3a o2 13.0421 0.0 + 1.0 4 c3a c3a c3a n2= 8.0000 0.0 + 1.0 4 c3a c3a c3a p4= 6.7090 0.0 + 1.0 6 c3a c3a c3a n3o 0.9194 0.0 + 1.0 6 c3a n3o o1= o1= 36.2612 0.0 + 1.0 6 c4 n3o o1= o1= 44.3062 0.0 + 1.0 6 h1 n3o o1= o1= 38.5581 0.0 + 1.0 6 o1= n3o o1= o2 45.0000 0.0 + 1.0 7 c3' c3' n3m c3a 0.0000 0.0 + 1.0 7 c3' c3a c3a c3a 17.0526 0.0 + 1.0 7 c3' n3m c3' c3a 0.0000 0.0 + 1.0 7 c3a c3a n3m c3a 17.0526 0.0 +!1.0 7 c3a c3a c3a n3m 17.0526 0.0 + 1.0 7 c3a c3' n3m o1= 30.0000 0.0 +!1.0 7 c3a c3a c3' c3a 17.0526 0.0 +!1.0 7 c3a c3' o1= n3m 30.0000 0.0 + 1.0 7 c3a o1= c3' n3m 30.0000 0.0 + 1.0 7 c4 c3' o2 o1= 46.9264 0.0 + 1.0 10 c3a c3a si4 c3a 5.3654 0.0 + + +#angle-angle compass + +> E = K * (Theta - Theta0) * (Theta' - Theta0') + +! J' I' K' +!Ver Ref I J K K +!---- --- ---- ---- ---- ---- ------- + 1.0 1 c3a c3a c3a c3a 0.0000 + 1.0 1 c3a c3a c3a h1 0.0000 + 1.0 1 c3a c3a h1 c3a 0.0000 + 1.0 1 c4 c4 c3a h1 2.0403 + 1.0 1 h1 c4 c3a h1 3.0118 + 1.0 1 c3a c4 c4 h1 -1.8202 + 1.0 1 c4 c4 c4 c4 -0.1729 + 1.0 1 c4 c4 c4 h1 -1.3199 + 1.0 1 h1 c4 c4 h1 -0.4825 + 1.0 1 c3a c4 h1 c4 1.0827 + 1.0 1 c3a c4 h1 h1 2.3794 + 1.0 1 c4 c4 h1 c4 0.1184 + 1.0 1 c4 c4 h1 h1 0.2738 + 1.0 1 h1 c4 h1 h1 -0.3157 + 1.0 3 c3a c3a c3a o2 0.0000 + 1.0 3 c3a c3a o2 c3a 0.0000 + 1.0 3 c4 c4 c4 o2 -0.8330 + 1.0 3 h1 c4 c4 o2 2.5926 + 1.0 3 c4 c4 h1 o2 3.9177 + 1.0 3 h1 c4 h1 o2 2.4259 + 1.0 3 c4 c4 o2 c4 -3.5744 + 1.0 3 c4 c4 o2 h1 0.1689 + 1.0 3 h1 c4 o2 h1 2.1283 + 1.0 4 h1 c4 c4 n2= 1.0910 + 1.0 4 c4 c4 h1 n2= 2.7530 + 1.0 4 h1 c4 h1 n2= 1.7680 + 1.0 4 c4 c4 n2= h1 -1.3060 + 1.0 4 h1 c4 n2= h1 -2.9470 + 1.0 7 h1 c4 c3' o2 4.7955 + 1.0 7 c3' c4 h1 h1 -1.7653 + 1.0 11 h1 c4 c3' h1 0.0 + 1.0 10 h1 c4 h1 si4 0.0000 + 1.0 10 h1 c4 si4 h1 2.2050 + 1.0 10 c4 si4 c4 h1 3.3827 + 1.0 10 c4 si4 c4 si4 1.3465 + 1.0 10 h1 si4 c4 h1 4.6809 + 1.0 10 si4 si4 c4 si4 -5.6849 + 1.0 10 c4 si4 h1 c4 2.7963 + 1.0 10 c4 si4 h1 h1 4.4559 + 1.0 10 c4 si4 h1 si4 3.4758 + 1.0 10 h1 si4 h1 h1 2.0665 + 1.0 10 si4 si4 h1 si4 3.4924 + 1.0 10 c4 si4 si4 c4 2.0805 + 1.0 10 c4 si4 si4 h1 -2.9623 + 1.0 10 c4 si4 si4 si4 4.5272 + 1.0 10 h1 si4 si4 h1 1.6082 + 1.0 10 si4 si4 si4 h1 4.1996 + + +#angle-angle-torsion_1 compass + +> E = K * (Theta - Theta0) * (Theta' - Theta0') * cos(Phi) + +!Ver Ref I J K L K(Ang,Ang,Tor) +!---- --- ---- ---- ---- ---- -------------- + 1.0 1 c3a c3a c3a c3a 0.0000 + 1.0 1 c3a c3a c3a c4 -14.4097 + 1.0 1 c3a c3a c3a h1 -4.8141 + 1.0 1 c4 c3a c3a h1 4.4444 + 1.0 1 h1 c3a c3a h1 0.3598 + 1.0 1 c3a c3a c4 h1 -5.8888 + 1.0 1 c4 c4 c4 c4 -22.0450 + 1.0 1 c4 c4 c4 h1 -16.1640 + 1.0 1 h1 c4 c4 h1 -12.5640 + 1.0 3 c3a c3a c3a o2 -21.0247 + 1.0 3 h1 c3a c3a o2 4.2296 + 1.0 3 c3a c3a o2 h1 -4.6072 + 1.0 3 c4 c4 c4 o2 -29.0420 + 1.0 3 h1 c4 c4 o2 -20.2006 + 1.0 3 o2 c4 c4 o2 -14.0484 + 1.0 3 c4 c4 o2 c4 -19.0059 + 1.0 3 c4 c4 o2 h1 -12.1038 + 1.0 3 h1 c4 o2 c4 -16.4438 + 1.0 3 h1 c4 o2 h1 -10.5093 + 1.0 4 c4 c4 c4 n2= 0.0000 + 1.0 4 h1 c4 c4 n2= -27.5060 + 1.0 4 c4 c4 n2= h1 -8.8980 + 1.0 4 h1 c4 n2= h1 -9.6280 + 1.0 4 h1 c4 p4= c4 -25.5460 + 1.0 4 h1 c4 p4= h1 -16.0180 + 1.0 4 h1 c4 p4= n2= -19.9340 + 1.0 4 h1 n2= p4= c4 -11.1020 + 1.0 4 h1 n2= p4= h1 -3.7880 + 1.0 6 c3a c3a c3a n3o -34.9681 + 1.0 6 h1 c3a c3a n3o 2.1508 + 1.0 6 c3a c3a n3o o1= -18.0436 + 1.0 6 h1 c4 n3o o1= -16.2615 + 1.0 7 o1= c3' n3m c3' -3.3556 + 1.0 7 c4 c4 o2 c3' -15.7082 + 1.0 7 h1 c4 o2 c3' -13.1500 + 1.0 7 c4 c3' o2 c4 -12.2070 + 1.0 7 o1= c3' o2 c4 -32.9368 + 1.0 7 o1= c3' c4 h1 -23.1923 + 1.0 7 o2 c3' c4 h1 -13.9734 + 1.0 10 c4 si4 c4 h1 -17.5802 + 1.0 10 h1 si4 c4 h1 -12.9341 + 1.0 10 h1 c4 si4 si4 -13.3679 + 1.0 10 c4 si4 si4 h1 -16.9141 + 1.0 10 h1 si4 si4 h1 -10.8232 + 1.0 10 h1 si4 si4 si4 -12.2900 + + +#nonbond(9-6) compass + +> E = eps(ij) [2(r(ij)*/r(ij))**9 - 3(r(ij)*/r(ij))**6] +> where r(ij) = [(r(i)**6 + r(j)**6))/2]**(1/6) +> +> eps(ij) = 2 sqrt(eps(i) * eps(j)) * +> r(i)^3 * r(j)^3/[r(i)^6 + r(j)^6] + +@combination sixth-power +@type r-eps + +!Ver Ref I r eps +!---- --- ---- --------- --------- + 1.0 1 c3a 3.9150 0.0680 + 1.0 1 c4 3.8540 0.0620 + 1.0 1 c43 3.8540 0.0400 + 1.0 1 c44 3.8540 0.0200 + 1.0 1 h1 2.8780 0.0230 + 1.0 2 o2z 3.3000 0.0800 + 1.0 2 si4 4.4050 0.1980 + 1.0 2 si4c 4.2900 0.1310 + 1.0 3 c4o 3.8150 0.0680 + 1.0 3 h1o 1.0870 0.0080 + 1.0 3 o2 3.3000 0.0800 + 1.0 3 o2e 3.3000 0.1200 + 1.0 3 o2h 3.5800 0.0960 + 1.0 4 n2= 3.8300 0.0960 + 1.0 4 p4= 4.2950 0.0650 + 1.0 5 he 2.9000 0.0050 + 1.0 5 ne 3.2000 0.0550 + 1.0 5 ar 3.8800 0.2000 + 1.0 5 kr 4.3000 0.2800 + 1.0 5 xe 4.2600 0.3900 + 1.0 5 h1h 1.4210 0.0216 + 1.0 5 n1n 3.8008 0.0598 + 1.0 5 c1o 4.0120 0.0530 + 1.0 5 o1o 3.4758 0.0780 + 1.0 5 o1c 3.6020 0.0850 + 1.0 5 n1o 3.4600 0.1280 + 1.0 5 o1n 3.3000 0.1560 + 1.0 5 c2= 3.9150 0.0680 + 1.0 5 s2= 4.0470 0.1250 + 1.0 5 n2o 3.5290 0.3330 + 1.0 5 o1= 3.4300 0.1920 + 1.0 5 o1=* 3.3600 0.0670 + 1.0 5 s1= 4.0070 0.3130 + 1.0 6 n3o 3.7600 0.0480 + 1.0 6 o12 3.4000 0.0480 + 1.0 6 o2n 3.6500 0.2000 + 1.0 7 c3' 3.9000 0.0640 + 1.0 7 n3m 3.7200 0.1500 + 1.0 7 o2s 3.3000 0.0960 + 1.1 8 c4o 3.8700 0.0748 + 1.1 8 c41o 3.8700 0.1080 + 1.1 8 c43o 3.6700 0.0498 + 1.0 9 c4z 3.6500 0.0800 + 1.0 9 n1z 3.5200 0.0850 + 1.0 9 n2t 3.3000 0.0500 + 1.0 9 n2z 3.4000 0.1200 + + +#bond_increments compass + +!Ver Ref I J DeltaIJ DeltaJI +!---- --- ---- ---- ------- ------- + 1.0 1 c3a c3a 0.0000 0.0000 + 1.0 1 c3a c4 0.0000 0.0000 + 1.0 1 c3a h1 -0.1268 0.1268 + 1.0 1 c4 c4 0.0000 0.0000 + 1.0 1 c4 h1 -0.0530 0.0530 + 1.0 2 o2z si4 -0.2225 0.2225 + 1.0 3 c3a o2e 0.0420 -0.0420 + 1.0 3 c3a o2h 0.0420 -0.0420 + 1.0 3 c4 o2e 0.1600 -0.1600 + 1.0 3 c4 o2h 0.1600 -0.1600 + 1.0 3 h1 o2 0.4200 -0.4200 + 1.0 3 h1 o2h 0.4200 -0.4200 + 1.0 4 c3a n2= 0.1990 -0.1990 + 1.0 4 c3a p4= -0.0600 0.0600 + 1.0 4 c4 n2= 0.3450 -0.3450 + 1.0 4 c4 p4= -0.0500 0.0500 + 1.0 4 cl1p p4= -0.1200 0.1200 + 1.0 4 f1p p4= -0.1800 0.1800 + 1.0 4 h1 n2= 0.3280 -0.3280 + 1.0 4 h1 p4= -0.0500 0.0500 + 1.0 4 n2= n2= 0.0000 0.0000 + 1.0 4 n2= n3 0.0250 -0.0250 + 1.0 4 n2= o2 -0.0430 0.0430 + 1.0 4 n2= p4= -0.3500 0.3500 + 1.0 4 n3 p4= -0.1200 0.1200 + 1.0 4 o2 p4= -0.1400 0.1400 + 1.0 5 c1o o1c -0.0203 0.0203 + 1.0 5 c2= o1= 0.4000 -0.4000 + 1.0 5 c2= s1= 0.0258 -0.0258 + 1.0 5 n2o o1= 0.0730 -0.0730 + 1.0 5 h1h h1h 0.0000 0.0000 + 1.0 5 n1n n1n 0.0000 0.0000 + 1.0 5 n1o o1n 0.0288 -0.0288 + 1.0 5 o1= s2= -0.2351 0.2351 + 1.0 5 o1o o1o 0.0000 0.0000 + 1.0 6 c3a n3o 0.2390 -0.2390 + 1.0 6 c4 n3o 0.2100 -0.2100 + 1.0 6 c4 o2n 0.3170 -0.3170 + 1.0 6 h1 n3o 0.1880 -0.1880 + 1.0 6 n3o o1= 0.4280 -0.4280 + 1.0 6 n3o o2n 0.0010 -0.0010 + 1.0 7 c3' o2e 0.1120 -0.1120 + 1.0 7 c3' c4 0.0000 0.0000 + 1.0 7 c3' o1= 0.4500 -0.4500 + 1.0 7 c3' c3a 0.0350 -0.0350 + 1.0 7 c3' n3m 0.0000 0.0000 + 1.0 7 c3a n3m 0.0950 -0.0950 + 1.1 8 h1 o2h 0.4100 -0.4100 + 1.0 9 n2z c4 -0.3110 0.3110 + 1.0 9 n2z h1 -0.3350 0.3350 + 1.0 9 n2t n1t 0.3860 -0.3860 + 1.0 9 n2t n2z 0.2470 -0.2470 + 1.0 10 c3a si4 -0.1170 0.1170 + 1.0 10 c4 si4 -0.1350 0.1350 + 1.0 10 h1 si4 -0.1260 0.1260 + +#templates compass + +type: ? + ! anything + template: (>*) +end_type + +type: ar + ! Argon atom + template: (>Ar) +end_type + +type:c1o + ! Carbon in CO + template: [>C[~O]] +end_type + +type:c2= + ! Carbon in =C= (e.g. CO2, CS2) + template: [>C[~*][~*]] +end_type + +type:c3' + ! Carbonyl carbon [one polar substituent such as O,N] + ! e.g. amide, acid and ester + template: (>C (~O) (~*) (~*)) + atom_test:1 + hybridization:sp2 + end_test + atom_test:3 + allowed_elements: C, H + end_test + atom_test:4 + allowed_elements: O, N + end_test +end_type + +type:c3a + ! SP2 aromatic carbon + template:(>C(~*)(~*)(~*)) + atom_test:1 + hybridization: SP2 + aromaticity:AROMATIC + end_test +end_type + +type:c3a + ! Transferred from pcff - may not be required. + ! This is used for aromatic carbons that fail the aromaticity test because + ! the current ring checker is too lame to figure on a ring with more than + ! seven or eight sides. The NON_AROMATIC test is to eliminate the conflict + ! with the above 'c3a' definition. This can be removed when the ring checker + ! is made more robust. + template: [>C(-*)(:*)(:*)] + atom_test:1 + hybridization:SP2 + aromaticity:NON_AROMATIC + end_test +end_type + +type:c4 + ! generic SP3 carbon + template: (>C(-*)(-*)(-*)(-*)) + atom_test:1 + hybridization:SP3 + end_test +end_type + +type:c41o + ! Carbon, sp3, in methanol (and dimethyl ether?) + template: [>C(-O(-*))(-H)(-H)(-H)] + atom_test:1 + hybridization:SP3 + end_test + atom_test:3 + allowed_elements:C,H +end_type + +type: c43 + ! sp3 carbon with 1 h and 3 heavy atoms + template: (>C(-H)(-*)(-*)(-*)) + atom_test:1 + hybridization:SP3 + atom_test:3 + disallowed_elements:H + atom_test:4 + disallowed_elements:H + atom_test:5 + disallowed_elements:H + end_test +end_type + +type:c43o + ! Carbon, sp3, in secondary alcohols + template: [>C(-O(-H))(-H)(-C)(-C)] + atom_test:1 + hybridization:SP3 + end_test +end_type + +type: c44 + ! sp3 carbon with four heavy atoms attached + template: (>C(-*)(-*)(-*)(-*)) + atom_test:1 + hybridization:SP3 + atom_test:2 + disallowed_elements:H + atom_test:3 + disallowed_elements:H + atom_test:4 + disallowed_elements:H + atom_test:5 + disallowed_elements:H + end_test +end_type + +type: c4o + ! alpha carbon (e.g. alpha to oxygen in ethers and alcohols) + template: (>C(-O)(-*)(-*)(-*)) + atom_test:1 + hybridization:SP3 + end_test +end_type + +type: c4z + ! Carbon, sp3, bonded to -N3 (azides) + template: (>C(-N(~N(~N)))(-*)(-*)(-*)) + atom_test:1 + hybridization:SP3 + end_test +end_type + +type:h1 + ! nonpolar hydrogen + template: (>H (-*) ) + atom_test:2 + allowed_elements:C,Si + end_test +end_type + +type:h1h + ! Hydrogen in H2 + template: [>H[-H]] +end_type + +type:h1o + ! strongly polar hydrogen (bonded to fluorine, nitrogen, Oxygen - h* in pcff) + template: (>H(-*)) + atom_test:2 + allowed_elements:O,N,F + end_test +end_type + +type: he + ! Helium atom + template: (>He) +end_type + +type: kr + ! Krypton atom + template: (>Kr) +end_type + +type:n1n + ! Nitrogen in N2 + template: [>N[~N]] +end_type + +type:n1o + ! Nitrogen in NO + template: [>N[~O]] +end_type + +type:n1z + ! Nitrogen, terminal atom in -N3 + template: [>N[~N[~N(~*)]]] +end_type + +type:n2= + ! Nitrogen (in phosphazenes, or generic???) + template: [>N(~*)(~*)] +end_type + +type:n2o + ! Nitrogen in NO2 + template: [>N[~O][~O]] +end_type + +type:n2t + ! Nitrogen, central atom in -N3 + template: [>N[~N][~N(~*)]] +end_type + +type:n2z + ! Nitrogen, first atom in -N3 + template: (>N[~N[~N]](~*)) +end_type + +type: n3m + ! sp3 nitrogen in amides without hydrogen + template: (>N(-C[=O])(-C)(-C)) + atom_test:1 + hybridization:SP3 + end_test +end_type + +type: n3o + ! Nitrogen in nitro group + template: (>N[~O][~O](~O(~C))) +end_type + +type: ne + ! Neon atom + template: (>Ne) +end_type + +type:o1= + ! Oxygen in NO2 and SO2 [and carbonyl] + template: (>O(~*)) + atom_test:2 + allowed_elements:N,S,C + end_test +end_type + +type:o1=* + ! Oxygen in CO2 + template: [>O[~C[~O]]] +end_type + +type:o12 + ! Oxygen in nitro group -NO2 + template: [>O[~N[~O](~*)]] +end_type + +type:o1c + ! Oxygen in CO + template: [>O[~C]] +end_type + +type:o1n + ! Oxygen in NO + template: [>O[~N]] +end_type + +type:o1o + ! Oxygen in O2 + template: [>O[~O]] +end_type + +type:o2 + ! Generic oxygen with two bonds attached + template: [>O(~*)(~*)] +end_type + +type:o2e + ! Ether oxygen + template: [>O(-C)(-C)] + atom_test: 1 + aromaticity:NON_AROMATIC + end_test +end_type + +type:o2h + ! Hydroxyl oxygen + template: (>O[-H](~*)) +end_type + +type:o2n + ! Oxygen in nitrates + template: (>O[~N[~O][~O]](~C)) +end_type + +type:o2s + ! Ester oxygen + template: (>O[~C[~O](~*)](~C)) +end_type + +type: o2z + ! Oxygen in siloxanes and zeolites + template: (>O(-Si)(-*) ) + atom_test: 3 + allowed_elements: Si, H + end_test +end_type + +type: p4= + ! Phosphorous [in phosphazenes] + template: (>P(~*)(~*)(~*)(~*)) +end_type + +type:s1= + ! Sulfur in CS2 + template: [>S[~C[~S]]] +end_type + +type:s2= + ! Sulfur in SO2 + template: [>S[~O][~O]] +end_type + +type: si4 + ! Generic silicon with four bonds attached + template: (>Si(-*)(-*)(-*)(-*)) +end_type + +type: si4c + ! A subset of si4, non-hydrogen atom attached [siloxanes??] + template: (>Si(-O)(-*)(-*)(-*)) + atom_test: 3 + allowed_elements: O, C + end_test + atom_test: 4 + allowed_elements: O, C + end_test + atom_test: 5 + allowed_elements: O, C + end_test +end_type + +type: xe + ! Xenon atom + template: (>Xe) +end_type + +precedence: +(? + (ar) + (c1o) + (c2=) + (c3a) (c3') + (c4 (c43 (c43o)) (c44) (c4o(c41o)) (c4z) ) + (h1) (h1h) (h1o) + (he) + (kr) + (n1n) (n1o) (n1z) + (n2= (n2o) (n2t) (n2z) ) + (n3m) (n3o) + (ne) + (o1= (o1=*) (o12) (o1c) (o1n) ) (o1o) + (o2 (o2e(o2s)) (o2h) (o2n) (o2z) ) + (p4=) + (s1=) + (s2=) + (si4 (si4c) ) + (xe) +) +end_precedence + + + +#reference 1 +@Author tester +@Date 01-Jun-09 +Barebones compass for aromatic & aliphatic hydrocarbons from H. Sun JCP B102, 7361-2 (1998) + +This file created by Materials Design, Inc. (www.materialsdesign.com) Please realize that +we neither support this version, nor make any warranty as to the correctness of the parameters. +We have checked the numbers against the literature, but of course there may still be errors, +including errors of interpretation. Also, the current version of COMPASS may well be different +that that originally published. + +If you have comments or suggestions, feel free to email Paul Saxe at psaxe (at) materialsdesign.com + +#reference 2 +@Author tester +@Date 27-Jun-09 +Parameters for siloxanes from Sun/Rigby Spectrochim. Acta A53, 1301-23 (1997) (o2 later renamed to o2z) + +#reference 3 +@Author tester +@Date 27-Jun-09 +Parameters for ethers and alcohols from Rigby/Sun/Eichinger Polym. Int. 44, 311-330 (1997) + +#reference 4 +@Author tester +@Date 30-Jun-09 +Parameters for phosphazenes from Comput. Theor. Polym. Sci. 8, 229-246 (1998) + +#reference 5 +@Author tester +@Date 28-Jun-09 +Parameters for He,Ne,Ar,Kr,Xe,H2,O2,N2,NO,CO,CO2,NO2,CS2,SO2 from JPC B104, 4951-7 (2000) + +#reference 6 +@Author tester +@Date 29-Jun-09 +Parameters for nitrate esters from JPC B104, 2477-89 (2000) + +#reference 7 +@Author tester +@Date 30-Jun-09 +Parameters for Ultem (imides) from Polymer 43, 599-607 (2002) + +#reference 8 +@Author tester +@Date 30-Jun-09 +Parameters for 2y and 3y alcohols from Fluid Phase Equilibria 217, 77-87 (2004) + +#reference 9 +@Author tester +@Date 30-Jun-09 +Parameters for aliphatic azides from J. Comput. Chem. 25, 61-71 (2004) + +#reference 10 +@Author tester +@Date 02-Jul-09 +Ref 2 missing -C-Si- params; assume values from Macromols 28, 701-712 (1995) (see pcff)