diff --git a/MindSPONGE/mindsponge/python/data/forcefield/amber.ff99sb.yaml b/MindSPONGE/mindsponge/python/data/forcefield/amber.ff99sb.yaml new file mode 100644 index 0000000000000000000000000000000000000000..3589bd48f55f66198b258efbc7d8d609ac1236dd --- /dev/null +++ b/MindSPONGE/mindsponge/python/data/forcefield/amber.ff99sb.yaml @@ -0,0 +1,1113 @@ +template: + base: protein0.yaml + ALA: + atom_type: [N, H, CT, H1, CT, HC, HC, HC, C, O] + atom_charge: [-0.4157, 0.2719, 0.0337, 0.0823, -0.1825, 0.0603, 0.0603, 0.0603, 0.5973, -0.5679] + ARG: + atom_type: [N, H, CT, H1, CT, HC, HC, CT, HC, HC, CT, H1, H1, N2, H, CA, N2, H, H, N2, H, H, C, O] + atom_charge: [-0.3479, 0.2747, -0.2637, 0.156, -0.0007, 0.0327, 0.0327, 0.039, 0.0285, 0.0285, 0.0486, 0.0687, + 0.0687, -0.5295, 0.3456, 0.8076, -0.8627, 0.4478, 0.4478, -0.8627, 0.4478, 0.4478, 0.7341, -0.5894] + ASN: + atom_type: [N, H, CT, H1, CT, HC, HC, C, O, N, H, H, C, O] + atom_charge: [-0.4157, 0.2719, 0.0143, 0.1048, -0.2041, 0.0797, 0.0797, 0.713, -0.5931, -0.9191, 0.4196, 0.4196, + 0.5973, -0.5679] + ASP: + atom_type: [N, H, CT, H1, CT, HC, HC, C, O2, O2, C, O] + atom_charge: [-0.5163, 0.2936, 0.0381, 0.088, -0.0303, -0.0122, -0.0122, 0.7994, -0.8014, -0.8014, 0.5366, -0.5819] + CYS: + atom_type: [N, H, CT, H1, CT, H1, H1, SH, HS, C, O] + atom_charge: [-0.4157, 0.2719, 0.0213, 0.1124, -0.1231, 0.1112, 0.1112, -0.3119, 0.1933, 0.5973, -0.5679] + GLN: + atom_type: [N, H, CT, H1, CT, HC, HC, CT, HC, HC, C, O, N, H, H, C, O] + atom_charge: [-0.4157, 0.2719, -0.0031, 0.085, -0.0036, 0.0171, 0.0171, -0.0645, 0.0352, 0.0352, 0.6951, -0.6086, + -0.9407, 0.4251, 0.4251, 0.5973, -0.5679] + GLU: + atom_type: [N, H, CT, H1, CT, HC, HC, CT, HC, HC, C, O2, O2, C, O] + atom_charge: [-0.5163, 0.2936, 0.0397, 0.1105, 0.056, -0.0173, -0.0173, 0.0136, -0.0425, -0.0425, 0.8054, -0.8188, + -0.8188, 0.5366, -0.5819] + GLY: + atom_type: [N, H, CT, H1, H1, C, O] + atom_charge: [-0.4157, 0.2719, -0.0252, 0.0698, 0.0698, 0.5973, -0.5679] + HID: + atom_type: [N, H, CT, H1, CT, HC, HC, CC, NA, H, CR, H5, NB, CV, H4, C, O] + atom_charge: [-0.4157, 0.2719, 0.0188, 0.0881, -0.0462, 0.0402, 0.0402, -0.0266, -0.3811, 0.3649, 0.2057, 0.1392, + -0.5727, 0.1292, 0.1147, 0.5973, -0.5679] + HIS: + atom_type: [N, H, CT, H1, CT, HC, HC, CC, NB, CR, H5, NA, H, CW, H4, C, O] + atom_charge: [-0.4157, 0.2719, -0.0581, 0.136, -0.0074, 0.0367, 0.0367, 0.1868, -0.5432, 0.1635, 0.1435, -0.2795, + 0.3339, -0.2207, 0.1862, 0.5973, -0.5679] + ILE: + atom_type: [N, H, CT, H1, CT, HC, CT, HC, HC, HC, CT, HC, HC, CT, HC, HC, HC, C, O] + atom_charge: [-0.4157, 0.2719, -0.0597, 0.0869, 0.1303, 0.0187, -0.3204, 0.0882, 0.0882, 0.0882, -0.043, 0.0236, + 0.0236, -0.066, 0.0186, 0.0186, 0.0186, 0.5973, -0.5679] + LEU: + atom_type: [N, H, CT, H1, CT, HC, HC, CT, HC, CT, HC, HC, HC, CT, HC, HC, HC, C, O] + atom_charge: [-0.4157, 0.2719, -0.0518, 0.0922, -0.1102, 0.0457, 0.0457, 0.3531, -0.0361, -0.4121, 0.1, 0.1, 0.1, + -0.4121, 0.1, 0.1, 0.1, 0.5973, -0.5679] + LYS: + atom_type: [N, H, CT, H1, CT, HC, HC, CT, HC, HC, CT, HC, HC, CT, HP, HP, N3, H, H, H, C, O] + atom_charge: [-0.3479, 0.2747, -0.24, 0.1426, -0.0094, 0.0362, 0.0362, 0.0187, 0.0103, 0.0103, -0.0479, 0.0621, + 0.0621, -0.0143, 0.1135, 0.1135, -0.3854, 0.34, 0.34, 0.34, 0.7341, -0.5894] + MET: + atom_type: [N, H, CT, H1, CT, HC, HC, CT, H1, H1, S, CT, H1, H1, H1, C, O] + atom_charge: [-0.4157, 0.2719, -0.0237, 0.088, 0.0342, 0.0241, 0.0241, 0.0018, 0.044, 0.044, -0.2737, -0.0536, + 0.0684, 0.0684, 0.0684, 0.5973, -0.5679] + PHE: + atom_type: [N, H, CT, H1, CT, HC, HC, CA, CA, HA, CA, HA, CA, HA, CA, HA, CA, HA, C, O] + atom_charge: [-0.4157, 0.2719, -0.0024, 0.0978, -0.0343, 0.0295, 0.0295, 0.0118, -0.1256, 0.133, -0.1704, 0.143, + -0.1072, 0.1297, -0.1704, 0.143, -0.1256, 0.133, 0.5973, -0.5679] + PRO: + atom_type: [N, CT, H1, H1, CT, HC, HC, CT, HC, HC, CT, H1, C, O] + atom_charge: [-0.2548, 0.0192, 0.0391, 0.0391, 0.0189, 0.0213, 0.0213, -0.007, 0.0253, 0.0253, -0.0266, 0.0641, + 0.5896, -0.5748] + SER: + atom_type: [N, H, CT, H1, CT, H1, H1, OH, HO, C, O] + atom_charge: [-0.4157, 0.2719, -0.0249, 0.0843, 0.2117, 0.0352, 0.0352, -0.6546, 0.4275, 0.5973, -0.5679] + THR: + atom_type: [N, H, CT, H1, CT, H1, CT, HC, HC, HC, OH, HO, C, O] + atom_charge: [-0.4157, 0.2719, -0.0389, 0.1007, 0.3654, 0.0043, -0.2438, 0.0642, 0.0642, 0.0642, -0.6761, 0.4102, + 0.5973, -0.5679] + TRP: + atom_type: [N, H, CT, H1, CT, HC, HC, C*, CW, H4, NA, H, CN, CA, HA, CA, HA, CA, HA, CA, HA, CB, C, O] + atom_charge: [-0.4157, 0.2719, -0.0275, 0.1123, -0.005, 0.0339, 0.0339, -0.1415, -0.1638, 0.2062, -0.3418, 0.3412, + 0.138, -0.2601, 0.1572, -0.1134, 0.1417, -0.1972, 0.1447, -0.2387, 0.17, 0.1243, 0.5973, -0.5679] + TYR: + atom_type: [N, H, CT, H1, CT, HC, HC, CA, CA, HA, CA, HA, C, OH, HO, CA, HA, CA, HA, C, O] + atom_charge: [-0.4157, 0.2719, -0.0014, 0.0876, -0.0152, 0.0295, 0.0295, -0.0011, -0.1906, 0.1699, -0.2341, 0.1656, + 0.3226, -0.5579, 0.3992, -0.2341, 0.1656, -0.1906, 0.1699, 0.5973, -0.5679] + VAL: + atom_type: [N, H, CT, H1, CT, HC, CT, HC, HC, HC, CT, HC, HC, HC, C, O] + atom_charge: [-0.4157, 0.2719, -0.0875, 0.0969, 0.2985, -0.0297, -0.3192, 0.0791, 0.0791, 0.0791, -0.3192, 0.0791, + 0.0791, 0.0791, 0.5973, -0.5679] + NALA: + atom_type: [N3, H, H, H, CT, HP, CT, HC, HC, HC, C, O] + atom_charge: [0.1414, 0.1997, 0.1997, 0.1997, 0.0962, 0.0889, -0.0597, 0.03, 0.03, 0.03, 0.6163, -0.5722] + NARG: + atom_type: [N3, H, H, H, CT, HP, CT, HC, HC, CT, HC, HC, CT, H1, H1, N2, H, CA, N2, H, H, N2, H, H, C, O] + atom_charge: [0.1305, 0.2083, 0.2083, 0.2083, -0.0223, 0.1242, 0.0118, 0.0226, 0.0226, 0.0236, 0.0309, 0.0309, + 0.0935, 0.0527, 0.0527, -0.565, 0.3592, 0.8281, -0.8693, 0.4494, 0.4494, -0.8693, 0.4494, 0.4494, + 0.7214, -0.6013] + NASN: + atom_type: [N3, H, H, H, CT, HP, CT, HC, HC, C, O, N, H, H, C, O] + atom_charge: [0.1801, 0.1921, 0.1921, 0.1921, 0.0368, 0.1231, -0.0283, 0.0515, 0.0515, 0.5833, -0.5744, -0.8634, + 0.4097, 0.4097, 0.6163, -0.5722] + NASP: + atom_type: [N3, H, H, H, CT, HP, CT, HC, HC, C, O2, O2, C, O] + atom_charge: [0.0782, 0.22, 0.22, 0.22, 0.0292, 0.1141, -0.0235, -0.0169, -0.0169, 0.8194, -0.8084, -0.8084, 0.5621, + -0.5889] + NCYS: + atom_type: [N3, H, H, H, CT, HP, CT, H1, H1, SH, HS, C, O] + atom_charge: [0.1325, 0.2023, 0.2023, 0.2023, 0.0927, 0.1411, -0.1195, 0.1188, 0.1188, -0.3298, 0.1975, 0.6123, + -0.5713] + NGLN: + atom_type: [N3, H, H, H, CT, HP, CT, HC, HC, CT, HC, HC, C, O, N, H, H, C, O] + atom_charge: [0.1493, 0.1996, 0.1996, 0.1996, 0.0536, 0.1015, 0.0651, 0.005, 0.005, -0.0903, 0.0331, 0.0331, 0.7354, + -0.6133, -1.0031, 0.4429, 0.4429, 0.6123, -0.5713] + NGLU: + atom_type: [N3, H, H, H, CT, HP, CT, HC, HC, CT, HC, HC, C, O2, O2, C, O] + atom_charge: [0.0017, 0.2391, 0.2391, 0.2391, 0.0588, 0.1202, 0.0909, -0.0232, -0.0232, -0.0236, -0.0315, -0.0315, + 0.8087, -0.8189, -0.8189, 0.5621, -0.5889] + NGLY: + atom_type: [N3, H, H, H, CT, HP, HP, C, O] + atom_charge: [0.2943, 0.1642, 0.1642, 0.1642, -0.01, 0.0895, 0.0895, 0.6163, -0.5722] + NHID: + atom_type: [N3, H, H, H, CT, HP, CT, HC, HC, CC, NA, H, CR, H5, NB, CV, H4, C, O] + atom_charge: [0.1542, 0.1963, 0.1963, 0.1963, 0.0964, 0.0958, 0.0259, 0.0209, 0.0209, -0.0399, -0.3819, 0.3632, + 0.2127, 0.1385, -0.5711, 0.1046, 0.1299, 0.6123, -0.5713] + NHIS: + atom_type: [N3, H, H, H, CT, HP, CT, HC, HC, CC, NB, CR, H5, NA, H, CW, H4, C, O] + atom_charge: [0.1472, 0.2016, 0.2016, 0.2016, 0.0236, 0.138, 0.0489, 0.0223, 0.0223, 0.174, -0.5579, 0.1804, 0.1397, + -0.2781, 0.3324, -0.2349, 0.1963, 0.6123, -0.5713] + NILE: + atom_type: [N3, H, H, H, CT, HP, CT, HC, CT, HC, HC, HC, CT, HC, HC, CT, HC, HC, HC, C, O] + atom_charge: [0.0311, 0.2329, 0.2329, 0.2329, 0.0257, 0.1031, 0.1885, 0.0213, -0.372, 0.0947, 0.0947, 0.0947, + -0.0387, 0.0201, 0.0201, -0.0908, 0.0226, 0.0226, 0.0226, 0.6123, -0.5713] + NLEU: + atom_type: [N3, H, H, H, CT, HP, CT, HC, HC, CT, HC, CT, HC, HC, HC, CT, HC, HC, HC, C, O] + atom_charge: [0.101, 0.2148, 0.2148, 0.2148, 0.0104, 0.1053, -0.0244, 0.0256, 0.0256, 0.3421, -0.038, -0.4106, + 0.098, 0.098, 0.098, -0.4104, 0.098, 0.098, 0.098, 0.6123, -0.5713] + NLYS: + atom_type: [N3, H, H, H, CT, HP, CT, HC, HC, CT, HC, HC, CT, HC, HC, CT, HP, HP, N3, H, H, H, C, O] + atom_charge: [0.0966, 0.2165, 0.2165, 0.2165, -0.0015, 0.118, 0.0212, 0.0283, 0.0283, -0.0048, 0.0121, 0.0121, + -0.0608, 0.0633, 0.0633, -0.0181, 0.1171, 0.1171, -0.3764, 0.3382, 0.3382, 0.3382, 0.7214, -0.6013] + NMET: + atom_type: [N3, H, H, H, CT, HP, CT, HC, HC, CT, H1, H1, S, CT, H1, H1, H1, C, O] + atom_charge: [0.1592, 0.1984, 0.1984, 0.1984, 0.0221, 0.1116, 0.0865, 0.0125, 0.0125, 0.0334, 0.0292, 0.0292, + -0.2774, -0.0341, 0.0597, 0.0597, 0.0597, 0.6123, -0.5713] + NPHE: + atom_type: [N3, H, H, H, CT, HP, CT, HC, HC, CA, CA, HA, CA, HA, CA, HA, CA, HA, CA, HA, C, O] + atom_charge: [0.1737, 0.1921, 0.1921, 0.1921, 0.0733, 0.1041, 0.033, 0.0104, 0.0104, 0.0031, -0.1392, 0.1374, + -0.1602, 0.1433, -0.1208, 0.1329, -0.1603, 0.1433, -0.1391, 0.1374, 0.6123, -0.5713] + NPRO: + atom_type: [N3, H, H, CT, HP, HP, CT, HC, HC, CT, HC, HC, CT, HP, C, O] + atom_charge: [-0.202, 0.312, 0.312, -0.012, 0.1, 0.1, -0.121, 0.1, 0.1, -0.115, 0.1, 0.1, 0.1, 0.1, 0.526, -0.5] + NSER: + atom_type: [N3, H, H, H, CT, HP, CT, H1, H1, OH, HO, C, O] + atom_charge: [0.1849, 0.1898, 0.1898, 0.1898, 0.0567, 0.0782, 0.2596, 0.0273, 0.0273, -0.6714, 0.4239, 0.6163, + -0.5722] + NTHR: + atom_type: [N3, H, H, H, CT, HP, CT, H1, CT, HC, HC, HC, OH, HO, C, O] + atom_charge: [0.1812, 0.1934, 0.1934, 0.1934, 0.0034, 0.1087, 0.4514, -0.0323, -0.2554, 0.0627, 0.0627, 0.0627, + -0.6764, 0.407, 0.6163, -0.5722] + NTRP: + atom_type: [N3, H, H, H, CT, HP, CT, HC, HC, C*, CW, H4, NA, H, CN, CA, HA, CA, HA, CA, HA, CA, HA, CB, C, O] + atom_charge: [0.1913, 0.1888, 0.1888, 0.1888, 0.0421, 0.1162, 0.0543, 0.0222, 0.0222, -0.1654, -0.1788, 0.2195, + -0.3444, 0.3412, 0.1575, -0.271, 0.1589, -0.108, 0.1411, -0.2034, 0.1458, -0.2265, 0.1646, 0.1132, + 0.6123, -0.5713] + NTYR: + atom_type: [N3, H, H, H, CT, HP, CT, HC, HC, CA, CA, HA, CA, HA, C, OH, HO, CA, HA, CA, HA, C, O] + atom_charge: [0.194, 0.1873, 0.1873, 0.1873, 0.057, 0.0983, 0.0659, 0.0102, 0.0102, -0.0205, -0.2002, 0.172, + -0.2239, 0.165, 0.3139, -0.5578, 0.4001, -0.2239, 0.165, -0.2002, 0.172, 0.6123, -0.5713] + NVAL: + atom_type: [N3, H, H, H, CT, HP, CT, HC, CT, HC, HC, HC, CT, HC, HC, HC, C, O] + atom_charge: [0.0577, 0.2272, 0.2272, 0.2272, -0.0054, 0.1093, 0.3196, -0.0221, -0.3129, 0.0735, 0.0735, 0.0735, + -0.3129, 0.0735, 0.0735, 0.0735, 0.6163, -0.5722] + CALA: + atom_type: [N, H, CT, H1, CT, HC, HC, HC, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.1747, 0.1067, -0.2093, 0.0764, 0.0764, 0.0764, 0.7731, -0.8055, -0.8055] + CARG: + atom_type: [N, H, CT, H1, CT, HC, HC, CT, HC, HC, CT, H1, H1, N2, H, CA, N2, H, H, N2, H, H, C, O2, O2] + atom_charge: [-0.3481, 0.2764, -0.3068, 0.1447, -0.0374, 0.0371, 0.0371, 0.0744, 0.0185, 0.0185, 0.1114, 0.0468, + 0.0468, -0.5564, 0.3479, 0.8368, -0.8737, 0.4493, 0.4493, -0.8737, 0.4493, 0.4493, 0.8557, -0.8266, + -0.8266] + CASN: + atom_type: [N, H, CT, H1, CT, HC, HC, C, O, N, H, H, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.208, 0.1358, -0.2299, 0.1023, 0.1023, 0.7153, -0.601, -0.9084, 0.415, 0.415, + 0.805, -0.8147, -0.8147] + CASP: + atom_type: [N, H, CT, H1, CT, HC, HC, C, O2, O2, C, O2, O2] + atom_charge: [-0.5192, 0.3055, -0.1817, 0.1046, -0.0677, -0.0212, -0.0212, 0.8851, -0.8162, -0.8162, 0.7256, + -0.7887, -0.7887] + CCYS: + atom_type: [N, H, CT, H1, CT, H1, H1, SH, HS, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.1635, 0.1396, -0.1996, 0.1437, 0.1437, -0.3102, 0.2068, 0.7497, -0.7981, -0.7981] + CGLN: + atom_type: [N, H, CT, H1, CT, HC, HC, CT, HC, HC, C, O, N, H, H, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.2248, 0.1232, -0.0664, 0.0452, 0.0452, -0.021, 0.0203, 0.0203, 0.7093, -0.6098, + -0.9574, 0.4304, 0.4304, 0.7775, -0.8042, -0.8042] + CGLU: + atom_type: [N, H, CT, H1, CT, HC, HC, CT, HC, HC, C, O2, O2, C, O2, O2] + atom_charge: [-0.5192, 0.3055, -0.2059, 0.1399, 0.0071, -0.0078, -0.0078, 0.0675, -0.0548, -0.0548, 0.8183, -0.822, + -0.822, 0.742, -0.793, -0.793] + CGLY: + atom_type: [N, H, CT, H1, H1, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.2493, 0.1056, 0.1056, 0.7231, -0.7855, -0.7855] + CHID: + atom_type: [N, H, CT, H1, CT, HC, HC, CC, NA, H, CR, H5, NB, CV, H4, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.1739, 0.11, -0.1046, 0.0565, 0.0565, 0.0293, -0.3892, 0.3755, 0.1925, 0.1418, + -0.5629, 0.1001, 0.1241, 0.7615, -0.8016, -0.8016] + CHIS: + atom_type: [N, H, CT, H1, CT, HC, HC, CC, NB, CR, H5, NA, H, CW, H4, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.2699, 0.165, -0.1068, 0.062, 0.062, 0.2724, -0.5517, 0.1558, 0.1448, -0.267, + 0.3319, -0.2588, 0.1957, 0.7916, -0.8065, -0.8065] + CILE: + atom_type: [N, H, CT, H1, CT, HC, CT, HC, HC, HC, CT, HC, HC, CT, HC, HC, HC, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.31, 0.1375, 0.0363, 0.0766, -0.3498, 0.1021, 0.1021, 0.1021, -0.0323, 0.0321, + 0.0321, -0.0699, 0.0196, 0.0196, 0.0196, 0.8343, -0.819, -0.819] + CLEU: + atom_type: [N, H, CT, H1, CT, HC, HC, CT, HC, CT, HC, HC, HC, CT, HC, HC, HC, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.2847, 0.1346, -0.2469, 0.0974, 0.0974, 0.3706, -0.0374, -0.4163, 0.1038, 0.1038, + 0.1038, -0.4163, 0.1038, 0.1038, 0.1038, 0.8326, -0.8199, -0.8199] + CLYS: + atom_type: [N, H, CT, H1, CT, HC, HC, CT, HC, HC, CT, HC, HC, CT, HP, HP, N3, H, H, H, C, O2, O2] + atom_charge: [-0.3481, 0.2764, -0.2903, 0.1438, -0.0538, 0.0482, 0.0482, 0.0227, 0.0134, 0.0134, -0.0392, 0.0611, + 0.0611, -0.0176, 0.1121, 0.1121, -0.3741, 0.3374, 0.3374, 0.3374, 0.8488, -0.8252, -0.8252] + CMET: + atom_type: [N, H, CT, H1, CT, HC, HC, CT, H1, H1, S, CT, H1, H1, H1, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.2597, 0.1277, -0.0236, 0.048, 0.048, 0.0492, 0.0317, 0.0317, -0.2692, -0.0376, + 0.0625, 0.0625, 0.0625, 0.8013, -0.8105, -0.8105] + CPHE: + atom_type: [N, H, CT, H1, CT, HC, HC, CA, CA, HA, CA, HA, CA, HA, CA, HA, CA, HA, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.1825, 0.1098, -0.0959, 0.0443, 0.0443, 0.0552, -0.13, 0.1408, -0.1847, 0.1461, + -0.0944, 0.128, -0.1847, 0.1461, -0.13, 0.1408, 0.766, -0.8026, -0.8026] + CPRO: + atom_type: [N, CT, H1, H1, CT, HC, HC, CT, HC, HC, CT, H1, C, O2, O2] + atom_charge: [-0.2802, 0.0434, 0.0331, 0.0331, 0.0466, 0.0172, 0.0172, -0.0543, 0.0381, 0.0381, -0.1336, 0.0776, + 0.6631, -0.7697, -0.7697] + CSER: + atom_type: [N, H, CT, H1, CT, H1, H1, OH, HO, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.2722, 0.1304, 0.1123, 0.0813, 0.0813, -0.6514, 0.4474, 0.8113, -0.8132, -0.8132] + CTHR: + atom_type: [N, H, CT, H1, CT, H1, CT, HC, HC, HC, OH, HO, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.242, 0.1207, 0.3025, 0.0078, -0.1853, 0.0586, 0.0586, 0.0586, -0.6496, 0.4119, + 0.781, -0.8044, -0.8044] + CTRP: + atom_type: [N, H, CT, H1, CT, HC, HC, C*, CW, H4, NA, H, CN, CA, HA, CA, HA, CA, HA, CA, HA, CB, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.2084, 0.1272, -0.0742, 0.0497, 0.0497, -0.0796, -0.1808, 0.2043, -0.3316, 0.3413, + 0.1222, -0.2594, 0.1567, -0.102, 0.1401, -0.2287, 0.1507, -0.1837, 0.1491, 0.1078, 0.7658, -0.8011, + -0.8011] + CTYR: + atom_type: [N, H, CT, H1, CT, HC, HC, CA, CA, HA, CA, HA, C, OH, HO, CA, HA, CA, HA, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.2015, 0.1092, -0.0752, 0.049, 0.049, 0.0243, -0.1922, 0.178, -0.2458, 0.1673, + 0.3395, -0.5643, 0.4017, -0.2458, 0.1673, -0.1922, 0.178, 0.7817, -0.807, -0.807] + CVAL: + atom_type: [N, H, CT, H1, CT, HC, CT, HC, HC, HC, CT, HC, HC, HC, C, O2, O2] + atom_charge: [-0.3821, 0.2681, -0.3438, 0.1438, 0.194, 0.0308, -0.3064, 0.0836, 0.0836, 0.0836, -0.3064, 0.0836, + 0.0836, 0.0836, 0.835, -0.8173, -0.8173] + ACE: + atom_type: [HC, CT, HC, HC, C, O] + atom_charge: [0.112298, -0.3661936, 0.112298, 0.112298, 0.5971897, -0.5678902] + NME: + atom_type: [N, H, CT, H1, H1, H1] + atom_charge: [-0.4156928, 0.2718953, -0.1489974, 0.0975983, 0.0975983, 0.0975983] + +parameters: + bond_energy: + length_unit: nm + energy_unit: kj/mol + parameter_names: + pattern: [bond_length, force_constant] + parameters: + C-C: [0.1525, 259408.0] + C-CA: [0.1409, 392459.2] + C-CB: [0.1419, 374049.6] + C-CM: [0.1444, 343088.0] + C-CT: [0.1522, 265265.6] + C-N: [0.1335, 410032.0] + C-N*: [0.1383, 354803.2] + C-NA: [0.1388, 349782.4] + C-NC: [0.1358, 382417.6] + C-O: [0.1229, 476976.0] + C-O2: [0.125, 548940.8] + C-OH: [0.1364, 376560.0] + C-OS: [0.1323, 376560.0] + C-H4: [0.108, 307105.6] + C-H5: [0.108, 307105.6] + CA-CA: [0.14, 392459.2] + CA-CB: [0.1404, 392459.2] + CA-CM: [0.1433, 357313.6] + CA-CN: [0.14, 392459.2] + CA-CT: [0.151, 265265.6] + CA-HA: [0.108, 307105.6] + CA-H4: [0.108, 307105.6] + CA-N2: [0.134, 402500.8] + CA-NA: [0.1381, 357313.6] + CA-NC: [0.1339, 404174.4] + CA-OH: [0.1364, 376560.0] + CB-CB: [0.137, 435136.0] + CB-N*: [0.1374, 364844.8] + CB-NB: [0.1391, 346435.2] + CB-NC: [0.1354, 385764.8] + CD-HA: [0.108, 307105.6] + CD-CD: [0.14, 392459.2] + CD-CM: [0.135, 459403.2] + CD-CT: [0.151, 265265.6] + CK-H5: [0.108, 307105.6] + CK-N*: [0.1371, 368192.0] + CK-NB: [0.1304, 442667.2] + CM-CM: [0.135, 459403.2] + CM-CT: [0.151, 265265.6] + CM-HA: [0.108, 307105.6] + CM-H4: [0.108, 307105.6] + CM-H5: [0.108, 307105.6] + CM-N*: [0.1365, 374886.4] + CM-OS: [0.124, 401664.0] + CQ-H5: [0.108, 307105.6] + CQ-NC: [0.1324, 420073.6] + CT-CT: [0.1526, 259408.0] + CT-HC: [0.109, 284512.0] + CT-H1: [0.109, 284512.0] + CT-H2: [0.109, 284512.0] + CT-H3: [0.109, 284512.0] + CT-HP: [0.109, 284512.0] + CT-N*: [0.1475, 282001.6] + CT-N2: [0.1463, 282001.6] + CT-OH: [0.141, 267776.0] + CT-OS: [0.141, 267776.0] + C*-HC: [0.108, 307105.6] + C*-CB: [0.1459, 324678.4] + C*-CT: [0.1495, 265265.6] + C*-CW: [0.1352, 456892.8] + CB-CN: [0.1419, 374049.6] + CC-CT: [0.1504, 265265.6] + CC-CV: [0.1375, 428441.6] + CC-CW: [0.1371, 433462.4] + CC-NA: [0.1385, 353129.6] + CC-NB: [0.1394, 343088.0] + CN-NA: [0.138, 358150.4] + CR-H5: [0.108, 307105.6] + CR-NA: [0.1343, 399153.6] + CR-NB: [0.1335, 408358.4] + CT-N: [0.1449, 282001.6] + CT-N3: [0.1471, 307105.6] + CT-NT: [0.1471, 307105.6] + CT-S: [0.181, 189953.6] + CT-SH: [0.181, 198321.6] + CT-CY: [0.1458, 334720.0] + CT-CZ: [0.1459, 334720.0] + CV-H4: [0.108, 307105.6] + CV-NB: [0.1394, 343088.0] + CW-H4: [0.108, 307105.6] + CW-NA: [0.1381, 357313.6] + CY-NY: [0.115, 502080.0] + CZ-CZ: [0.1206, 502080.0] + CZ-HZ: [0.1056, 334720.0] + O2-P: [0.148, 439320.0] + OH-P: [0.161, 192464.0] + OS-P: [0.161, 192464.0] + H-N2: [0.101, 363171.2] + H-N*: [0.101, 363171.2] + H-NA: [0.101, 363171.2] + H-N: [0.101, 363171.2] + H-N3: [0.101, 363171.2] + H-NT: [0.101, 363171.2] + HO-OH: [0.096, 462750.4] + HO-OS: [0.096, 462750.4] + HS-SH: [0.1336, 229283.2] + S-S: [0.2038, 138908.8] + F-CT: [0.138, 307105.6] + Cl-CT: [0.1766, 194137.6] + Br-CT: [0.1944, 133051.2] + I-CT: [0.2166, 123846.4] + F-CA: [0.1359, 323004.8] + Cl-CA: [0.1727, 161502.4] + I-CA: [0.2075, 143092.8] + Br-CA: [0.189, 143929.6] + LP-O: [0.02, 502080.0] + LP-OH: [0.02, 502080.0] + LP-OS: [0.02, 502080.0] + LP-N3: [0.02, 502080.0] + LP-NT: [0.02, 502080.0] + LP-NB: [0.02, 502080.0] + LP-NC: [0.02, 502080.0] + LP-S: [0.07, 502080.0] + LP-SH: [0.07, 502080.0] + angle_energy: + length_unit: nm + energy_unit: kj/mol + parameter_names: + pattern: [bond_angle, force_constant] + parameters: + C-C-O: [120.0, 669.44] + C-C-OH: [120.0, 669.44] + CA-C-CA: [120.0, 527.184] + CA-C-OH: [120.0, 585.76] + CB-C-NA: [111.3, 585.76] + CB-C-O: [128.8, 669.44] + CM-C-NA: [114.1, 585.76] + CM-C-O: [125.3, 669.44] + CT-C-O: [120.4, 669.44] + CT-C-O2: [117.0, 585.76] + CT-C-N: [116.6, 585.76] + CT-C-CT: [117.0, 527.184] + CT-C-OS: [115.0, 669.44] + CT-C-OH: [110.0, 669.44] + N*-C-NA: [115.4, 585.76] + N*-C-NC: [118.6, 585.76] + N*-C-O: [120.9, 669.44] + NA-C-O: [120.6, 669.44] + NC-C-O: [122.5, 669.44] + N-C-O: [122.9, 669.44] + O-C-O: [126.0, 669.44] + O-C-OH: [120.0, 669.44] + O-C-OS: [125.0, 669.44] + O2-C-O2: [126.0, 669.44] + H4-C-C: [120.0, 418.4] + H4-C-CM: [115.0, 418.4] + H4-C-CT: [115.0, 418.4] + H4-C-O: [120.0, 418.4] + H4-C-OH: [120.0, 418.4] + H5-C-N: [120.0, 418.4] + H5-C-O: [119.0, 418.4] + H5-C-OH: [107.0, 418.4] + H5-C-OS: [107.0, 418.4] + C-CA-CA: [120.0, 527.184] + C-CA-HA: [120.0, 418.4] + CA-CA-CA: [120.0, 527.184] + CA-CA-CB: [120.0, 527.184] + CA-CA-CT: [120.0, 585.76] + CA-CA-HA: [120.0, 418.4] + CA-CA-H4: [120.0, 418.4] + CA-CA-OH: [120.0, 585.76] + CA-CA-CN: [120.0, 527.184] + CB-CA-HA: [120.0, 418.4] + CB-CA-H4: [120.0, 418.4] + CB-CA-N2: [123.5, 585.76] + CB-CA-NC: [117.3, 585.76] + CM-CA-N2: [120.1, 585.76] + CM-CA-NC: [121.5, 585.76] + CN-CA-HA: [120.0, 418.4] + NA-CA-NC: [123.3, 585.76] + N2-CA-NA: [116.0, 585.76] + N2-CA-NC: [119.3, 585.76] + N2-CA-N2: [120.0, 585.76] + F-CA-CA: [121.0, 585.76] + Cl-CA-CA: [118.8, 585.76] + Br-CA-CA: [118.8, 585.76] + I-CA-CA: [118.8, 585.76] + C-CB-CB: [119.2, 527.184] + C-CB-NB: [130.0, 585.76] + CA-CB-CB: [117.3, 527.184] + CA-CB-NB: [132.4, 585.76] + CB-CB-N*: [106.2, 585.76] + CB-CB-NB: [110.4, 585.76] + CB-CB-NC: [127.7, 585.76] + C*-CB-CA: [134.9, 527.184] + C*-CB-CN: [108.8, 527.184] + CA-CB-CN: [116.2, 527.184] + N*-CB-NC: [126.2, 585.76] + CD-CD-CM: [120.0, 527.184] + CD-CD-CT: [120.0, 585.76] + CM-CD-CT: [120.0, 585.76] + HA-CD-HA: [119.0, 292.88] + HA-CD-CD: [120.0, 418.4] + HA-CD-CM: [120.0, 418.4] + H5-CK-N*: [123.05, 418.4] + H5-CK-NB: [123.05, 418.4] + N*-CK-NB: [113.9, 585.76] + C-CM-CM: [120.7, 527.184] + C-CM-CT: [119.7, 585.76] + C-CM-HA: [119.7, 418.4] + C-CM-H4: [119.7, 418.4] + CA-CM-CM: [117.0, 527.184] + CA-CM-HA: [123.3, 418.4] + CA-CM-H4: [123.3, 418.4] + CM-CM-CT: [119.7, 585.76] + CM-CM-HA: [119.7, 418.4] + CM-CM-H4: [119.7, 418.4] + CM-CM-N*: [121.2, 585.76] + CM-CM-OS: [125.0, 669.44] + H4-CM-N*: [119.1, 418.4] + H4-CM-OS: [113.0, 418.4] + HA-CM-HA: [120.0, 292.88] + HA-CM-CD: [120.0, 418.4] + HA-CM-CT: [120.0, 418.4] + NC-CQ-NC: [129.1, 585.76] + H5-CQ-NC: [115.45, 418.4] + H1-CT-H1: [109.5, 292.88] + H1-CT-N*: [109.5, 418.4] + H1-CT-OH: [109.5, 418.4] + H1-CT-OS: [109.5, 418.4] + H1-CT-CM: [109.5, 418.4] + H1-CT-CY: [110.0, 418.4] + H1-CT-CZ: [110.0, 418.4] + H1-CT-N: [109.5, 418.4] + H1-CT-S: [109.5, 418.4] + H1-CT-SH: [109.5, 418.4] + H1-CT-N2: [109.5, 418.4] + H1-CT-NT: [109.5, 418.4] + H2-CT-H2: [109.5, 292.88] + H2-CT-N*: [109.5, 418.4] + H2-CT-OS: [109.5, 418.4] + HP-CT-HP: [109.5, 292.88] + HP-CT-N3: [109.5, 418.4] + HC-CT-HC: [109.5, 292.88] + HC-CT-CM: [109.5, 418.4] + HC-CT-CD: [109.5, 418.4] + HC-CT-CZ: [110.0, 418.4] + C-CT-H1: [109.5, 418.4] + C-CT-HP: [109.5, 418.4] + C-CT-HC: [109.5, 418.4] + C-CT-N: [110.1, 527.184] + C-CT-N3: [111.2, 669.44] + C-CT-CT: [111.1, 527.184] + C-CT-OS: [109.5, 502.08] + CA-CT-HC: [109.5, 418.4] + CC-CT-CT: [113.1, 527.184] + CC-CT-HC: [109.5, 418.4] + CM-CT-CT: [111.0, 527.184] + CM-CT-OS: [109.5, 418.4] + CT-CT-CT: [109.5, 334.72] + CT-CT-HC: [109.5, 418.4] + CT-CT-H1: [109.5, 418.4] + CT-CT-H2: [109.5, 418.4] + CT-CT-HP: [109.5, 418.4] + CT-CT-N*: [109.5, 418.4] + CT-CT-OH: [109.5, 418.4] + CT-CT-OS: [109.5, 418.4] + CT-CT-S: [114.7, 418.4] + CT-CT-SH: [108.6, 418.4] + CT-CT-CA: [114.0, 527.184] + CT-CT-N2: [111.2, 669.44] + CT-CT-N: [109.7, 669.44] + CT-CT-N3: [111.2, 669.44] + CT-CT-NT: [111.2, 669.44] + CT-CT-CY: [110.0, 527.184] + CT-CT-CZ: [110.0, 527.184] + C*-CT-CT: [115.6, 527.184] + C*-CT-HC: [109.5, 418.4] + OS-CT-OS: [101.0, 1338.88] + OS-CT-CY: [110.0, 418.4] + OS-CT-CZ: [110.0, 418.4] + OS-CT-N*: [109.5, 418.4] + F-CT-F: [109.1, 644.336] + F-CT-H1: [109.5, 418.4] + F-CT-CT: [109.0, 418.4] + F-CT-H2: [109.5, 418.4] + Cl-CT-CT: [108.5, 418.4] + Cl-CT-H1: [108.5, 418.4] + Br-CT-CT: [108.0, 418.4] + Br-CT-H1: [106.5, 418.4] + I-CT-CT: [106.0, 418.4] + CT-CC-NA: [120.0, 585.76] + CT-CC-CV: [120.0, 585.76] + CT-CC-NB: [120.0, 585.76] + CV-CC-NA: [120.0, 585.76] + CW-CC-NA: [120.0, 585.76] + CW-CC-NB: [120.0, 585.76] + CT-CC-CW: [120.0, 585.76] + H5-CR-NA: [120.0, 418.4] + H5-CR-NB: [120.0, 418.4] + NA-CR-NA: [120.0, 585.76] + NA-CR-NB: [120.0, 585.76] + CC-CV-H4: [120.0, 418.4] + CC-CV-NB: [120.0, 585.76] + H4-CV-NB: [120.0, 418.4] + CC-CW-H4: [120.0, 418.4] + CC-CW-NA: [120.0, 585.76] + C*-CW-H4: [120.0, 418.4] + C*-CW-NA: [108.7, 585.76] + H4-CW-NA: [120.0, 418.4] + CB-C*-CT: [128.6, 585.76] + CB-C*-CW: [106.4, 527.184] + CT-C*-CW: [125.0, 585.76] + CA-CN-CB: [122.7, 527.184] + CA-CN-NA: [132.8, 585.76] + CB-CN-NA: [104.4, 585.76] + CT-CY-NY: [180.0, 669.44] + CT-CZ-CZ: [180.0, 669.44] + CZ-CZ-HZ: [180.0, 418.4] + C-N-CT: [121.9, 418.4] + C-N-H: [120.0, 418.4] + CT-N-H: [118.04, 418.4] + CT-N-CT: [118.0, 418.4] + H-N-H: [120.0, 292.88] + C-N*-CM: [121.6, 585.76] + C-N*-CT: [117.6, 585.76] + C-N*-H: [119.2, 418.4] + CB-N*-CK: [105.4, 585.76] + CB-N*-CT: [125.8, 585.76] + CB-N*-H: [125.8, 418.4] + CK-N*-CT: [128.8, 585.76] + CK-N*-H: [128.8, 418.4] + CM-N*-CT: [121.2, 585.76] + CM-N*-H: [121.2, 418.4] + CA-N2-H: [120.0, 418.4] + CA-N2-CT: [123.2, 418.4] + CT-N2-H: [118.4, 418.4] + H-N2-H: [120.0, 292.88] + CT-N3-H: [109.5, 418.4] + CT-N3-CT: [109.5, 418.4] + H-N3-H: [109.5, 292.88] + CT-NT-H: [109.5, 418.4] + CT-NT-CT: [109.5, 418.4] + H-NT-H: [109.5, 292.88] + C-NA-C: [126.4, 585.76] + C-NA-CA: [125.2, 585.76] + C-NA-H: [116.8, 418.4] + CA-NA-H: [118.0, 418.4] + CC-NA-CR: [120.0, 585.76] + CC-NA-H: [120.0, 418.4] + CR-NA-CW: [120.0, 585.76] + CR-NA-H: [120.0, 418.4] + CW-NA-H: [120.0, 418.4] + CN-NA-CW: [111.6, 585.76] + CN-NA-H: [123.1, 418.4] + CB-NB-CK: [103.8, 585.76] + CC-NB-CR: [117.0, 585.76] + CR-NB-CV: [117.0, 585.76] + C-NC-CA: [120.5, 585.76] + CA-NC-CB: [112.2, 585.76] + CA-NC-CQ: [118.6, 585.76] + CB-NC-CQ: [111.0, 585.76] + C-OH-HO: [113.0, 418.4] + CA-OH-HO: [113.0, 418.4] + CT-OH-HO: [108.5, 460.24] + HO-OH-P: [108.5, 376.56] + C-OS-CT: [117.0, 502.08] + CM-OS-CT: [117.0, 502.08] + CT-OS-CT: [109.5, 502.08] + CT-OS-P: [120.5, 836.8] + P-OS-P: [120.5, 836.8] + O2-P-OH: [108.23, 376.56] + O2-P-O2: [119.9, 1171.52] + O2-P-OS: [108.23, 836.8] + OH-P-OS: [102.6, 376.56] + OS-P-OS: [102.6, 376.56] + CT-S-CT: [98.9, 518.816] + CT-S-S: [103.7, 569.024] + CT-SH-HS: [96.0, 359.824] + HS-SH-HS: [92.07, 292.88] + CB-NB-LP: [126.0, 1255.2] + CC-NB-LP: [126.0, 1255.2] + CK-NB-LP: [126.0, 1255.2] + CR-NB-LP: [126.0, 1255.2] + CV-NB-LP: [126.0, 1255.2] + C-NC-LP: [120.0, 1255.2] + CA-NC-LP: [120.0, 1255.2] + CB-NC-LP: [120.0, 1255.2] + CQ-NC-LP: [120.0, 1255.2] + CT-N3-LP: [109.5, 1255.2] + H-N3-LP: [109.5, 1255.2] + CT-NT-LP: [109.5, 1255.2] + H-NT-LP: [109.5, 1255.2] + C-O-LP: [120.0, 1255.2] + LP-O-LP: [120.0, 1255.2] + C-OH-LP: [120.0, 1255.2] + CT-OH-LP: [109.5, 1255.2] + HO-OH-LP: [109.5, 1255.2] + LP-OH-LP: [109.5, 1255.2] + C-OS-LP: [109.5, 1255.2] + CM-OS-LP: [109.5, 1255.2] + CT-OS-LP: [109.5, 1255.2] + LP-OS-LP: [109.5, 1255.2] + CT-S-LP: [90.0, 1255.2] + CT-SH-LP: [90.0, 1255.2] + P-OS-LP: [109.5, 1255.2] + LP-S-LP: [180.0, 1255.2] + LP-SH-LP: [180.0, 1255.2] + HS-SH-LP: [90.0, 1255.2] + dihedral_energy: + length_unit: nm + energy_unit: kj/mol + parameter_names: + pattern: + - [phase, force_constant, periodicity] + parameters: + ?-C-C-?: + - [180.0, 30.334, 2.0] + ?-C-CA-?: + - [180.0, 30.334, 2.0] + ?-C-CB-?: + - [180.0, 25.104, 2.0] + ?-C-CM-?: + - [180.0, 18.2, 2.0] + ?-C-CT-?: + - [0.0, 0.0, 2.0] + ?-C-N-?: + - [180.0, 20.92, 2.0] + ?-C-N*-?: + - [180.0, 12.134, 2.0] + ?-C-NA-?: + - [180.0, 11.297, 2.0] + ?-C-NC-?: + - [180.0, 33.472, 2.0] + ?-C-O-?: + - [180.0, 23.43, 2.0] + ?-C-OH-?: + - [180.0, 19.246, 2.0] + ?-C-OS-?: + - [180.0, 22.594, 2.0] + ?-CA-CA-?: + - [180.0, 30.334, 2.0] + ?-CA-CB-?: + - [180.0, 29.288, 2.0] + ?-CA-CM-?: + - [180.0, 21.338, 2.0] + ?-CA-CN-?: + - [180.0, 30.334, 2.0] + ?-CA-CT-?: + - [0.0, 0.0, 2.0] + ?-CA-N2-?: + - [180.0, 20.083, 2.0] + ?-CA-NA-?: + - [180.0, 12.552, 2.0] + ?-CA-NC-?: + - [180.0, 40.166, 2.0] + ?-CA-OH-?: + - [180.0, 7.531, 2.0] + ?-CB-CB-?: + - [180.0, 45.606, 2.0] + ?-CB-CN-?: + - [180.0, 25.104, 2.0] + ?-CB-N*-?: + - [180.0, 13.807, 2.0] + ?-CB-NB-?: + - [180.0, 21.338, 2.0] + ?-CB-NC-?: + - [180.0, 34.727, 2.0] + ?-CC-CT-?: + - [0.0, 0.0, 2.0] + ?-CC-CV-?: + - [180.0, 43.095, 2.0] + ?-CC-CW-?: + - [180.0, 44.978, 2.0] + ?-CC-NA-?: + - [180.0, 11.715, 2.0] + ?-CC-NB-?: + - [180.0, 20.083, 2.0] + ?-CD-CD-?: + - [180.0, 8.368, 2.0] + ?-CD-CT-?: + - [0.0, 0.0, 2.0] + ?-CD-CM-?: + - [180.0, 55.647, 2.0] + ?-CK-N*-?: + - [180.0, 14.226, 2.0] + ?-CK-NB-?: + - [180.0, 83.68, 2.0] + ?-CM-CM-?: + - [180.0, 55.647, 2.0] + ?-CM-CT-?: + - [0.0, 0.0, 3.0] + ?-CM-N*-?: + - [180.0, 15.481, 2.0] + ?-CM-OS-?: + - [180.0, 8.786, 2.0] + ?-CN-NA-?: + - [180.0, 12.761, 2.0] + ?-CQ-NC-?: + - [180.0, 56.902, 2.0] + ?-CT-CT-?: + - [0.0, 1.302, 3.0] + ?-CT-CY-?: + - [0.0, 0.0, 1.0] + ?-CT-CZ-?: + - [0.0, 0.0, 1.0] + ?-CT-N-?: + - [0.0, 0.0, 2.0] + ?-CT-N*-?: + - [0.0, 0.0, 2.0] + ?-CT-N2-?: + - [0.0, 0.0, 3.0] + ?-CT-NT-?: + - [0.0, 2.51, 3.0] + ?-CT-N3-?: + - [0.0, 1.302, 3.0] + ?-CT-OH-?: + - [0.0, 1.395, 3.0] + ?-CT-OS-?: + - [0.0, 3.208, 3.0] + ?-CT-S-?: + - [0.0, 2.789, 3.0] + ?-CT-SH-?: + - [0.0, 2.092, 3.0] + ?-C*-CB-?: + - [180.0, 14.016, 2.0] + ?-C*-CT-?: + - [0.0, 0.0, 2.0] + ?-C*-CW-?: + - [180.0, 54.601, 2.0] + ?-CR-NA-?: + - [180.0, 19.456, 2.0] + ?-CR-NB-?: + - [180.0, 41.84, 2.0] + ?-CV-NB-?: + - [180.0, 20.083, 2.0] + ?-CW-NA-?: + - [180.0, 12.552, 2.0] + ?-OH-P-?: + - [0.0, 2.092, 3.0] + ?-OS-P-?: + - [0.0, 2.092, 3.0] + N-CT-C-N: + - [0.0, 0.0, -4.0] + - [180.0, 4.602, -3.0] + - [180.0, 13.221, -2.0] + - [180.0, 3.766, 1.0] + C-N-CT-C: + - [0.0, 0.0, -4.0] + - [0.0, 3.515, -3.0] + - [0.0, 2.259, -2.0] + - [0.0, 0.0, 1.0] + CT-CT-N-C: + - [0.0, 0.0, -4.0] + - [0.0, 3.347, -3.0] + - [0.0, 16.736, -2.0] + - [0.0, 16.736, 1.0] + CT-CT-C-N: + - [0.0, 0.0, -4.0] + - [0.0, 3.347, -3.0] + - [0.0, 1.674, -2.0] + - [0.0, 1.674, 1.0] + H-N-C-O: + - [180.0, 20.92, -2.0] + - [0.0, 16.736, 1.0] + CT-S-S-CT: + - [0.0, 29.288, -2.0] + - [0.0, 5.021, 3.0] + OH-P-OS-CT: + - [0.0, 2.092, -3.0] + - [0.0, 10.042, 2.0] + OS-P-OS-CT: + - [0.0, 2.092, -3.0] + - [0.0, 10.042, 2.0] + H1-CT-C-O: + - [0.0, 6.694, -1.0] + - [0.0, 0.0, -2.0] + - [180.0, 0.669, 3.0] + HC-CT-C-O: + - [0.0, 6.694, -1.0] + - [0.0, 0.0, -2.0] + - [180.0, 0.669, 3.0] + HC-CT-CT-HC: + - [0.0, 1.255, 3.0] + HC-CT-CT-CT: + - [0.0, 1.339, 3.0] + HC-CT-CM-CM: + - [180.0, 3.18, -3.0] + - [0.0, 9.623, 1.0] + HO-OH-CT-CT: + - [0.0, 1.339, -3.0] + - [0.0, 2.092, 1.0] + HO-OH-C-O: + - [180.0, 19.246, -2.0] + - [0.0, 15.899, 1.0] + CM-CM-C-O: + - [180.0, 18.2, -2.0] + - [0.0, 2.51, 3.0] + CT-CM-CM-CT: + - [180.0, 55.647, -2.0] + - [180.0, 15.899, 1.0] + CT-CT-CT-CT: + - [0.0, 1.506, -3.0] + - [180.0, 2.092, -2.0] + - [180.0, 1.674, 1.0] + CT-CT-NT-CT: + - [0.0, 2.51, -3.0] + - [180.0, 4.017, 2.0] + CT-CT-OS-CT: + - [0.0, 3.205, -3.0] + - [180.0, 0.837, 2.0] + CT-CT-OS-C: + - [0.0, 3.205, -3.0] + - [180.0, 6.694, 1.0] + CT-OS-CT-OS: + - [0.0, 0.837, -3.0] + - [180.0, 7.113, -2.0] + - [180.0, 11.297, 1.0] + CT-OS-CT-N*: + - [0.0, 3.205, -3.0] + - [0.0, 5.439, 2.0] + CT-CZ-CZ-HZ: + - [0.0, 0.0, 1.0] + O-C-OS-CT: + - [180.0, 22.594, -2.0] + - [180.0, 11.715, 1.0] + OS-CT-N*-CK: + - [0.0, 0.0, -2.0] + - [0.0, 20.92, 1.0] + OS-CT-N*-CM: + - [0.0, 0.0, -2.0] + - [0.0, 20.92, 1.0] + OS-CT-CT-OS: + - [0.0, 1.205, -3.0] + - [0.0, 9.832, 2.0] + OS-CT-CT-OH: + - [0.0, 1.205, -3.0] + - [0.0, 9.832, 2.0] + OH-CT-CT-OH: + - [0.0, 1.205, -3.0] + - [0.0, 9.832, 2.0] + F-CT-CT-F: + - [0.0, 0.0, -3.0] + - [180.0, 10.042, 1.0] + Cl-CT-CT-Cl: + - [0.0, 0.0, -3.0] + - [180.0, 3.766, 1.0] + Br-CT-CT-Br: + - [0.0, 0.0, -3.0] + - [180.0, 0.0, 1.0] + H1-CT-CT-OS: + - [0.0, 0.0, -3.0] + - [0.0, 2.092, 1.0] + H1-CT-CT-OH: + - [0.0, 0.0, -3.0] + - [0.0, 2.092, 1.0] + H1-CT-CT-F: + - [0.0, 0.0, -3.0] + - [0.0, 1.59, 1.0] + H1-CT-CT-Cl: + - [0.0, 0.0, -3.0] + - [0.0, 2.092, 1.0] + H1-CT-CT-Br: + - [0.0, 0.0, -3.0] + - [0.0, 4.602, 1.0] + HC-CT-CT-OS: + - [0.0, 0.0, -3.0] + - [0.0, 2.092, 1.0] + HC-CT-CT-OH: + - [0.0, 0.0, -3.0] + - [0.0, 2.092, 1.0] + HC-CT-CT-F: + - [0.0, 0.0, -3.0] + - [0.0, 1.59, 1.0] + HC-CT-CT-Cl: + - [0.0, 0.0, -3.0] + - [0.0, 2.092, 1.0] + HC-CT-CT-Br: + - [0.0, 0.0, -3.0] + - [0.0, 4.602, 1.0] + H1-CT-NT-LP: + - [0.0, 0.0, 3.0] + CT-CT-NT-LP: + - [0.0, 0.0, 3.0] + CT-C-N-LP: + - [180.0, 0.0, 2.0] + O-C-N-LP: + - [180.0, 0.0, 2.0] + H1-CT-OH-LP: + - [0.0, 0.0, 3.0] + CT-CT-OH-LP: + - [0.0, 0.0, 3.0] + H1-CT-OS-LP: + - [0.0, 0.0, 3.0] + H2-CT-OS-LP: + - [0.0, 0.0, 3.0] + CT-CT-OS-LP: + - [0.0, 0.0, 3.0] + CM-CM-OS-LP: + - [180.0, 0.0, 2.0] + HA-CM-OS-LP: + - [180.0, 0.0, 2.0] + H4-CM-OS-LP: + - [180.0, 0.0, 2.0] + improper_energy: + length_unit: nm + energy_unit: kj/mol + parameter_names: + pattern: + - [phase, force_constant, periodicity] + parameters: + ?-?-C-O: + - [180.0, 87.864, 2] + ?-O2-C-O2: + - [180.0, 87.864, 2] + ?-?-N-H: + - [180.0, 8.368, 2] + ?-?-N2-H: + - [180.0, 8.368, 2] + ?-?-NA-H: + - [180.0, 8.368, 2] + ?-N2-CA-N2: + - [180.0, 87.864, 2] + ?-CT-N-CT: + - [180.0, 8.368, 2] + ?-?-CA-HA: + - [180.0, 9.205, 2] + ?-?-CW-H4: + - [180.0, 9.205, 2] + ?-?-CR-H5: + - [180.0, 9.205, 2] + ?-?-CV-H4: + - [180.0, 9.205, 2] + ?-?-CQ-H5: + - [180.0, 9.205, 2] + ?-?-CK-H5: + - [180.0, 9.205, 2] + ?-?-CM-H4: + - [180.0, 9.205, 2] + ?-?-CM-HA: + - [180.0, 9.205, 2] + ?-?-CA-H4: + - [180.0, 9.205, 2] + ?-?-CA-H5: + - [180.0, 9.205, 2] + CB-CK-N*-CT: + - [180.0, 8.368, 2] + C-CM-N*-CT: + - [180.0, 8.368, 2] + CT-O-C-OH: + - [180.0, 87.864, 2] + CT-CV-CC-NA: + - [180.0, 9.205, 2] + CT-CW-CC-NB: + - [180.0, 9.205, 2] + CT-CW-CC-NA: + - [180.0, 9.205, 2] + CB-CT-C*-CW: + - [180.0, 9.205, 2] + CA-CA-CA-CT: + - [180.0, 9.205, 2] + C-CM-CM-CT: + - [180.0, 9.205, 2] + CM-N2-CA-NC: + - [180.0, 9.205, 2] + CB-N2-CA-NC: + - [180.0, 9.205, 2] + N2-NA-CA-NC: + - [180.0, 9.205, 2] + CA-CA-C-OH: + - [180.0, 9.205, 2] + CA-CA-CA-OH: + - [180.0, 9.205, 2] + H5-O-C-OH: + - [180.0, 9.205, 2] + H5-O-C-OS: + - [180.0, 9.205, 2] + CM-CT-CM-HA: + - [180.0, 9.205, 2] + Br-CA-CA-CA: + - [180.0, 9.205, 2] + CM-H4-C-O: + - [180.0, 9.205, 2] + C-CT-N-H: + - [180.0, 9.205, 2] + C-CT-N-O: + - [180.0, 9.205, 2] + coulomb_energy: + length_unit: nm + energy_unit: kj/mol + vdw_energy: + length_unit: nm + energy_unit: kj/mol + parameter_names: + pattern: [sigma, epsilon] + parameters: + H: [0.1069078, 0.0656888] + HO: [0.0, 0.0] + HS: [0.1069078, 0.0656888] + HC: [0.2649533, 0.0656888] + H1: [0.2471353, 0.0656888] + H2: [0.2293173, 0.0656888] + H3: [0.2114994, 0.0656888] + HP: [0.1959977, 0.0656888] + HA: [0.2599642, 0.06276] + H4: [0.2510553, 0.06276] + H5: [0.2421463, 0.06276] + HZ: [0.2599642, 0.06276] + O: [0.2959922, 0.87864] + O2: [0.2959922, 0.87864] + OH: [0.3066473, 0.8803136] + OS: [0.3000012, 0.71128] + C*: [0.339967, 0.359824] + CA: [0.339967, 0.359824] + CB: [0.339967, 0.359824] + CC: [0.339967, 0.359824] + CD: [0.339967, 0.359824] + CK: [0.339967, 0.359824] + CM: [0.339967, 0.359824] + CN: [0.339967, 0.359824] + CQ: [0.339967, 0.359824] + CR: [0.339967, 0.359824] + CV: [0.339967, 0.359824] + CW: [0.339967, 0.359824] + CY: [0.339967, 0.359824] + CZ: [0.339967, 0.359824] + CT: [0.339967, 0.4577296] + C: [0.339967, 0.359824] + N: [0.3249999, 0.71128] + NA: [0.3249999, 0.71128] + N2: [0.3249999, 0.71128] + N*: [0.3249999, 0.71128] + NC: [0.3249999, 0.71128] + NB: [0.3249999, 0.71128] + NT: [0.3249999, 0.71128] + NY: [0.3249999, 0.71128] + N3: [0.3249999, 0.71128] + S: [0.3563595, 1.046] + SH: [0.3563595, 1.046] + P: [0.3741775, 0.8368] + IM: [0.440104, 0.4184] + Li: [0.2025904, 0.0765672] + IP: [0.3328398, 0.0115897] + Na: [0.3328398, 0.0115897] + K: [0.4736018, 0.0013724] + Rb: [0.5266993, 0.0007113] + Cs: [0.6049202, 0.0003372] + MG: [0.1412253, 3.7434248] + C0: [0.3052397, 1.9237572] + Zn: [0.1959977, 0.0523] + F: [0.3118146, 0.255224] + Cl: [0.3470941, 1.10876] + Br: [0.395559, 1.33888] + I: [0.4187224, 1.6736] + IB: [0.8908987, 0.4184] + LP: [0.0, 0.0] + nb_pair_energy: + length_unit: nm + energy_unit: kj/mol + parameter_names: + pattern: [r_scale, r6_scale, r12_scale] + parameters: + ?: [0.8333333, 0.5, 0.5]