/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp is in gromacs-data 2018.1-1.
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1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 | ; New format introduced in Gromacs 3.1.4.
; Dont use this forcefield with earlier versions.
; This residue database includes new reparameterized sidechain dihedrals
; from Kaminski et al (JPCB, 2001) that override the default atomtype-based
; dihedrals. We use set 2 for SER and THR, set 2 for ASP, and the better
; separate dihedrals for LEU and VAL instead of the combined ones, since we
; can specify them here without using introducing extra atom types.
; (That was the reason they were combined in the paper).
; NB: OPLS chargegroups are not strictly neutral, since we mainly
; use them to optimize the neighborsearching. For accurate simulations
; you should use PME.
[ bondedtypes ]
; Column 1 : default bondtype
; Column 2 : default angletype
; Column 3 : default proper dihedraltype
; Column 4 : default improper dihedraltype
; Column 5 : This controls the generation of dihedrals from the bonding.
; All possible dihedrals are generated automatically. A value of
; 1 here means that all these are retained. A value of
; 0 here requires generated dihedrals be removed if
; * there are any dihedrals on the same central atoms
; specified in the residue topology, or
; * there are other identical generated dihedrals
; sharing the same central atoms, or
; * there are other generated dihedrals sharing the
; same central bond that have fewer hydrogen atoms
; Column 6 : number of neighbors to exclude from non-bonded interactions
; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms
; 0 = do not generate such
; Column 8 : 1 = remove proper dihedrals if found centered on the same
; bond as an improper dihedral
; 0 = do not generate such
; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
1 1 3 1 1 3 1 0
[ ACE ]
[ atoms ]
CH3 opls_135 -0.180 1
HH31 opls_140 0.060 1
HH32 opls_140 0.060 1
HH33 opls_140 0.060 1
C opls_235 0.500 2
O opls_236 -0.500 2
[ bonds ]
CH3 HH31
CH3 HH32
CH3 HH33
CH3 C
C O
[ impropers ]
CH3 +N C O improper_O_C_X_Y
[ ALA ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_135 -0.180 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
HB3 opls_140 0.060 2
C opls_235 0.500 3
O opls_236 -0.500 3
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB HB3
C O
-C N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ AIB ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_225B 0.200 1
CB1 opls_135 -0.180 2
HB11 opls_140 0.060 2
HB12 opls_140 0.060 2
HB13 opls_140 0.060 2
CB2 opls_135 -0.180 3
HB21 opls_140 0.060 3
HB22 opls_140 0.060 3
HB23 opls_140 0.060 3
C opls_235 0.500 4
O opls_236 -0.500 4
[ bonds ]
N H
N CA
CA CB1
CA CB2
CA C
CB1 HB11
CB1 HB12
CB1 HB13
CB2 HB21
CB2 HB22
CB2 HB23
C O
-C N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ ARG ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_308 -0.050 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_307 0.190 4
HD1 opls_140 0.060 4
HD2 opls_140 0.060 4
NE opls_303 -0.700 5
HE opls_304 0.440 5
CZ opls_302 0.640 5
NH1 opls_300 -0.800 6
HH11 opls_301 0.460 6
HH12 opls_301 0.460 6
NH2 opls_300 -0.800 7
HH21 opls_301 0.460 7
HH22 opls_301 0.460 7
C opls_235 0.500 8
O opls_236 -0.500 8
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD NE
NE HE
NE CZ
CZ NH1
CZ NH2
NH1 HH11
NH1 HH12
NH2 HH21
NH2 HH22
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_ARG_chi1_N_C_C_C
CG CB CA C dih_ARG_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CD CZ NE HE improper_Z_N_X_Y
NE NH1 CZ NH2 improper_O_C_X_Y
CZ HH11 NH1 HH12 improper_Z_N_X_Y
CZ HH21 NH2 HH22 improper_Z_N_X_Y
[ ARGN ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_308 -0.050 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_748 0.040 4
HD1 opls_140 0.060 4
HD2 opls_140 0.060 4
NE opls_749 -0.620 5
HE opls_304 0.350 5; guessed charge
CZ opls_752 0.550 6
NH1 opls_750 -0.785 6
HH1 opls_301 0.340 6; guessed charge
NH2 opls_751 -0.785 7
HH21 opls_301 0.360 7; guessed charge
HH22 opls_301 0.360 7; guessed charge
C opls_235 0.500 8
O opls_236 -0.500 8
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD NE
NE HE
NE CZ
CZ NH1
CZ NH2
NH1 HH1
NH2 HH21
NH2 HH22
C O
-C N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CD CZ NE HE improper_Z_N_X_Y
NE NH1 CZ NH2 improper_O_C_X_Y
CZ HH21 NH2 HH22 improper_Z_N_X_Y
[ ASN ]
[ atoms ]
N opls_238 -0.500 0
H opls_241 0.300 0
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_235 0.500 3
OD1 opls_236 -0.500 3
ND2 opls_237 -0.760 4
HD21 opls_240 0.380 4
HD22 opls_240 0.380 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG ND2
ND2 HD21
ND2 HD22
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_ASN_chi1_N_C_C_C
CG CB CA C dih_ASN_chi1_C_C_C_CO
CA CB CG ND2 dih_ASN_chi2_C_C_CO_N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CB ND2 CG OD1 improper_O_C_X_Y
CG HD21 ND2 HD22 improper_Z_N_X_Y
[ ASP ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_274 -0.220 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_271 0.700 3
OD1 opls_272 -0.800 3
OD2 opls_272 -0.800 3
C opls_235 0.500 4
O opls_236 -0.500 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG OD2
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_ASP_chi1_N_C_C_C
CG CB CA C dih_ASP_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CB OD1 CG OD2 improper_O_C_X_Y
[ ASPH ]
[ atoms ]
N opls_238 -0.500 0
H opls_241 0.300 0
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_267 0.520 3
OD1 opls_269 -0.440 3
OD2 opls_268 -0.530 4
HD2 opls_270 0.450 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG OD1
CG OD2
OD2 HD2
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_ASP_chi1_N_C_C_C
CG CB CA C dih_ASP_chi1_C_C_C_CO
CB CG OD2 HD2 dih_sidechain_COOH_C_C_O_H
OD1 CG OD2 HD2 dih_sidechain_COOH_O_C_O_H
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CB OD1 CG OD2 improper_O_C_X_Y
[ CYS2 ] ; aka CYX
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_214 0.0975 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
SG opls_203 -0.2175 2
C opls_235 0.500 3
O opls_236 -0.500 3
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
C O
-C N
[ dihedrals ] ; override some of the typebased dihedrals
N CA CB SG dih_CYS_chi1_N_C_C_S
C CA CB SG dih_CYS_chi1_CO_C_C_S
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ CYSH ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_206 0.060 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
SG opls_200 -0.335 3
HG opls_204 0.155 3
C opls_235 0.500 4
O opls_236 -0.500 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB SG
SG HG
C O
-C N
[ dihedrals ] ; override some of the typebased dihedrals
N CA CB SG dih_CYS_chi1_N_C_C_S
C CA CB SG dih_CYS_chi1_CO_C_C_S
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ GLN ]
[ atoms ]
N opls_238 -0.500 0
H opls_241 0.300 0
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_136 -0.120 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_235 0.500 4
OE1 opls_236 -0.500 4
NE2 opls_237 -0.760 5
HE21 opls_240 0.380 5
HE22 opls_240 0.380 5
C opls_235 0.500 6
O opls_236 -0.500 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD NE2
NE2 HE21
NE2 HE22
C O
-C N
[ dihedrals ] ; override some of the typebased dihedrals
N CA CB CG dih_GLN_chi1_N_C_C_C
CG CB CA C dih_GLN_chi1_C_C_C_CO
CB CG CD NE2 dih_GLN_chi3_C_C_CO_N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CG NE2 CD OE1 improper_O_C_X_Y
CD HE21 NE2 HE22 improper_Z_N_X_Y
; Charged Glutamine
; See. Patriksson et al. Int. J. Mass. Spectrom. 248 pp 124-135 (2006)
[ QLN ]
[ atoms ]
N opls_238 -0.500 0
H opls_241 0.300 0
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_136 0.054 3
HG1 opls_140 0.131 3
HG2 opls_140 0.131 3
CD opls_235 0.544 4
OE1 opls_154 -0.496 4
HE1 opls_155 0.498 4
NE2 opls_237 -0.720 5
HE21 opls_240 0.429 5
HE22 opls_240 0.429 5
C opls_235 0.500 6
O opls_236 -0.500 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
OE1 HE1
CD NE2
NE2 HE21
NE2 HE22
C O
-C N
[ dihedrals ] ; override some of the typebased dihedrals
N CA CB CG dih_GLN_chi1_N_C_C_C
CG CB CA C dih_GLN_chi1_C_C_C_CO
CB CG CD NE2 dih_GLN_chi3_C_C_CO_N
CG CD OE1 HE1 dih_GLN_chi4_C_C_O_H
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CG NE2 CD OE1 improper_O_C_X_Y
CD HE21 NE2 HE22 improper_Z_N_X_Y
HE1 OE1 CD NE2 improper_O_C_X_Y
[ GLU ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_274 -0.220 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_271 0.700 4
OE1 opls_272 -0.800 4
OE2 opls_272 -0.800 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD OE2
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_GLU_chi1_N_C_C_C
CG CB CA C dih_GLU_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CG OE1 CD OE2 improper_O_C_X_Y
[ PGLU ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_274 -0.120 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_235 0.500 4
OE opls_236 -0.500 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE
CD N
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_GLU_chi1_N_C_C_C
CG CB CA C dih_GLU_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
; CG OE1 CD OE2 improper_O_C_X_Y
[ GLUH ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_136 -0.120 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_267 0.520 4
OE1 opls_269 -0.440 4
OE2 opls_268 -0.530 5
HE2 opls_270 0.450 5
C opls_235 0.500 6
O opls_236 -0.500 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD OE2
OE2 HE2
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_GLU_chi1_N_C_C_C
CG CB CA C dih_GLU_chi1_C_C_C_CO
CG CD OE2 HE2 dih_sidechain_COOH_C_C_O_H
OE1 CD OE2 HE2 dih_sidechain_COOH_O_C_O_H
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CG OE1 CD OE2 improper_O_C_X_Y
[ GLY ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_223B 0.080 1
HA1 opls_140 0.060 1
HA2 opls_140 0.060 1
C opls_235 0.500 2
O opls_236 -0.500 2
[ bonds ]
N H
N CA
CA HA1
CA HA2
CA C
C O
-C N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ HISD ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_505 -0.005 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_508 0.015 3
ND1 opls_503 -0.570 4
HD1 opls_504 0.420 4
CD2 opls_507 -0.015 5
HD2 opls_146 0.115 5
CE1 opls_506 0.295 6
HE1 opls_146 0.115 6
NE2 opls_511 -0.490 7
C opls_235 0.500 8
O opls_236 -0.500 8
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_HIS_chi1_N_C_C_C
CG CB CA C dih_HIS_chi1_C_C_C_CO
CA CB CG ND1 dih_HIS_chi2_C_C_C_N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
ND1 CD2 CG CB improper_Z_CA_X_Y
CG CE1 ND1 HD1 improper_Z_N_X_Y
CG NE2 CD2 HD2 improper_Z_CA_X_Y
ND1 NE2 CE1 HE1 improper_Z_CA_X_Y
[ HISE ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_505 -0.005 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_507 -0.015 3
ND1 opls_511 -0.490 3
CD2 opls_508 0.015 4
HD2 opls_146 0.115 4
CE1 opls_506 0.295 5
HE1 opls_146 0.115 5
NE2 opls_503 -0.570 6
HE2 opls_504 0.420 6
C opls_235 0.500 7
O opls_236 -0.500 7
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 CE1
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
NE2 HE2
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_HIS_chi1_N_C_C_C
CG CB CA C dih_HIS_chi1_C_C_C_CO
CA CB CG ND1 dih_HIS_chi2_C_C_C_N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CE1 CD2 NE2 HE2 improper_Z_N_X_Y
CG NE2 CD2 HD2 improper_Z_CA_X_Y
ND1 NE2 CE1 HE1 improper_Z_CA_X_Y
ND1 CD2 CG CB improper_Z_CA_X_Y
[ HISH ] ; also known as HISP (or HIS+)
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_505 -0.005 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_510 0.215 3
ND1 opls_512 -0.540 4
HD1 opls_513 0.460 4
CD2 opls_510 0.215 5
HD2 opls_146 0.115 5
CE1 opls_509 0.385 6
HE1 opls_146 0.115 6
NE2 opls_512 -0.540 7
HE2 opls_513 0.460 7
C opls_235 0.500 8
O opls_236 -0.500 8
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG ND1
CG CD2
ND1 HD1
ND1 CE1
CD2 HD2
CD2 NE2
CE1 HE1
CE1 NE2
NE2 HE2
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_HIP_chi1_N_C_C_C
CG CB CA C dih_HIP_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CG CE1 ND1 HD1 improper_Z_N_X_Y
CE1 CD2 NE2 HE2 improper_Z_N_X_Y
CG NE2 CD2 HD2 improper_Z_CA_X_Y
ND1 NE2 CE1 HE1 improper_Z_CA_X_Y
ND1 CD2 CG CB improper_Z_CA_X_Y
[ HOH ]
; We believe SPC has slightly better properties than TIP3P...
[ atoms ]
OW opls_116 -0.82 0
HW1 opls_117 0.41 0
HW2 opls_117 0.41 0
[ bonds ]
OW HW1
OW HW2
[ HO4 ]
; TIP4P
[ atoms ]
OW opls_113 0.00 0
HW1 opls_114 0.52 0
HW2 opls_114 0.52 0
MW opls_115 -1.04 0
[ bonds ]
OW HW1
OW HW2
[ HO5 ]
; TIP5P
[ atoms ]
OW opls_118 0.00 0
HW1 opls_119 0.248 0
HW2 opls_119 0.248 0
LP1 opls_120 -0.248 0
LP2 opls_120 -0.248 0
[ bonds ]
OW HW1
OW HW2
[ ILE ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_137 -0.060 2
HB opls_140 0.060 2
CG1 opls_136 -0.120 3
HG11 opls_140 0.060 3
HG12 opls_140 0.060 3
CG2 opls_135 -0.180 4
HG21 opls_140 0.060 4
HG22 opls_140 0.060 4
HG23 opls_140 0.060 4
CD opls_135 -0.180 5
HD1 opls_140 0.060 5
HD2 opls_140 0.060 5
HD3 opls_140 0.060 5
C opls_235 0.500 6
O opls_236 -0.500 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB CG1
CB CG2
CG1 HG11
CG1 HG12
CG1 CD
CG2 HG21
CG2 HG22
CG2 HG23
CD HD1
CD HD2
CD HD3
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG1 dih_ILE_chi1_N_C_C_C
N CA CB CG2 dih_ILE_chi1_N_C_C_C
CG1 CB CA C dih_ILE_chi1_C_C_C_CO
CG2 CB CA C dih_ILE_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ LEU ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_137 -0.060 3
HG opls_140 0.060 3
CD1 opls_135 -0.180 4
HD11 opls_140 0.060 4
HD12 opls_140 0.060 4
HD13 opls_140 0.060 4
CD2 opls_135 -0.180 5
HD21 opls_140 0.060 5
HD22 opls_140 0.060 5
HD23 opls_140 0.060 5
C opls_235 0.500 6
O opls_236 -0.500 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG
CG CD1
CG CD2
CD1 HD11
CD1 HD12
CD1 HD13
CD2 HD21
CD2 HD22
CD2 HD23
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_LEU_chi1_N_C_C_C
CG CB CA C dih_LEU_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ LYS ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_136 -0.120 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_136 -0.120 4
HD1 opls_140 0.060 4
HD2 opls_140 0.060 4
CE opls_906 0.060 5
HE1 opls_911 0.060 5
HE2 opls_911 0.060 5
NZ opls_900 -0.900 6
HZ1 opls_909 0.360 6
HZ2 opls_909 0.360 6
C opls_235 0.500 7
O opls_236 -0.500 7
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD CE
CE HE1
CE HE2
CE NZ
NZ HZ1
NZ HZ2
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_LYS_chi1_N_C_C_C
CG CB CA C dih_LYS_chi1_C_C_C_CO
CD CE NZ HZ1 dih_LYS_chi5_C_C_N_H
CD CE NZ HZ2 dih_LYS_chi5_C_C_N_H
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ LYSH ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_136 -0.120 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_136 -0.120 4
HD1 opls_140 0.060 4
HD2 opls_140 0.060 4
CE opls_292 0.190 5
HE1 opls_140 0.060 5
HE2 opls_140 0.060 5
NZ opls_287 -0.300 6
HZ1 opls_290 0.330 6
HZ2 opls_290 0.330 6
HZ3 opls_290 0.330 6
C opls_235 0.500 7
O opls_236 -0.500 7
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD CE
CE HE1
CE HE2
CE NZ
NZ HZ1
NZ HZ2
NZ HZ3
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_LYS_chi1_N_C_C_C
CG CB CA C dih_LYS_chi1_C_C_C_CO
CD CE NZ HZ1 dih_LYS_chi5_C_C_N_H
CD CE NZ HZ2 dih_LYS_chi5_C_C_N_H
CD CE NZ HZ3 dih_LYS_chi5_C_C_N_H
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ MET ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_210 0.048 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
SD opls_202 -0.335 4
CE opls_209 -0.013 5
HE1 opls_140 0.060 5
HE2 opls_140 0.060 5
HE3 opls_140 0.060 5
C opls_235 0.500 6
O opls_236 -0.500 6
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG SD
SD CE
CE HE1
CE HE2
CE HE3
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_MET_chi1_N_C_C_C
CG CB CA C dih_MET_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ NAC ] ; metylamide, a.k.a NMA.
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CH3 opls_242 0.020 2
HH31 opls_140 0.060 2
HH32 opls_140 0.060 2
HH33 opls_140 0.060 2
[ bonds ]
N H
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
-C N
[ impropers ]
-C CH3 N H improper_Z_N_X_Y
[ NH2 ]
[ atoms ]
N opls_237 -0.760 1
H1 opls_240 0.380 1
H2 opls_240 0.380 1
[ bonds ]
-C N
N H1
N H2
[ impropers ]
-C H1 N H2 improper_Z_N_X_Y
[ NHE ]
; same as NH2
[ atoms ]
N opls_237 -0.760 1
H1 opls_240 0.380 1
H2 opls_240 0.380 1
[ bonds ]
-C N
N H1
N H2
[ impropers ]
-C H1 N H2 improper_Z_N_X_Y
[ PHE ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_149 -0.005 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_145 -0.115 2
CD1 opls_145 -0.115 3
HD1 opls_146 0.115 3
CD2 opls_145 -0.115 4
HD2 opls_146 0.115 4
CE1 opls_145 -0.115 5
HE1 opls_146 0.115 5
CE2 opls_145 -0.115 6
HE2 opls_146 0.115 6
CZ opls_145 -0.115 7
HZ opls_146 0.115 7
C opls_235 0.500 8
O opls_236 -0.500 8
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CD2 HD2
CD2 CE2
CE1 HE1
CE1 CZ
CE2 HE2
CE2 CZ
CZ HZ
C O
-C N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CG CE2 CD2 HD2 improper_Z_CA_X_Y
CD2 CZ CE2 HE2 improper_Z_CA_X_Y
CE1 CE2 CZ HZ improper_Z_CA_X_Y
CD1 CZ CE1 HE1 improper_Z_CA_X_Y
CG CE1 CD1 HD1 improper_Z_CA_X_Y
CD1 CD2 CG CB improper_Z_CA_X_Y
[ PRO ]
[ atoms ]
N opls_239 -0.140 1
CA opls_246 0.010 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_136 -0.120 3
HG1 opls_140 0.060 3
HG2 opls_140 0.060 3
CD opls_245 -0.050 4
HD1 opls_140 0.060 4
HD2 opls_140 0.060 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ bonds ]
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD N
C O
-C N
[ impropers ]
-C CA N CD improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ SER ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_157 0.145 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
OG opls_154 -0.683 3
HG opls_155 0.418 3
C opls_235 0.500 4
O opls_236 -0.500 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB OG
OG HG
C O
-C N
[ dihedrals ] ; override some of the typebased dihedrals
N CA CB OG dih_SER_THR_chi1_N_C_C_O
C CA CB OG dih_SER_THR_chi1_CO_C_C_O
CA CB OG HG dih_SER_THR_chi2_C_C_OH_HO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ THR ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_158 0.205 2
HB opls_140 0.060 2
OG1 opls_154 -0.683 2
HG1 opls_155 0.418 2
CG2 opls_135 -0.180 3
HG21 opls_140 0.060 3
HG22 opls_140 0.060 3
HG23 opls_140 0.060 3
C opls_235 0.500 4
O opls_236 -0.500 4
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB OG1
CB CG2
OG1 HG1
CG2 HG21
CG2 HG22
CG2 HG23
C O
-C N
[ dihedrals ] ; override some of the typebased dihedrals
N CA CB OG1 dih_SER_THR_chi1_N_C_C_O
C CA CB OG1 dih_SER_THR_chi1_CO_C_C_O
CA CB OG1 HG1 dih_SER_THR_chi2_C_C_OH_HO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ TRP ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_136 -0.120 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_500 0.075 3
CD1 opls_514 -0.115 4
HD1 opls_146 0.115 4
CD2 opls_501 -0.055 5
NE1 opls_503 -0.570 6
HE1 opls_504 0.420 6
CE2 opls_502 0.130 6
CE3 opls_145 -0.115 7
HE3 opls_146 0.115 7
CZ2 opls_145 -0.115 8
HZ2 opls_146 0.115 8
CZ3 opls_145 -0.115 9
HZ3 opls_146 0.115 9
CH2 opls_145 -0.115 10
HH2 opls_146 0.115 10
C opls_235 0.500 11
O opls_236 -0.500 11
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 NE1
CD2 CE2
CD2 CE3
NE1 HE1
NE1 CE2
CE2 CZ2
CE3 HE3
CE3 CZ3
CZ2 HZ2
CZ2 CH2
CZ3 HZ3
CZ3 CH2
CH2 HH2
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG dih_TRP_chi1_N_C_C_C
CG CB CA C dih_TRP_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CD1 CE2 NE1 HE1 improper_Z_N_X_Y
CE2 CH2 CZ2 HZ2 improper_Z_CA_X_Y
CZ2 CZ3 CH2 HH2 improper_Z_CA_X_Y
CH2 CE3 CZ3 HZ3 improper_Z_CA_X_Y
CZ3 CD2 CE3 HE3 improper_Z_CA_X_Y
CG NE1 CD1 HD1 improper_Z_CA_X_Y
CD1 CD2 CG CB improper_Z_CA_X_Y
[ TYR ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_149 -0.005 2
HB1 opls_140 0.060 2
HB2 opls_140 0.060 2
CG opls_145 -0.115 2
CD1 opls_145 -0.115 4
HD1 opls_146 0.115 4
CD2 opls_145 -0.115 5
HD2 opls_146 0.115 5
CE1 opls_145 -0.115 6
HE1 opls_146 0.115 6
CE2 opls_145 -0.115 7
HE2 opls_146 0.115 7
CZ opls_166 0.150 8
OH opls_167 -0.585 8
HH opls_168 0.435 8
C opls_235 0.500 9
O opls_236 -0.500 9
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 HD1
CD1 CE1
CD2 HD2
CD2 CE2
CE1 HE1
CE1 CZ
CE2 HE2
CE2 CZ
CZ OH
OH HH
C O
-C N
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
CG CE2 CD2 HD2 improper_Z_CA_X_Y
CD2 CZ CE2 HE2 improper_Z_CA_X_Y
CD1 CZ CE1 HE1 improper_Z_CA_X_Y
CG CE1 CD1 HD1 improper_Z_CA_X_Y
CD1 CD2 CG CB improper_Z_CA_X_Y
CE1 CE2 CZ OH improper_Z_CA_X_Y
[ VAL ]
[ atoms ]
N opls_238 -0.500 1
H opls_241 0.300 1
CA opls_224B 0.140 1
HA opls_140 0.060 1
CB opls_137 -0.060 2
HB opls_140 0.060 2
CG1 opls_135 -0.180 3
HG11 opls_140 0.060 3
HG12 opls_140 0.060 3
HG13 opls_140 0.060 3
CG2 opls_135 -0.180 4
HG21 opls_140 0.060 4
HG22 opls_140 0.060 4
HG23 opls_140 0.060 4
C opls_235 0.500 5
O opls_236 -0.500 5
[ bonds ]
N H
N CA
CA HA
CA CB
CA C
CB HB
CB CG1
CB CG2
CG1 HG11
CG1 HG12
CG1 HG13
CG2 HG21
CG2 HG22
CG2 HG23
C O
-C N
[ dihedrals ] ; override some with residue-specific ones
N CA CB CG1 dih_VAL_chi1_N_C_C_C
N CA CB CG2 dih_VAL_chi1_N_C_C_C
CG1 CB CA C dih_VAL_chi1_C_C_C_CO
CG2 CB CA C dih_VAL_chi1_C_C_C_CO
[ impropers ]
-C CA N H improper_Z_N_X_Y
CA +N C O improper_O_C_X_Y
[ F ]
[ atoms ]
F opls_400 -1.000 0
[ CL ]
[ atoms ]
CL opls_401 -1.000 0
[ BR ]
[ atoms ]
BR opls_402 -1.000 0
; Aqvists cation parameters
[ LI ]
[ atoms ]
LI opls_406 1.000 0 ; Jorgensen ion type would be opls_404
[ NA ]
[ atoms ]
NA opls_407 1.000 0 ; Jorgensen ion type would be opls_405
[ K ]
[ atoms ]
K opls_408 1.000 0
[ RB ]
[ atoms ]
RB opls_409 1.000 0
[ CS ]
[ atoms ]
CS opls_410 1.000 0
[ MG ]
[ atoms ]
MG opls_411 2.000 0
[ CA ]
[ atoms ]
CA opls_412 2.000 0
[ SR ]
[ atoms ]
SR opls_413 2.000 0
[ BA ]
[ atoms ]
BA opls_414 2.000 0
; Ethanol - CA is the carbon bound to the OH group
[ EtOH ]
[ atoms ]
CB opls_135 -0.180 1
HB1 opls_140 0.060 1
HB2 opls_140 0.060 1
HB3 opls_140 0.060 1
CA opls_157 0.145 2
HA1 opls_140 0.060 2
HA2 opls_140 0.060 2
OH opls_154 -0.683 2
HO opls_155 0.418 2
[ bonds ]
CB HB1
CB HB2
CB HB3
CB CA
CA HA1
CA HA2
CA OH
OH HO
; New All atom DMSO model, DvdS, 17/06/2006
; Use at your own risk!
[ DMSO ]
[ atoms ]
OD opls_125 -0.459 1
SD opls_124 0.139 1
CD1 opls_139 -0.020 1
HD11 opls_140 0.060 1
HD12 opls_140 0.060 1
HD13 opls_140 0.060 1
CD2 opls_139 -0.020 1
HD21 opls_140 0.060 1
HD22 opls_140 0.060 1
HD23 opls_140 0.060 1
[ bonds ]
OD SD
SD CD1
SD CD2
CD1 HD11
CD1 HD12
CD1 HD13
CD2 HD21
CD2 HD22
CD2 HD23
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