2 ; Encad residue topology file.
3 ; Note that this is only a subset of all molecules described
4 ; in Encad. If you need to use a new one, it might help to
5 ; study the parameter files of Encad.
8 ; Column 1 : default bondtype
9 ; Column 2 : default angletype
10 ; Column 3 : default proper dihedraltype
11 ; Column 4 : default improper dihedraltype
12 ; Column 5 : This controls the generation of dihedrals from the bonding.
13 ; All possible dihedrals are generated automatically. A value of
14 ; 1 here means that all these are retained. A value of
15 ; 0 here requires generated dihedrals be removed if
16 ; * there are any dihedrals on the same central atoms
17 ; specified in the residue topology, or
18 ; * there are other identical generated dihedrals
19 ; sharing the same central atoms, or
20 ; * there are other generated dihedrals sharing the
21 ; same central bond that have fewer hydrogen atoms
22 ; Column 6 : number of neighbors to exclude from non-bonded interactions
23 ; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms
24 ; 0 = do not generate such
25 ; Column 8 : 1 = remove proper dihedrals if found centered on the same
26 ; bond as an improper dihedral
27 ; 0 = do not generate such
28 ; bonds angles dihedrals impropers all_dihedrals nrexcl bHH14 bRemoveDih
50 C HH33 CH3 HH31 improper_X_X_C_X
51 C HH33 CH3 HH32 improper_X_X_C_X
52 CH3 +N C O improper_X_X_A_X
84 -C CA N H improper_X_X_N_X
85 N C CA HA improper_X_X_C_X
86 N C CA CB improper_N_A_C1_C
87 CA HB3 CB HB1 improper_X_X_C_X
88 CA HB3 CB HB2 improper_X_X_C_X
89 CA +N C O improper_X_X_A_X
156 -C CA N H improper_X_X_N_X
157 N C CA HA improper_X_X_C_X
158 N C CA CB improper_N_A_C1_C
159 CA +N C O improper_X_X_A_X
160 CA CG CB HB1 improper_X_X_C_X
161 CA CG CB HB2 improper_X_X_C_X
162 CB CD CG HG1 improper_X_X_C_X
163 CB CD CG HG2 improper_X_X_C_X
164 CG NE CD HD1 improper_X_X_C_X
165 CG NE CD HD2 improper_X_X_C_X
166 CD CZ NE HE improper_X_X_M_X
167 NE NH2 CZ NH1 improper_X_X_A_X
168 CZ HH12 NH1 HH11 improper_X_X_M_X
169 CZ HH22 NH2 HH21 improper_X_X_M_X
233 -C CA N H improper_X_X_N_X
234 N C CA HA improper_X_X_C_X
235 N C CA CB improper_N_A_C1_C
236 CA +N C O improper_X_X_A_X
237 CA CG CB HB1 improper_X_X_C_X
238 CA CG CB HB2 improper_X_X_C_X
239 CB CD CG HG1 improper_X_X_C_X
240 CB CD CG HG2 improper_X_X_C_X
241 CG NE CD HD1 improper_X_X_C_X
242 CG NE CD HD2 improper_X_X_C_X
243 CD CZ NE HE improper_X_X_M_X
244 NE NH1 CZ NH2 improper_X_X_A_X
245 CZ HH21 NH2 HH22 improper_X_X_M_X
287 -C CA N H improper_X_X_N_X
288 N C CA HA improper_X_X_C_X
289 N C CA CB improper_N_A_C1_C
290 CA +N C O improper_X_X_A_X
291 CA CG CB HB1 improper_X_X_C_X
292 CA CG CB HB2 improper_X_X_C_X
293 CB ND2 CG OD1 improper_X_X_A_X
294 CG HD22 ND2 HD21 improper_X_X_N_X
331 -C CA N H improper_X_X_N_X
332 N C CA HA improper_X_X_C_X
333 N C CA CB improper_N_A_C1_C
334 CA +N C O improper_X_X_A_X
335 CA CG CB HB1 improper_X_X_C_X
336 CA CG CB HB2 improper_X_X_C_X
337 CB OD2 CG OD1 improper_X_X_A_X
377 -C CA N H improper_X_X_N_X
378 N C CA HA improper_X_X_C_X
379 N C CA CB improper_N_A_C1_C
380 CA +N C O improper_X_X_A_X
381 CA CG CB HB1 improper_X_X_C_X
382 CA CG CB HB2 improper_X_X_C_X
383 OD2 CB CG OD1 improper_X_X_A_X
416 -C CA N H improper_X_X_N_X
417 N C CA HA improper_X_X_C_X
418 N C CA CB improper_N_A_C1_C
419 CA +N C O improper_X_X_A_X
420 CA SG CB HB1 improper_X_X_C_X
421 CA SG CB HB2 improper_X_X_C_X
456 -C CA N H improper_X_X_N_X
457 N C CA HA improper_X_X_C_X
458 N C CA CB improper_N_A_C1_C
459 CA +N C O improper_X_X_A_X
460 CA SG CB HB1 improper_X_X_C_X
461 CA SG CB HB2 improper_X_X_C_X
464 [ CYH ] ; same as cysh
496 -C CA N H improper_X_X_N_X
497 N C CA HA improper_X_X_C_X
498 N C CA CB improper_N_A_C1_C
499 CA +N C O improper_X_X_A_X
500 CA SG CB HB1 improper_X_X_C_X
501 CA SG CB HB2 improper_X_X_C_X
551 -C CA N H improper_X_X_N_X
552 N C CA HA improper_X_X_C_X
553 N C CA CB improper_N_A_C1_C
554 CA +N C O improper_X_X_A_X
555 CA CG CB HB1 improper_X_X_C_X
556 CA CG CB HB2 improper_X_X_C_X
557 CB CD CG HG1 improper_X_X_C_X
558 CB CD CG HG2 improper_X_X_C_X
559 CG NE2 CD OE1 improper_X_X_A_X
560 CD HE22 NE2 HE21 improper_X_X_N_X
604 -C CA N H improper_X_X_N_X
605 N C CA HA improper_X_X_C_X
606 N C CA CB improper_N_A_C1_C
607 CA CG CB HB1 improper_X_X_C_X
608 CA CG CB HB2 improper_X_X_C_X
609 CA +N C O improper_X_X_A_X
610 CB CD CG HG1 improper_X_X_C_X
611 CB CD CG HG2 improper_X_X_C_X
612 CG OE2 CD OE1 improper_X_X_A_X
659 -C CA N H improper_X_X_N_X
660 N C CA HA improper_X_X_C_X
661 N C CA CB improper_N_A_C1_C
662 CA CG CB HB1 improper_X_X_C_X
663 CA CG CB HB2 improper_X_X_C_X
664 CB CD CG HG1 improper_X_X_C_X
665 CB CD CG HG2 improper_X_X_C_X
666 CG OE2 CD OE1 improper_X_X_A_X
667 CA +N C O improper_X_X_A_X
692 -C CA N H improper_X_X_N_X
693 N C CA HA1 improper_X_X_C_X
694 N C CA HA2 improper_X_X_C_X
695 CA +N C O improper_X_X_A_X
699 [ HISA ] ; A.K.A. HISD/HID
748 -C CA N H improper_X_X_N_X
749 N C CA HA improper_X_X_C_X
750 N C CA CB improper_N_A_C1_C
751 CA CG CB HB1 improper_X_X_C_X
752 CA CG CB HB2 improper_X_X_C_X
753 CB CD2 CG ND1 improper_X_X_A_X
754 CG CE1 ND1 HD1 improper_X_X_N_X
755 ND1 NE2 CE1 HE1 improper_X_X_A_X
756 NE2 CG CD2 HD2 improper_X_X_A_X
757 CA +N C O improper_X_X_A_X
761 [ HID ] ; same as HISA
810 -C CA N H improper_X_X_N_X
811 N C CA HA improper_X_X_C_X
812 N C CA CB improper_N_A_C1_C
813 CA CG CB HB1 improper_X_X_C_X
814 CA CG CB HB2 improper_X_X_C_X
815 CB CD2 CG ND1 improper_X_X_A_X
816 CG CE1 ND1 HD1 improper_X_X_N_X
817 ND1 NE2 CE1 HE1 improper_X_X_A_X
818 NE2 CG CD2 HD2 improper_X_X_A_X
819 CA +N C O improper_X_X_A_X
823 [ HIS1 ] Identical to HISA
872 -C CA N H improper_X_X_N_X
873 N C CA HA improper_X_X_C_X
874 N C CA CB improper_N_A_C1_C
875 CA CG CB HB1 improper_X_X_C_X
876 CA CG CB HB2 improper_X_X_C_X
877 CB CD2 CG ND1 improper_X_X_A_X
878 CG CE1 ND1 HD1 improper_X_X_N_X
879 ND1 NE2 CE1 HE1 improper_X_X_A_X
880 NE2 CG CD2 HD2 improper_X_X_A_X
881 CA +N C O improper_X_X_A_X
884 [ HISB ] ; A.K.A. HISE/HIE
933 -C CA N H improper_X_X_N_X
934 N C CA HA improper_X_X_C_X
935 N C CA CB improper_N_A_C1_C
936 CA CG CB HB1 improper_X_X_C_X
937 CA CG CB HB2 improper_X_X_C_X
938 CB CD2 CG ND1 improper_X_X_A_X
939 ND1 NE2 CE1 HE1 improper_X_X_A_X
940 CE1 CD2 NE2 HE2 improper_X_X_N_X
941 NE2 CG CD2 HD2 improper_X_X_A_X
942 CA +N C O improper_X_X_A_X
945 [ HIE ] ; same as HISB
994 -C CA N H improper_X_X_N_X
995 N C CA HA improper_X_X_C_X
996 N C CA CB improper_N_A_C1_C
997 CA CG CB HB1 improper_X_X_C_X
998 CA CG CB HB2 improper_X_X_C_X
999 CB CD2 CG ND1 improper_X_X_A_X
1000 ND1 NE2 CE1 HE1 improper_X_X_A_X
1001 CE1 CD2 NE2 HE2 improper_X_X_N_X
1002 NE2 CG CD2 HD2 improper_X_X_A_X
1003 CA +N C O improper_X_X_A_X
1007 [ HISH ] ; also known as HISP (or HIS+)
1058 -C CA N H improper_X_X_N_X
1059 N C CA HA improper_X_X_C_X
1060 N C CA CB improper_N_A_C1_C
1061 CA CG CB HB1 improper_X_X_C_X
1062 CA CG CB HB2 improper_X_X_C_X
1063 CB CD2 CG ND1 improper_X_X_A_X
1064 CG CE1 ND1 HD1 improper_X_X_N_X
1065 ND1 NE2 CE1 HE1 improper_X_X_A_X
1066 CE1 CD2 NE2 HE2 improper_X_X_N_X
1067 NE2 CG CD2 HD2 improper_X_X_A_X
1068 CA +N C O improper_X_X_A_X
1071 [ HIP ] ; same as HISH
1122 -C CA N H improper_X_X_N_X
1123 N C CA HA improper_X_X_C_X
1124 N C CA CB improper_N_A_C1_C
1125 CA CG CB HB1 improper_X_X_C_X
1126 CA CG CB HB2 improper_X_X_C_X
1127 CB CD2 CG ND1 improper_X_X_A_X
1128 CG CE1 ND1 HD1 improper_X_X_N_X
1129 ND1 NE2 CE1 HE1 improper_X_X_A_X
1130 CE1 CD2 NE2 HE2 improper_X_X_N_X
1131 NE2 CG CD2 HD2 improper_X_X_A_X
1132 CA +N C O improper_X_X_A_X
1137 ; SPC and encad water have identical charges.
1138 ; Include encadwater.itp instead of spc.itp to use the flexible encad bonds/angles
1139 ; instead of the rigid SPC model.
1199 -C CA N H improper_X_X_N_X
1200 N C CA HA improper_X_X_C_X
1201 N C CA CB improper_N_A_C1_C
1202 CA CG1 CB CG2 improper_C1_C2_C1_C3
1203 CA CG1 CB HB improper_X_X_C_X
1204 CB CD CG1 HG11 improper_X_X_C_X
1205 CB CD CG1 HG12 improper_X_X_C_X
1206 CG1 HD3 CD HD1 improper_X_X_C_X
1207 CG1 HD3 CD HD2 improper_X_X_C_X
1208 CB HG23 CG2 HG21 improper_X_X_C_X
1209 CB HG23 CG2 HG22 improper_X_X_C_X
1210 CA +N C O improper_X_X_A_X
1264 -C CA N H improper_X_X_N_X
1265 N C CA HA improper_X_X_C_X
1266 N C CA CB improper_N_A_C1_C
1267 CA CG CB HB1 improper_X_X_C_X
1268 CA CG CB HB2 improper_X_X_C_X
1269 CB CD2 CG HG improper_X_X_C_X
1270 CB CD2 CG CD1 improper_X_X_C_X
1271 CG HD13 CD1 HD11 improper_X_X_C_X
1272 CG HD13 CD1 HD12 improper_X_X_C_X
1273 CG HD23 CD2 HD21 improper_X_X_C_X
1274 CG HD23 CD2 HD22 improper_X_X_C_X
1275 CA +N C O improper_X_X_A_X
1278 [ LYS ] ; non-protonated - see LYSH for the most common state.
1333 -C CA N H improper_X_X_N_X
1334 N C CA HA improper_X_X_C_X
1335 N C CA CB improper_N_A_C1_C
1336 CA CG CB HB1 improper_X_X_C_X
1337 CA CG CB HB2 improper_X_X_C_X
1338 CB CD CG HG1 improper_X_X_C_X
1339 CB CD CG HG2 improper_X_X_C_X
1340 CG CE CD HD1 improper_X_X_C_X
1341 CG CE CD HD2 improper_X_X_C_X
1342 CD NZ CE HE1 improper_X_X_C_X
1343 CD NZ CE HE2 improper_X_X_C_X
1344 CE HZ2 NZ HZ1 improper_X_X_M_X
1345 CA +N C O improper_X_X_A_X
1406 -C CA N H improper_X_X_N_X
1407 N C CA HA improper_X_X_C_X
1408 N C CA CB improper_N_A_C1_C
1409 CA CG CB HB1 improper_X_X_C_X
1410 CA CG CB HB2 improper_X_X_C_X
1411 CB CD CG HG1 improper_X_X_C_X
1412 CB CD CG HG2 improper_X_X_C_X
1413 CG CE CD HD1 improper_X_X_C_X
1414 CG CE CD HD2 improper_X_X_C_X
1415 CD NZ CE HE1 improper_X_X_C_X
1416 CD NZ CE HE2 improper_X_X_C_X
1417 CE HZ3 NZ HZ1 improper_X_X_M3_X
1418 CE HZ3 NZ HZ2 improper_X_X_M3_X
1419 CA +N C O improper_X_X_A_X
1468 -C CA N H improper_X_X_N_X
1469 N C CA HA improper_X_X_C_X
1470 N C CA CB improper_N_A_C1_C
1471 CA CG CB HB1 improper_X_X_C_X
1472 CA CG CB HB2 improper_X_X_C_X
1473 CB SD CG HG1 improper_X_X_C_X
1474 CB SD CG HG2 improper_X_X_C_X
1475 SD HE3 CE HE1 improper_X_X_C_X
1476 SD HE3 CE HE2 improper_X_X_C_X
1477 CA +N C O improper_X_X_A_X
1480 [ NAC ] ; metylamide, a.k.a NMA.
1499 -C CH3 N H improper_X_X_N_X
1500 N HH33 CH3 HH31 improper_X_X_C_X
1501 N HH33 CH3 HH32 improper_X_X_C_X
1516 -C H2 N H1 improper_X_X_N_X
1532 -C H2 N H1 improper_X_X_N_X
1592 -C CA N H improper_X_X_N_X
1593 N C CA HA improper_X_X_C_X
1594 N C CA CB improper_N_A_C1_C
1595 CA CG CB HB1 improper_X_X_C_X
1596 CA CG CB HB2 improper_X_X_C_X
1597 CB CD2 CG CD1 improper_X_X_A_X
1598 CG CE1 CD1 HD1 improper_X_X_A_X
1599 CD1 CZ CE1 HE1 improper_X_X_A_X
1600 CE1 CE2 CZ HZ improper_X_X_A_X
1601 CE2 CG CD2 HD2 improper_X_X_A_X
1602 CZ CD2 CE2 HE2 improper_X_X_A_X
1603 CA +N C O improper_X_X_A_X
1646 -C CA N H improper_X_X_N_X
1647 N C CA HA improper_X_X_C_X
1648 N C CA CB improper_N_A_C1_C
1649 CA CG CB HB1 improper_X_X_C_X
1650 CA CG CB HB2 improper_X_X_C_X
1651 CB CD CG HG1 improper_X_X_C_X
1652 CB CD CG HG2 improper_X_X_C_X
1653 CG N CD HD1 improper_X_X_C_X
1654 CG N CD HD2 improper_X_X_C_X
1655 -C CD N CA improper_X_X_N_X
1656 CA +N C O improper_X_X_A_X
1692 -C CA N H improper_X_X_N_X
1693 N C CA HA improper_X_X_C_X
1694 N C CA CB improper_N_A_C1_C
1695 CA OG CB HB1 improper_X_X_C_X
1696 CA OG CB HB2 improper_X_X_C_X
1697 CA +N C O improper_X_X_A_X
1739 -C CA N H improper_X_X_N_X
1740 N C CA HA improper_X_X_C_X
1741 N C CA CB improper_N_A_C1_C
1742 CA CG2 CB OG1 improper_X_X_C_X
1743 CA CG2 CB HB improper_X_X_C_X
1744 CB HG23 CG2 HG21 improper_X_X_C_X
1745 CB HG23 CG2 HG22 improper_X_X_C_X
1746 CA +N C O improper_X_X_A_X
1819 -C CA N H improper_X_X_N_X
1820 CA +N C O improper_X_X_A_X
1821 N C CA CB improper_N_A_C1_C
1822 N C CA HA improper_X_X_C_X
1823 CA CG CB HB1 improper_X_X_C_X
1824 CA CG CB HB2 improper_X_X_C_X
1825 CB CD2 CG CD1 improper_X_X_A_X
1826 CG NE1 CD1 HD1 improper_X_X_A_X
1827 CD1 CE2 NE1 HE1 improper_X_X_N_X
1828 NE1 CD2 CE2 CZ2 improper_X_X_A_X
1829 CE2 CH2 CZ2 HZ2 improper_X_X_A_X
1830 CZ2 CZ3 CH2 HH2 improper_X_X_A_X
1831 CH2 CE3 CZ3 HZ3 improper_X_X_A_X
1832 CZ3 CD2 CE3 HE3 improper_X_X_A_X
1833 CG CD2 CE2 CE3 improper_X_X_A_X
1896 -C CA N H improper_X_X_N_X
1897 N C CA HA improper_X_X_C_X
1898 N C CA CB improper_N_A_C1_C
1899 CA CG CB HB1 improper_X_X_C_X
1900 CA CG CB HB2 improper_X_X_C_X
1901 CB CD2 CG CD1 improper_X_X_A_X
1902 CG CE1 CD1 HD1 improper_X_X_A_X
1903 CD1 CZ CE1 HE1 improper_X_X_A_X
1904 CE1 CE2 CZ OH improper_X_X_A_X
1905 CE2 CG CD2 HD2 improper_X_X_A_X
1906 CZ CD2 CE2 HE2 improper_X_X_A_X
1907 CA +N C O improper_X_X_A_X
1955 -C CA N H improper_X_X_N_X
1956 N C CA HA improper_X_X_C_X
1957 N C CA CB improper_N_A_C1_C
1958 CA CG2 CB HB improper_X_X_C_X
1959 CA CG2 CB CG1 improper_X_X_C_X
1960 CB HG13 CG1 HG11 improper_X_X_C_X
1961 CB HG13 CG1 HG12 improper_X_X_C_X
1962 CB HG23 CG2 HG21 improper_X_X_C_X
1963 CB HG23 CG2 HG22 improper_X_X_C_X
1964 CA +N C O improper_X_X_A_X