One nice thing of AMBER10 is to use generalized torsional restraints, but
I could not use pmemd but sander.MPI. The manual is not clear on this and
therefore I was wondering if pmemd accepts generalized torsional
restraints. The rst file I am using is as follows.
------------rst------------
# TOR :2-6,41-45 :10-14,33-37 :18-22,57-61 :26-30,49-53 0
&rst iat = -1, -1, -1, -1,
igr1 =
34,37,38,41,43,44,46,47,49,50,51,52,55,56,58,59,60,62,65,66,69,70,73,75,76,78,79,81,82,83,84,85,87,88,91,92,93,95,98,99,102,103,106,108,109,111,112,114,115,116,117,118,120,121,124,125,126,128,131,132,135,136,139,141,142,144,145,147,148,149,150,153,154,156,157,158,160,163,164,167,168,171,173,174,176,177,179,180,181,182,185,186,188,189,190,192,195,1303,1306,1307,1310,1312,1313,1315,1316,1318,1319,1323,1324,1325,1327,1328,1329,1331,1334,1335,1338,1339,1342,1344,1345,1347,1348,1350,1351,1355,1356,1357,1359,1360,1361,1363,1366,1367,1370,1371,1374,1376,1377,1379,1380,1382,1384,1385,1388,1389,1390,1391,1393,1396,1397,1400,1401,1404,1406,1407,1409,1410,1412,1414,1415,1418,1419,1420,1421,1423,1426,1427,1430,1431,1434,1436,1437,1439,1440,1442,1443,1447,1448,1449,1451,1452,1453,1455,1458,
igr2 =
293,296,297,300,302,303,305,306,308,309,313,314,315,317,318,319,321,324,325,328,329,332,334,335,337,338,340,341,345,346,347,349,350,351,353,356,357,360,361,364,366,367,369,370,372,373,374,375,378,379,381,382,383,385,388,389,392,393,396,398,399,401,402,404,405,409,410,411,413,414,415,417,420,421,424,425,428,430,431,433,434,436,437,438,439,442,443,445,446,447,449,452,1049,1052,1053,1056,1058,1059,1061,1062,1064,1065,1069,1070,1071,1073,1074,1075,1077,1080,1081,1084,1085,1088,1090,1091,1093,1094,1096,1097,1098,1099,1102,1103,1105,1106,1107,1109,1112,1113,1116,1117,1120,1122,1123,1125,1126,1128,1129,1133,1134,1135,1137,1138,1139,1141,1144,1145,1148,1149,1152,1154,1155,1157,1158,1160,1161,1162,1163,1166,1167,1169,1170,1171,1173,1176,1177,1180,1181,1184,1186,1187,1189,1190,1192,1193,1194,1195,1198,1199,1201,1202,1203,1205,1208,
igr3 =
573,576,577,580,582,583,585,586,588,589,593,594,595,597,598,599,601,604,605,608,609,612,614,615,617,618,620,621,622,623,626,627,629,630,631,633,636,637,640,641,644,646,647,649,650,652,653,657,658,659,661,662,663,665,668,669,672,673,676,678,679,681,682,684,685,686,687,690,691,693,694,695,697,700,701,704,705,708,710,711,713,714,716,717,718,719,722,723,725,726,727,729,732,1838,1841,1842,1845,1847,1848,1850,1851,1853,1854,1858,1859,1860,1862,1863,1864,1866,1869,1870,1873,1874,1877,1879,1880,1882,1883,1885,1886,1890,1891,1892,1894,1895,1896,1898,1901,1902,1905,1906,1909,1911,1912,1914,1915,1917,1918,1919,1920,1923,1924,1926,1927,1928,1930,1933,1934,1937,1938,1941,1943,1944,1946,1947,1949,1950,1954,1955,1956,1958,1959,1960,1962,1965,1966,1969,1970,1973,1975,1976,1978,1979,1981,1982,1983,1984,1987,1988,1990,1991,1992,1994,1997,
igr4 =
827,830,831,834,836,837,839,840,842,843,847,848,849,851,852,853,855,858,859,862,863,866,868,869,871,872,874,875,879,880,881,883,884,885,887,890,891,894,895,898,900,901,903,904,906,908,909,912,913,914,915,917,920,921,924,925,928,930,931,933,934,936,938,939,942,943,944,945,947,950,951,954,955,958,960,961,963,964,966,967,971,972,973,975,976,977,979,982,1579,1582,1583,1586,1588,1589,1591,1592,1594,1595,1596,1597,1600,1601,1603,1604,1605,1607,1610,1611,1614,1615,1618,1620,1621,1623,1624,1626,1627,1628,1629,1630,1632,1633,1636,1637,1638,1640,1643,1644,1647,1648,1651,1653,1654,1656,1657,1659,1660,1661,1662,1663,1665,1666,1669,1670,1671,1673,1676,1677,1680,1681,1684,1686,1687,1689,1690,1692,1693,1694,1695,1698,1699,1701,1702,1703,1705,1708,1709,1712,1713,1716,1718,1719,1721,1722,1724,1725,1726,1727,1730,1731,1733,1734,1735,1737,1740,
r1 = -180, r2 = 0, r3 = 0, r4 = 180,
rk2 = 50.0, rk3 = 50.0, ialtd=0, &end
---------------------------
Thanks in advance. Best regards,
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
= Department of Chemistry - 2145 Sheridan Road =
= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
=
http://www.pas.rochester.edu/~yildirim/ =
-----------------------------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 23 2011 - 17:00:02 PDT
