/usr/share/gromacs/top/charmm27.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 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 | [ 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
; bondtype angletype dihedraltype impropertype all_dih nrexcl HH14 bRemoveDih
1 5 9 2 1 3 1 0
[ ALA ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT3 -0.27 4
HB1 HA 0.09 5
HB2 HA 0.09 6
HB3 HA 0.09 7
C C 0.51 8
O O -0.51 9
[ bonds ]
CB CA
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CB HB3
O C
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ ARG ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CT2 -0.18 7
HG1 HA 0.09 8
HG2 HA 0.09 9
CD CT2 0.20 10
HD1 HA 0.09 11
HD2 HA 0.09 12
NE NC2 -0.70 13
HE HC 0.44 14
CZ C 0.64 15
NH1 NC2 -0.80 16
HH11 HC 0.46 17
HH12 HC 0.46 18
NH2 NC2 -0.80 19
HH21 HC 0.46 20
HH22 HC 0.46 21
C C 0.51 22
O O -0.51 23
[ bonds ]
CB CA
CG CB
CD CG
NE CD
CZ NE
NH2 CZ
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CG HG1
CG HG2
CD HD1
CD HD2
NE HE
NH1 HH11
NH1 HH12
NH2 HH21
NH2 HH22
O C
CZ NH1
[ impropers ]
N -C CA HN
C CA +N O
CZ NH1 NH2 NE
[ cmap ]
-C N CA C +N
[ ASN ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CC 0.55 7
OD1 O -0.55 8
ND2 NH2 -0.62 9
HD21 H 0.32 10
HD22 H 0.30 11
C C 0.51 12
O O -0.51 13
[ bonds ]
CB CA
CG CB
ND2 CG
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
ND2 HD21
ND2 HD22
C O
CG OD1
[ impropers ]
N -C CA HN
C CA +N O
CG ND2 CB OD1
CG CB ND2 OD1
ND2 CG HD21 HD22
ND2 CG HD22 HD21
[ cmap ]
-C N CA C +N
[ ASP ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.28 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CC 0.62 7
OD1 OC -0.76 8
OD2 OC -0.76 9
C C 0.51 10
O O -0.51 11
[ bonds ]
CB CA
CG CB
OD2 CG
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
O C
CG OD1
[ impropers ]
N -C CA HN
C CA +N O
CG CB OD2 OD1
[ cmap ]
-C N CA C +N
[ ASPP ] ; protonated ASP
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.21 4 ;
HB1 HA 0.09 5 ; HB1 OD1
HB2 HA 0.09 6 ; | //
CG CD 0.75 7 ; -CB--CG
OD1 OB -0.55 8 ; | \
OD2 OH1 -0.61 9 ; HB2 OD2-HD2
HD2 H 0.44 10;
C C 0.51 11
O O -0.51 12
[ bonds ]
CB CA
CG CB
OD2 CG
OD2 HD2
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
O C
CG OD1
[ impropers ]
N -C CA HN
C CA +N O
CG CB OD2 OD1
[ cmap ]
-C N CA C +N
[ CYS ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.11 4
HB1 HA 0.09 5
HB2 HA 0.09 6
SG S -0.23 7
HG1 HS 0.16 8
C C 0.51 9
O O -0.51 10
[ bonds ]
CB CA
SG CB
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
SG HG1
O C
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ CYS2 ] ; disulfide cystine
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.10 4
HB1 HA 0.09 5
HB2 HA 0.09 6
SG SM -0.08 7
C C 0.51 8
O O -0.51 9
[ bonds ]
CB CA
SG CB
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
O C
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ GLN ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CT2 -0.18 7
HG1 HA 0.09 8
HG2 HA 0.09 9
CD CC 0.55 10
OE1 O -0.55 11
NE2 NH2 -0.62 12
HE21 H 0.32 13
HE22 H 0.30 14
C C 0.51 15
O O -0.51 16
[ bonds ]
CB CA
CG CB
CD CG
NE2 CD
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CG HG1
CG HG2
NE2 HE21
NE2 HE22
O C
CD OE1
[ impropers ]
N -C CA HN
C CA +N O
CD NE2 CG OE1
CD CG NE2 OE1
NE2 CD HE21 HE22
NE2 CD HE22 HE21
[ cmap ]
-C N CA C +N
[ GLU ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CT2 -0.28 7
HG1 HA 0.09 8
HG2 HA 0.09 9
CD CC 0.62 10
OE1 OC -0.76 11
OE2 OC -0.76 12
C C 0.51 13
O O -0.51 14
[ bonds ]
CB CA
CG CB
CD CG
OE2 CD
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CG HG1
CG HG2
O C
CD OE1
[ impropers ]
N -C CA HN
C CA +N O
CD CG OE2 OE1
[ cmap ]
-C N CA C +N
[ GLUP ] ; protonated GLU
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CT2 -0.21 7 ;
HG1 HA 0.09 8 ; HG1 OE1
HG2 HA 0.09 9 ; | //
CD CD 0.75 10; -CG--CD
OE1 OB -0.55 11; | \
OE2 OH1 -0.61 12; HG2 OE2-HE2
HE2 H 0.44 13;
C C 0.51 14
O O -0.51 15
[ bonds ]
CB CA
CG CB
CD CG
OE2 CD
OE2 HE2
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CG HG1
CG HG2
O C
CD OE1
[ impropers ]
N -C CA HN
C CA +N O
CD CG OE2 OE1
[ cmap ]
-C N CA C +N
[ GLY ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT2 -0.02 2
HA1 HB 0.09 3
HA2 HB 0.09 4
C C 0.51 5
O O -0.51 6
[ bonds ]
N HN
N CA
C CA
C +N
CA HA1
CA HA2
O C
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ HSD ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.09 4
HB1 HA 0.09 5
HB2 HA 0.09 6
ND1 NR1 -0.36 7
HD1 H 0.32 8
CG CPH1 -0.05 9
CE1 CPH2 0.25 10
HE1 HR1 0.13 11
NE2 NR2 -0.70 12
CD2 CPH1 0.22 13
HD2 HR3 0.10 14
C C 0.51 15
O O -0.51 16
[ bonds ]
CB CA
CG CB
ND1 CG
CE1 ND1
NE2 CD2
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
ND1 HD1
CD2 HD2
CE1 HE1
O C
CG CD2
CE1 NE2
[ impropers ]
ND1 CG CE1 HD1
CD2 CG NE2 HD2
CE1 ND1 NE2 HE1
ND1 CE1 CG HD1
CD2 NE2 CG HD2
CE1 NE2 ND1 HE1
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ HSE ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.08 4
HB1 HA 0.09 5
HB2 HA 0.09 6
ND1 NR2 -0.70 7
CG CPH1 0.22 8
CE1 CPH2 0.25 9
HE1 HR1 0.13 10
NE2 NR1 -0.36 11
HE2 H 0.32 12
CD2 CPH1 -0.05 13
HD2 HR3 0.09 14
C C 0.51 15
O O -0.51 16
[ bonds ]
CB CA
CG CB
ND1 CG
NE2 CD2
N HN
N CA
C CA
C +N
NE2 CE1
CA HA
CB HB1
CB HB2
NE2 HE2
CD2 HD2
CE1 HE1
O C
CD2 CG
CE1 ND1
[ impropers ]
NE2 CD2 CE1 HE2
CD2 CG NE2 HD2
CE1 ND1 NE2 HE1
NE2 CE1 CD2 HE2
CD2 NE2 CG HD2
CE1 NE2 ND1 HE1
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ HSP ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.05 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CD2 CPH1 0.19 7
HD2 HR1 0.13 8
CG CPH1 0.19 9
NE2 NR3 -0.51 10
HE2 H 0.44 11
ND1 NR3 -0.51 12
HD1 H 0.44 13
CE1 CPH2 0.32 14
HE1 HR2 0.18 15
C C 0.51 16
O O -0.51 17
[ bonds ]
CB CA
CG CB
ND1 CG
CE1 ND1
NE2 CD2
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
ND1 HD1
NE2 HE2
CD2 HD2
CE1 HE1
O C
CD2 CG
NE2 CE1
[ impropers ]
ND1 CG CE1 HD1
ND1 CE1 CG HD1
NE2 CD2 CE1 HE2
NE2 CE1 CD2 HE2
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ ILE ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT1 -0.09 4
HB HA 0.09 5
CG2 CT3 -0.27 6
HG21 HA 0.09 7
HG22 HA 0.09 8
HG23 HA 0.09 9
CG1 CT2 -0.18 10
HG11 HA 0.09 11
HG12 HA 0.09 12
CD CT3 -0.27 13
HD1 HA 0.09 14
HD2 HA 0.09 15
HD3 HA 0.09 16
C C 0.51 17
O O -0.51 18
[ bonds ]
CB CA
CG1 CB
CG2 CB
CD CG1
N HN
N CA
C CA
C +N
CA HA
CB HB
CG1 HG11
CG1 HG12
CG2 HG21
CG2 HG22
CG2 HG23
CD HD1
CD HD2
CD HD3
O C
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ LEU ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CT1 -0.09 7
HG HA 0.09 8
CD1 CT3 -0.27 9
HD11 HA 0.09 10
HD12 HA 0.09 11
HD13 HA 0.09 12
CD2 CT3 -0.27 13
HD21 HA 0.09 14
HD22 HA 0.09 15
HD23 HA 0.09 16
C C 0.51 17
O O -0.51 18
[ bonds ]
CB CA
CG CB
CD1 CG
CD2 CG
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CG HG
CD1 HD11
CD1 HD12
CD1 HD13
CD2 HD21
CD2 HD22
CD2 HD23
O C
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ LYS ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CT2 -0.18 7
HG1 HA 0.09 8
HG2 HA 0.09 9
CD CT2 -0.18 10
HD1 HA 0.09 11
HD2 HA 0.09 12
CE CT2 0.21 13
HE1 HA 0.05 14
HE2 HA 0.05 15
NZ NH3 -0.30 16
HZ1 HC 0.33 17
HZ2 HC 0.33 18
HZ3 HC 0.33 19
C C 0.51 20
O O -0.51 21
[ bonds ]
CB CA
CG CB
CD CG
CE CD
NZ CE
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CG HG1
CG HG2
CD HD1
CD HD2
CE HE1
CE HE2
O C
NZ HZ1
NZ HZ2
NZ HZ3
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ LSN ] ; neutral lysine residue
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CT2 -0.18 7
HG1 HA 0.09 8
HG2 HA 0.09 9
CD CT2 -0.18 10
HD1 HA 0.09 11
HD2 HA 0.09 12
CE CT2 0.13 13
HE1 HA 0.075 14
HE2 HA 0.075 15
NZ NH2 -0.96 16
HZ1 HC 0.34 17
HZ2 HC 0.34 18
C C 0.51 19
O O -0.51 20
[ bonds ]
CB CA
CG CB
CD CG
CE CD
NZ CE
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CG HG1
CG HG2
CD HD1
CD HD2
CE HE1
CE HE2
O C
NZ HZ1
NZ HZ2
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ MET ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CT2 -0.14 7
HG1 HA 0.09 8
HG2 HA 0.09 9
SD S -0.09 10
CE CT3 -0.22 11
HE1 HA 0.09 12
HE2 HA 0.09 13
HE3 HA 0.09 14
C C 0.51 15
O O -0.51 16
[ bonds ]
CB CA
CG CB
SD CG
CE SD
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CG HG1
CG HG2
CE HE1
CE HE2
CE HE3
O C
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ PHE ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CA 0.00 7
CD1 CA -0.115 8
HD1 HP 0.115 9
CE1 CA -0.115 10
HE1 HP 0.115 11
CZ CA -0.115 12
HZ HP 0.115 13
CD2 CA -0.115 14
HD2 HP 0.115 15
CE2 CA -0.115 16
HE2 HP 0.115 17
C C 0.51 18
O O -0.51 19
[ bonds ]
CB CA
CG CB
CD2 CG
CE1 CD1
CZ CE2
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CD1 HD1
CD2 HD2
CE1 HE1
O C
CD1 CG
CZ CE1
CE2 CD2
CE2 HE2
CZ HZ
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ PRO ]
[ atoms ]
N N -0.29 0
CD CP3 0.00 1
HD1 HA 0.09 2
HD2 HA 0.09 3
CA CP1 0.02 4
HA HB 0.09 5
CB CP2 -0.18 6
HB1 HA 0.09 7
HB2 HA 0.09 8
CG CP2 -0.18 9
HG1 HA 0.09 10
HG2 HA 0.09 11
C C 0.51 12
O O -0.51 13
[ bonds ]
C CA
C +N
N CA
CA CB
CB CG
CG CD
N CD
HA CA
HG1 CG
HG2 CG
HD1 CD
HD2 CD
HB1 CB
HB2 CB
O C
[ impropers ]
N -C CA CD
C CA +N O
[ cmap ]
-C N CA C +N
[ SER ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 0.05 4
HB1 HA 0.09 5
HB2 HA 0.09 6
OG OH1 -0.66 7
HG1 H 0.43 8
C C 0.51 9
O O -0.51 10
[ bonds ]
CB CA
OG CB
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
OG HG1
O C
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ THR ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT1 0.14 4
HB HA 0.09 5
OG1 OH1 -0.66 6
HG1 H 0.43 7
CG2 CT3 -0.27 8
HG21 HA 0.09 9
HG22 HA 0.09 10
HG23 HA 0.09 11
C C 0.51 12
O O -0.51 13
[ bonds ]
CB CA
OG1 CB
CG2 CB
N HN
N CA
C CA
C +N
CA HA
CB HB
OG1 HG1
CG2 HG21
CG2 HG22
CG2 HG23
O C
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ TRP ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CY -0.03 7
CD1 CA 0.035 8
HD1 HP 0.115 9
NE1 NY -0.61 10
HE1 H 0.38 11
CE2 CPT 0.13 12
CD2 CPT -0.02 13
CE3 CA -0.115 14
HE3 HP 0.115 15
CZ3 CA -0.115 16
HZ3 HP 0.115 17
CZ2 CA -0.115 18
HZ2 HP 0.115 19
CH2 CA -0.115 20
HH2 HP 0.115 21
C C 0.51 22
O O -0.51 23
[ bonds ]
CB CA
CG CB
CD2 CG
NE1 CD1
CZ2 CE2
N HN
N CA
C CA
C +N
CZ3 CH2
CD2 CE3
NE1 CE2
CA HA
CB HB1
CB HB2
CD1 HD1
NE1 HE1
CE3 HE3
CZ2 HZ2
CZ3 HZ3
CH2 HH2
O C
CD1 CG
CE2 CD2
CZ3 CE3
CH2 CZ2
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ TYR ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT2 -0.18 4
HB1 HA 0.09 5
HB2 HA 0.09 6
CG CA 0.00 7
CD1 CA -0.115 8
HD1 HP 0.115 9
CE1 CA -0.115 10
HE1 HP 0.115 11
CZ CA 0.11 12
OH OH1 -0.54 13
HH H 0.43 14
CD2 CA -0.115 15
HD2 HP 0.115 16
CE2 CA -0.115 17
HE2 HP 0.115 18
C C 0.51 19
O O -0.51 20
[ bonds ]
CB CA
CG CB
CD2 CG
CE1 CD1
CZ CE2
OH CZ
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CD1 HD1
CD2 HD2
CE1 HE1
CE2 HE2
OH HH
O C
CD1 CG
CE1 CZ
CE2 CD2
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ VAL ]
[ atoms ]
N NH1 -0.47 0
HN H 0.31 1
CA CT1 0.07 2
HA HB 0.09 3
CB CT1 -0.09 4
HB HA 0.09 5
CG1 CT3 -0.27 6
HG11 HA 0.09 7
HG12 HA 0.09 8
HG13 HA 0.09 9
CG2 CT3 -0.27 10
HG21 HA 0.09 11
HG22 HA 0.09 12
HG23 HA 0.09 13
C C 0.51 14
O O -0.51 15
[ bonds ]
CB CA
CG1 CB
CG2 CB
N HN
N CA
C CA
C +N
CA HA
CB HB
CG1 HG11
CG1 HG12
CG1 HG13
CG2 HG21
CG2 HG22
CG2 HG23
O C
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N
[ ALAD ] ; Alanine dipeptide
[ atoms ]
CL CT3 -0.27 0
HL1 HA 0.09 1
HL2 HA 0.09 2
HL3 HA 0.09 3
CLP C 0.51 4
OL O -0.51 5
NL NH1 -0.47 6
HL H 0.31 7
CA CT1 0.07 8
HA HB 0.09 9
CB CT3 -0.27 10
HB1 HA 0.09 11
HB2 HA 0.09 12
HB3 HA 0.09 13
CRP C 0.51 14
OR O -0.51 15
NR NH1 -0.47 16
HR H 0.31 17
CR CT3 -0.11 18
HR1 HA 0.09 19
HR2 HA 0.09 20
HR3 HA 0.09 21
[ bonds ]
CL CLP
CLP NL
NL CA
CA CRP
CRP NR
NR CR
CLP OL
CRP OR
NL HL
NR HR
CA HA
CA CB
CL HL1
CL HL2
CL HL3
CB HB1
CB HB2
CB HB3
CR HR1
CR HR2
CR HR3
[ impropers ]
CLP CL NL OL
NL CLP CA HL
CRP CA NR OR
NR CRP CR HR
[ cmap ]
CLP NL CA CRP NR
[ HEME ]
[ atoms ]
FE FE 0.24 0
NA NPH -0.18 1
NB NPH -0.18 2
NC NPH -0.18 3
ND NPH -0.18 4
C1A CPA 0.12 5
C2A CPB -0.06 6
C3A CPB -0.06 7
C4A CPA 0.12 8
C1B CPA 0.12 9
C2B CPB -0.06 10
C3B CPB -0.06 11
C4B CPA 0.12 12
C1C CPA 0.12 13
C2C CPB -0.06 14
C3C CPB -0.06 15
C4C CPA 0.12 16
C1D CPA 0.12 17
C2D CPB -0.06 18
C3D CPB -0.06 19
C4D CPA 0.12 20
CHA CPM -0.10 21
HA HA 0.10 22
CHB CPM -0.10 23
HB HA 0.10 24
CHC CPM -0.10 25
HC HA 0.10 26
CHD CPM -0.10 27
HD HA 0.10 28
CMA CT3 -0.27 29
HMA1 HA 0.09 30
HMA2 HA 0.09 31
HMA3 HA 0.09 32
CAA CT2 -0.18 33
HAA1 HA 0.09 34
HAA2 HA 0.09 35
CBA CT2 -0.28 36
HBA1 HA 0.09 37
HBA2 HA 0.09 38
CGA CC 0.62 39
O1A OC -0.76 40
O2A OC -0.76 41
CMB CT3 -0.27 42
HMB1 HA 0.09 43
HMB2 HA 0.09 44
HMB3 HA 0.09 45
CAB CE1 -0.15 46
HAB HE1 0.15 47
CBB CE2 -0.42 48
HBB1 HE2 0.21 49
HBB2 HE2 0.21 50
CMC CT3 -0.27 51
HMC1 HA 0.09 52
HMC2 HA 0.09 53
HMC3 HA 0.09 54
CAC CE1 -0.15 55
HAC HE1 0.15 56
CBC CE2 -0.42 57
HBC1 HE2 0.21 58
HBC2 HE2 0.21 59
CMD CT3 -0.27 60
HMD1 HA 0.09 61
HMD2 HA 0.09 62
HMD3 HA 0.09 63
CAD CT2 -0.18 64
HAD1 HA 0.09 65
HAD2 HA 0.09 66
CBD CT2 -0.28 67
HBD1 HA 0.09 68
HBD2 HA 0.09 69
CGD CC 0.62 70
O1D OC -0.76 71
O2D OC -0.76 72
[ bonds ]
FE NA
FE NB
FE NC
FE ND
NA C1A
C1A C2A
C2A C3A
C3A C4A
NA C4A
C2A CAA
CAA CBA
CBA CGA
CGA O1A
CGA O2A
C3A CMA
CHB C4A
CHB C1B
NB C1B
C1B C2B
C2B C3B
C3B C4B
NB C4B
C2B CMB
C3B CAB
CAB CBB
CHC C4B
CHC C1C
NC C1C
C1C C2C
C2C C3C
C3C C4C
NC C4C
C2C CMC
C3C CAC
CAC CBC
CHD C4C
CHD C1D
ND C1D
C1D C2D
C2D C3D
C3D C4D
ND C4D
C2D CMD
C3D CAD
CAD CBD
CBD CGD
CGD O1D
CGD O2D
CHA C4D
CHA C1A
CHA HA
CHB HB
CHC HC
CHD HD
CAA HAA1
CAA HAA2
CBA HBA1
CBA HBA2
CMA HMA1
CMA HMA2
CMA HMA3
CMB HMB1
CMB HMB2
CMB HMB3
CAB HAB
CBB HBB1
CBB HBB2
CMC HMC1
CMC HMC2
CMC HMC3
CAC HAC
CBC HBC1
CBC HBC2
CMD HMD1
CMD HMD2
CMD HMD3
CAD HAD1
CAD HAD2
CBD HBD1
CBD HBD2
[ angles ]
; ai aj ak th0 cth ub0 cub
NA FE NC 180.0 0.0 0.0 0.0
NB FE ND 180.0 0.0 0.0 0.0
[ impropers ]
C2A C1A C3A CAA
C3A C2A C4A CMA
C2B C1B C3B CMB
C3B C2B C4B CAB
C2C C1C C3C CMC
C3C C2C C4C CAC
C2D C1D C3D CMD
C3D C2D C4D CAD
CGA CBA O2A O1A
CGD CBD O2D O1D
C4A NA C1A C2A
C1A NA C4A C3A
C4B NB C1B C2B
C1B NB C4B C3B
C4C NC C1C C2C
C1C NC C4C C3C
C4D ND C1D C2D
C1D ND C4D C3D
NA C1A C2A C3A
NA C4A C3A C2A
NB C1B C2B C3B
NB C4B C3B C2B
NC C1C C2C C3C
NC C4C C3C C2C
ND C1D C2D C3D
ND C4D C3D C2D
NA C1A CHA C4D
NA C4A CHB C1B
NB C1B CHB C4A
NB C4B CHC C1C
NC C1C CHC C4B
NC C4C CHD C1D
ND C1D CHD C4C
ND C4D CHA C1A
CHA C1A C4D HA
CHB C1B C4A HB
CHC C1C C4B HC
CHD C1D C4C HD
C1A C2A CHA NA
C4A C3A CHB NA
C1B C2B CHB NB
C4B C3B CHC NB
C1C C2C CHC NC
C4C C3C CHD NC
C1D C2D CHD ND
C4D C3D CHA ND
NA C1A C4A FE
NB C1B C4B FE
NC C1C C4C FE
ND C1D C4D FE
[ HEO2 ]
[ atoms ]
FE FE 0.24 0
NA NPH -0.18 1
NB NPH -0.18 2
NC NPH -0.18 3
ND NPH -0.18 4
C1A CPA 0.12 5
C2A CPB -0.06 6
C3A CPB -0.06 7
C4A CPA 0.12 8
C1B CPA 0.12 9
C2B CPB -0.06 10
C3B CPB -0.06 11
C4B CPA 0.12 12
C1C CPA 0.12 13
C2C CPB -0.06 14
C3C CPB -0.06 15
C4C CPA 0.12 16
C1D CPA 0.12 17
C2D CPB -0.06 18
C3D CPB -0.06 19
C4D CPA 0.12 20
CHA CPM -0.10 21
HA HA 0.10 22
CHB CPM -0.10 23
HB HA 0.10 24
CHC CPM -0.10 25
HC HA 0.10 26
CHD CPM -0.10 27
HD HA 0.10 28
CMA CT3 -0.27 29
HMA1 HA 0.09 30
HMA2 HA 0.09 31
HMA3 HA 0.09 32
CAA CT2 -0.18 33
HAA1 HA 0.09 34
HAA2 HA 0.09 35
CBA CT2 -0.28 36
HBA1 HA 0.09 37
HBA2 HA 0.09 38
CGA CC 0.62 39
O1A OC -0.76 40
O2A OC -0.76 41
CMB CT3 -0.27 42
HMB1 HA 0.09 43
HMB2 HA 0.09 44
HMB3 HA 0.09 45
CAB CE1 -0.15 46
HAB HE1 0.15 47
CBB CE2 -0.42 48
HBB1 HE2 0.21 49
HBB2 HE2 0.21 50
CMC CT3 -0.27 51
HMC1 HA 0.09 52
HMC2 HA 0.09 53
HMC3 HA 0.09 54
CAC CE1 -0.15 55
HAC HE1 0.15 56
CBC CE2 -0.42 57
HBC1 HE2 0.21 58
HBC2 HE2 0.21 59
CMD CT3 -0.27 60
HMD1 HA 0.09 61
HMD2 HA 0.09 62
HMD3 HA 0.09 63
CAD CT2 -0.18 64
HAD1 HA 0.09 65
HAD2 HA 0.09 66
CBD CT2 -0.28 67
HBD1 HA 0.09 68
HBD2 HA 0.09 69
CGD CC 0.62 70
O1D OC -0.76 71
O2D OC -0.76 72
O1 OM 0.021 73
O2 OM -0.021 74
[ bonds ]
FE NA
FE NB
FE NC
FE ND
NA C1A
C1A C2A
C2A C3A
C3A C4A
NA C4A
C2A CAA
CAA CBA
CBA CGA
CGA O1A
CGA O2A
C3A CMA
CHB C4A
CHB C1B
NB C1B
C1B C2B
C2B C3B
C3B C4B
NB C4B
C2B CMB
C3B CAB
CAB CBB
CHC C4B
CHC C1C
NC C1C
C1C C2C
C2C C3C
C3C C4C
NC C4C
C2C CMC
C3C CAC
CAC CBC
CHD C4C
CHD C1D
ND C1D
C1D C2D
C2D C3D
C3D C4D
ND C4D
C2D CMD
C3D CAD
CAD CBD
CBD CGD
CGD O1D
CGD O2D
CHA C4D
CHA C1A
CHA HA
CHB HB
CHC HC
CHD HD
CAA HAA1
CAA HAA2
CBA HBA1
CBA HBA2
CMA HMA1
CMA HMA2
CMA HMA3
CMB HMB1
CMB HMB2
CMB HMB3
CAB HAB
CBB HBB1
CBB HBB2
CMC HMC1
CMC HMC2
CMC HMC3
CAC HAC
CBC HBC1
CBC HBC2
CMD HMD1
CMD HMD2
CMD HMD3
CAD HAD1
CAD HAD2
CBD HBD1
CBD HBD2
O1 O2
O1 FE
[ angles ]
; ai aj ak th0 cth ub0 cub
NA FE NC 180.0 0.0 0.0 0.0
NB FE ND 180.0 0.0 0.0 0.0
FE O1 O2 122.0 50.00 0.0 0.0
[ impropers ]
C2A C1A C3A CAA
C3A C2A C4A CMA
C2B C1B C3B CMB
C3B C2B C4B CAB
C2C C1C C3C CMC
C3C C2C C4C CAC
C2D C1D C3D CMD
C3D C2D C4D CAD
CGA CBA O2A O1A
CGD CBD O2D O1D
C4A NA C1A C2A
C1A NA C4A C3A
C4B NB C1B C2B
C1B NB C4B C3B
C4C NC C1C C2C
C1C NC C4C C3C
C4D ND C1D C2D
C1D ND C4D C3D
NA C1A C2A C3A
NA C4A C3A C2A
NB C1B C2B C3B
NB C4B C3B C2B
NC C1C C2C C3C
NC C4C C3C C2C
ND C1D C2D C3D
ND C4D C3D C2D
NA C1A CHA C4D
NA C4A CHB C1B
NB C1B CHB C4A
NB C4B CHC C1C
NC C1C CHC C4B
NC C4C CHD C1D
ND C1D CHD C4C
ND C4D CHA C1A
CHA C1A C4D HA
CHB C1B C4A HB
CHC C1C C4B HC
CHD C1D C4C HD
C1A C2A CHA NA
C4A C3A CHB NA
C1B C2B CHB NB
C4B C3B CHC NB
C1C C2C CHC NC
C4C C3C CHD NC
C1D C2D CHD ND
C4D C3D CHA ND
NA C1A C4A FE
NB C1B C4B FE
NC C1C C4C FE
ND C1D C4D FE
[ O2 ] ; O2 ligand for HEME
[ atoms ]
O1 OM 0.021 0
O2 OM -0.021 1
[ bonds ]
O1 O2
[ CO ] ; CO ligand for HEME
[ atoms ]
C CM 0.021 0
O OM -0.021 1
[ bonds ]
C O
[ HOH ]
[ atoms ]
OW OT -0.834 0
HW1 HT 0.417 1
HW2 HT 0.417 2
[ bonds ]
OW HW1
OW HW2
HW1 HW2
[ TIP3 ]
[ atoms ]
OH2 OT -0.834 0
H1 HT 0.417 1
H2 HT 0.417 2
[ bonds ]
OH2 H1
OH2 H2
H1 H2
[ TP3M ]
[ atoms ]
OH2 OT -0.834 0
H1 HT 0.417 1
H2 HT 0.417 2
[ bonds ]
OH2 H1
OH2 H2
[ HO4 ]
; TIP4P
[ atoms ]
OW OWT4 0.00 0
HW1 HWT4 0.52 0
HW2 HWT4 0.52 0
MW MWT4 -1.04 0
[ bonds ]
OW HW1
OW HW2
[ SOD ]
[ atoms ]
SOD SOD 1.00 0
[ MG ]
[ atoms ]
MG MG 2.00 0
[ POT ]
[ atoms ]
POT POT 1.00 0
[ CES ]
[ atoms ]
CES CES 1.00 0
[ CAL ]
[ atoms ]
CAL CAL 2.00 0
[ CLA ]
[ atoms ]
CLA CLA -1.00 0
[ ZN2 ]
[ atoms ]
ZN ZN 2.00 0
[ ACE ]
[ atoms ]
CH3 CT3 -0.270 0
HH31 HA 0.090 1
HH32 HA 0.090 2
HH33 HA 0.090 3
C C 0.510 4
O O -0.510 5
[ bonds ]
C CH3
C +N
CH3 HH31
CH3 HH32
CH3 HH33
O C
[ impropers ]
C CH3 +N O
[ CT3 ]
; this can also be done with the .c.tdb, but the atom naming is different
; and this can matter
[ atoms ]
N NH1 -0.470 0
HN H 0.310 1
CH3 CT3 -0.110 2
HH31 HA 0.090 3
HH32 HA 0.090 4
HH33 HA 0.090 5
[ bonds ]
-C N
N HN
N CH3
CH3 HH31
CH3 HH32
CH3 HH33
[ impropers ]
N -C CH3 HN
-C CH3 N -O
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