1; Table 2.5.2.1 2; GROMOS bond-stretching parameters 3; 4; 5; Bond type code 6; Force constant 7; Ideal bond length 8; Examples of usage in terms of non-bonded atom types 9; 10; 11; ICB(H)[N] CB[N] B0[N] 12; 13#define gb_1 0.1000 1.5700e+07 14; H - OA 750 15; 16#define gb_2 0.1000 1.8700e+07 17; H - N (all) 895 18; 19#define gb_3 0.1090 1.2300e+07 20; HC - C 700 21; 22#define gb_4 0.112 3.7000e+07 23; C - O (CO in heme) 2220 24; 25#define gb_5 0.1230 1.6600e+07 26; C - O 1200 27; 28#define gb_6 0.1250 1.3400e+07 29; C - OM 1000 30; 31#define gb_7 0.1320 1.2000e+07 32; CR1 - NR (6-ring) 1000 33; 34#define gb_8 0.1330 8.8700e+06 35; H - S 750 36; 37#define gb_9 0.1330 1.0600e+07 38; C - NT, NL 900 39; 40#define gb_10 0.1330 1.1800e+07 41; C, CR1 - N, NR, CR1, C (peptide, 5-ring) 1000 42; 43#define gb_11 0.1340 1.0500e+07 44; C - N, NZ, NE 900 45; 46#define gb_12 0.1340 1.1700e+07 47; C - NR (no H) (6-ring) 1000 48; 49#define gb_13 0.1360 1.0200e+07 50; C - OA 900 51; 52#define gb_14 0.1380 1.1000e+07 53; C - NR (heme) 1000 54; 55#define gb_15 0.1390 8.6600e+06 56; CH2 - C, CR1 (6-ring) 800 57; 58#define gb_16 0.1390 1.0800e+07 59; C, CR1 - CH2, C, CR1 (6-ring) 1000 60; 61#define gb_17 0.1400 8.5400e+06 62; C, CR1, CH2 - NR (6-ring) 800 63; 64#define gb_18 0.1430 8.1800e+06 65; CHn - OA 800 66; 67#define gb_19 0.1430 9.2100e+06 68; CHn - OM 900 69; 70#define gb_20 0.1435 6.1000e+06 71; CHn - OA (sugar) 600 72; 73#define gb_21 0.1470 8.7100e+06 74; CHn - N, NT, NL, NZ, NE 900 75; 76#define gb_22 0.1480 5.7300e+06 77; CHn - NR (5-ring) 600 78; 79#define gb_23 0.1480 7.6400e+06 80; CHn - NR (6-ring) 800 81; 82#define gb_24 0.1480 8.6000e+06 83; O, OM - P 900 84; 85#define gb_25 0.1500 8.3700e+06 86; O - S 900 87; 88#define gb_26 0.1520 5.4300e+06 89; CHn - CHn (sugar) 600 90; 91#define gb_27 0.1530 7.1500e+06 92; C, CHn - C, CHn 800 93; 94#define gb_28 0.1610 4.8400e+06 95; OA - P 600 96; 97#define gb_29 0.1630 4.7200e+06 98; OA - SI 600 99; 100#define gb_30 0.1780 2.7200e+06 101; FE - C (Heme) 102; 103#define gb_31 0.1780 5.9400e+06 104; CH3 - S 900 105; 106#define gb_32 0.1830 5.6200e+06 107; CH2 - S 900 108; 109#define gb_33 0.1870 3.5900e+06 110; CH1 - SI 600 111; 112#define gb_34 0.198 0.6400e+06 113; NR - FE 120 114; 115#define gb_35 0.200 0.6280e+06 116; NR (heme) - FE 120 117; 118#define gb_36 0.2040 5.0300e+06 119; S - S 1000 120; 121#define gb_37 0.221 0.5400e+06 122; NR - FE 126 123; 124#define gb_38 0.1000 2.3200e+07 125; HWat - OWat 1110 126; 127#define gb_39 0.1100 1.2100e+07 128; HChl - CChl 700 129; 130#define gb_40 0.1758 8.1200e+06 131; CChl - CLChl 1200 132; 133#define gb_41 0.1530 8.0400e+06 134; ODmso - SDmso 900 135; 136#define gb_42 0.193799 4.9500e+06 137; SDmso - CDmso 890 138; 139#define gb_43 0.1760 8.1000e+06 140; CCl4 - CLCl4 1200 141; 142#define gb_44 0.1265 1.3100e+07 143; CUrea - OUrea 1000 144; 145#define gb_45 0.135 1.0300e+07 146; CUrea - NUrea 900 147; 148#define gb_46 0.163299 8.7100e+06 149; HWat - HWat 1110 150; 151#define gb_47 0.233839 2.6800e+06 152; HChl - CLChl 700 153; 154#define gb_48 0.290283 2.9800e+06 155; CLChl - CLChl 1200 156; 157#define gb_49 0.279388 2.3900e+06 158; ODmso - CDmso 890 159; 160#define gb_50 0.291189 2.1900e+06 161; CDmso - CDmso 890 162; 163#define gb_51 0.2077 3.9700e+06 164; HMet - CMet 820 165; 166#define gb_52 0.287407 3.0400e+06 167; CLCl4 - CLCl4 1200 168; 169;--- 170; Table 2.5.3.1. 171; GROMOS bond-angle bending parameters 172; 173; 174; Bond-angle type code 175; Force constant 176; Ideal bond angle 177; Example of usage in terms of non-bonded atom types 178; 179; 180; ICT(H)[N] CT[N] (T0[N]) 181; 182#define ga_1 90.00 380.00 183; NR(heme) - FE - C 90 184; 185#define ga_2 90.00 420.00 186; NR(heme) - FE - NR(heme) 100 187; 188#define ga_3 96.00 405.00 189; H - S - CH2 95 190; 191#define ga_4 100.00 475.00 192; CH2 - S - CH3 110 193; 194#define ga_5 103.00 420.00 195; OA - P - OA 95 196; 197#define ga_6 104.00 490.00 198; CH2 - S - S 110 199; 200#define ga_7 108.00 465.00 201; NR, C, CR1(5-ring) 100 202; 203#define ga_8 109.50 285.00 204; CHn - CHn - CHn, NR(6-ring) (sugar) 60 205; 206#define ga_9 109.50 320.00 207; CHn, OA - CHn - OA, NR(ring) (sugar) 68 208; 209#define ga_10 109.50 380.00 210; H - NL, NT - H, CHn - OA - CHn(sugar) 80 211; 212#define ga_11 109.50 425.00 213; H - NL - C, CHn H - NT - CHn 90 214; 215#define ga_12 109.50 450.00 216; X - OA, SI - X 95 217; 218#define ga_13 109.50 520.00 219; CHn,C - CHn - C, CHn, OA, OM, N, NE 110 220; 221#define ga_14 109.60 450.00 222; OM - P - OA 95 223; 224#define ga_15 111.00 530.00 225; CHn - CHn - C, CHn, OA, NR, NT, NL 110 226; 227#define ga_16 113.00 545.00 228; CHn - CH2 - S 110 229; 230#define ga_17 115.00 50.00 231; NR(heme) - FE - NR 10 232; 233#define ga_18 115.00 460.00 234; H - N - CHn 90 235; 236#define ga_19 115.00 610.00 237; CHn, C - C - OA, N, NT, NL 120 238; 239#define ga_20 116.00 465.00 240; H - NE - CH2 90 241; 242#define ga_21 116.00 620.00 243; CH2 - N - CH1 120 244; 245#define ga_22 117.00 635.00 246; CH3 - N - C, CHn - C - OM 120 247; 248#define ga_23 120.00 390.00 249; H - NT, NZ, NE - C 70 250; 251#define ga_24 120.00 445.00 252; H - NT, NZ - H 80 253; 254#define ga_25 120.00 505.00 255; H - N - CH3, H, HC - 6-ring, H - NT - CHn 90 256; 257#define ga_26 120.00 530.00 258; P, SI - OA - CHn, P 95 259; 260#define ga_27 120.00 560.00 261; N, C, CR1 (6-ring, no H) 100 262; 263#define ga_28 120.00 670.00 264; NZ - C - NZ, NE 120 265; 266#define ga_29 120.00 780.00 267; OM - P - OM 140 268; 269#define ga_30 121.00 685.00 270; O - C - CHn, C CH3 - N - CHn 120 271; 272#define ga_31 122.00 700.00 273; CH1, CH2 - N - C 120 274; 275#define ga_32 123.00 415.00 276; H - N - C 70 277; 278#define ga_33 124.00 730.00 279; O - C - OA, N, NT, NL C - NE - CH2 120 280; 281#define ga_34 125.00 375.00 282; FE - NR - CR1 (5-ring) 60 283; 284#define ga_35 125.00 750.00 285; - 120 286; 287#define ga_36 126.00 575.00 288; H, HC - 5-ring 90 289; 290#define ga_37 126.00 640.00 291; X(noH) - 5-ring 100 292; 293#define ga_38 126.00 770.00 294; OM - C - OM 120 295; 296#define ga_39 132.00 760.00 297; 5, 6 ring connnection 100 298; 299#define ga_40 155.00 2215.00 300; SI - OA - SI 95 301; 302#define ga_41 180.00 91350.00 303; Fe - C - O (heme) 57 304; 305#define ga_42 109.50 434.00 306; HWat - OWat - HWat 92 307; 308#define ga_43 107.57 484.00 309; HChl - CChl - CLChl 105 310; 311#define ga_44 111.30 632.00 312; CLChl - CChl - CLChl 131 313; 314#define ga_45 97.40 469.00 315; CDmso - SDmso - CDmso 110 316; 317#define ga_46 106.75 503.00 318; CDmso - SDmso - ODmso 110 319; 320#define ga_47 108.53 443.00 321; HMet - OMet - CMet 95 322; 323#define ga_48 109.50 618.00 324; CLCl4 - CCl4 - CLCl4 131 325; 326#define ga_49 107.60 507.00 327; FTFE - CTFE - FTFE 100 328; 329#define ga_50 109.50 448.00 330; HTFE - OTFE - CHTFE 85 331; 332#define ga_51 110.3 524.00 333; OTFE - CHTFE - CTFE 97 334; 335#define ga_52 111.4 532.00 336; CHTFE - CTFE - FTFE 95 337; 338#define ga_53 117.2 636.00 339; NUrea - CUrea - NUrea 120 340; 341#define ga_54 121.4 690.00 342; OUrea - CUrea - NUrea 120 343; 344; Table 2.5.4.1 345; GROMOS improper (harmonic) dihedral angle parameters 346; 347; 348; Improper dihedral-angle type code 349; Force constant 350; Ideal improper dihedral angle 351; Example of usage 352; 353; 354; ICQ(H)[N] CQ[N] (Q0[N]) 355; 356#define gi_1 0.0 167.42309 357; planar groups 40 358; 359#define gi_2 35.26439 334.84617 360; tetrahedral centres 80 361; 362#define gi_3 0.0 669.69235 363; heme iron 160 364; 365; Table 2.5.5.1 (Note: changes with respect to the 43A1 table) 366; GROMOS (trigonometric) dihedral torsional angle parameters 367; 368; 369; Dihedral-angle type code 370; Force constant 371; Phase shift 372; Multiplicity 373; Example of usage in terms of non-bonded atom types 374; 375; 376; ICP(H)[N] CP[N] PD[N] NP[N] 377; 378#define gd_1 180.000 2.67 1 379; CHn-CHn-CHn-OA (sugar) 0.6 380; 381#define gd_2 180.000 3.41 1 382; OA-CHn-OA-CHn,H (beta sugar) 0.8 383; 384#define gd_3 180.000 4.97 1 385; OA-CHn-CHn-OA (sugar) 1.2 386; 387#define gd_4 180.000 5.86 1 388; N-CHn-CHn-OA (lipid) 1.4 389; 390#define gd_5 180.000 9.35 1 391; OA-CHn-CHn-OA (sugar) 2.2 392; 393#define gd_6 180.000 9.45 1 394; OA-CHn-OA-CHn,H (alpha sugar) 2.3 395; 396#define gd_7 0.000 2.79 1 397; P-O5*-C5*-C4* (dna) 0.7 398; 399#define gd_8 0.000 5.35 1 400; O5*-C5*-C4*-O4* (dna) 1.3 401; 402#define gd_9 180.000 1.53 2 403; C1-C2-CAB-CBB (heme) 0.4 404; 405#define gd_10 180.000 5.86 2 406; -C-C- 1.4 407; 408#define gd_11 180.000 7.11 2 409; -C-OA,OE- (at ring) 1.7 410; 411#define gd_12 180.000 16.7 2 412; -C-OA,OE- (carboxyl) 4.0 413; 414#define gd_13 180.000 24.0 2 415; CHn-OE-C-CHn (ester lipid) 5.7 416; 417#define gd_14 180.000 33.5 2 418; -C-N,NT,NE,NZ,NR- 8.0 419; 420#define gd_15 180.000 41.8 2 421; -C-CR1- (6-ring) 10.0 422; 423#define gd_16 0.000 0.0 2 424; -CH1(sugar)-NR(base) 0.0 425; 426#define gd_17 0.000 0.418 2 427; O-CH1-CHn-no O 0.1 428; 429#define gd_18 0.000 2.09 2 430; O-CH1-CHn-O 0.5 431; 432#define gd_19 0.000 3.14 2 433; -OA-P- 0.75 434; 435#define gd_20 0.000 5.09 2 436; O-P-O- (dna, lipids) 1.2 437; 438#define gd_21 0.000 16.7 2 439; -S-S- 4.0 440; 441#define gd_22 0.000 1.05 3 442; -OA-P- 0.25 443; 444#define gd_23 0.000 1.26 3 445; -CHn-OA(no sugar)- 0.3 446; 447#define gd_24 0.000 1.30 3 448; HTFE-OTFE-CHTFE-CTFE 0.3 449; 450#define gd_25 0.000 2.53 3 451; O5*-C5*-C4*-O4* (dna) 0.6 452; 453#define gd_26 0.000 2.93 3 454; -CH2-S- 0.7 455; 456#define gd_27 0.000 3.19 3 457; O-P-O- (dna, lipids) 0.8 458; 459#define gd_28 0.000 3.65 3 460; OA-CHn-OA-CHn,H (alpha sugar) 0.9 461; 462#define gd_29 0.000 3.77 3 463; -C,CHn,SI- 0.9 464; 465#define gd_30 0.000 3.90 3 466; CHn-CHn-OA-H (sugar) 0.9 467; 468#define gd_31 0.000 4.18 3 469; HC-C-S- 1.0 470; 471#define gd_32 0.000 4.69 3 472; AO-CHn-OA-CHn,H (beta sugar) 473; 474#define gd_33 0.000 5.44 3 475; HC-C-C- 1.3 476; 477#define gd_34 0.000 5.92 3 478; -CHn,SI-CHn- 1.4 479; 480#define gd_35 0.000 7.69 3 481; OA-CHn-CHn-OA (sugar) 1.8 482; 483#define gd_36 0.000 8.62 3 484; N-CHn-CHn-OA (lipid) 2.1 485; 486#define gd_37 0.000 9.50 3 487; OA-CHn-CHn-OA (sugar) 2.3 488; 489#define gd_38 0.000 0.0 4 490; -NR-FE- 0.0 491; 492#define gd_39 180.000 1.0 6 493; -CHn-N,NE- 0.24 494; 495#define gd_40 0.000 1.0 6 496; -CHn-C,NR(ring), CR1- 0.24 497; 498#define gd_41 0.000 3.77 6 499; -CHn-NT- 0.9 500; 501; get the constraint distances for dummy atom constructions 502 503#include "ff_dum.itp" 504 505[ constrainttypes ] 506; now the constraints for the rigid NH3 groups 507 MNH3 C 2 DC_MNC1 508 MNH3 CH1 2 DC_MNC2 509 MNH3 CH2 2 DC_MNC2 510 MNH3 MNH3 2 DC_MNMN 511; and the angle-constraints for OH and SH groups in proteins: 512 CH2 H 2 DC_CO 513 CH1 H 2 DC_CO 514 C H 2 DC_CO 515 P H 2 DC_PO 516 517; bond-, angle- and dihedraltypes for specbonds: 518[ bondtypes ] 519S S 2 gb_36 520NR FE 2 gb_34 521 522[ angletypes ] 523CH1 CH2 S 2 ga_16 524CH2 S S 2 ga_6 525CR1 NR FE 2 ga_34 526NR FE NR 2 ga_17 527 528[ dihedraltypes ] 529S S 1 gd_21 530NR FE 1 gd_38 531CH2 S 1 gd_26 532