Hi Ilyas,
Yes it does support natural language. sander in this context is generic and
simply used to differentiate it from pmemd.
Back to the generalized torsion restraints: there is only igr1 and igr2 in
the pmemd &rst namelist, but such a generalized torsion angle requires 4
groups. Therefore, pmemd does not support that capability.
I'm not sure why igr3,4 were omitted (historical reasons, since torsion
constraints were added after-the-fact and it was just never thought of?) or
if there were actual implementation obstacles.
If it's easy enough to add, I'll look into dropping that in for the next
Amber release.
Thanks!
Jason
On Wed, Mar 23, 2011 at 5:14 PM, Ilyas Yildirim <i-yildirim.northwestern.edu
> wrote:
> Thanks Jason. The manual says "New to AMBER 10 (sander only), users may
> now use a "natural language" system to define restraints by using the
> RESTRAINT character variable". I assume that sander.MPI is not supporting
> this version of restraint definitions, or is it?
>
> 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/ =
> -----------------------------------------------------------
>
>
> On Wed, 23 Mar 2011, Jason Swails wrote:
>
> > It does not.
> >
> > Another thing perhaps worth checking into is the natural language added
> with
> > the generalized distance restraint that makes the input a little cleaner
> and
> > easier.
> >
> > Hope this helps,
> > Jason
> >
> > On Wed, Mar 23, 2011 at 4:48 PM, Ilyas Yildirim <
> i-yildirim.northwestern.edu
> >> wrote:
> >
> >> 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
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Mar 23 2011 - 17:30:05 PDT
