On Tue, Oct 22, 2013 at 6:39 AM, Mike Limb <mikeallimb.gmail.com> wrote:
> Dear Jason,
>
> Many thanks for your help. I have one more question to do with the layout
> of the input.
>
> My input currently reads:
>
> Restrainted initial optimisation of intermediate for adiabatic mapping
> &cntrl
> imin=1, ncyc=20, maxcyc=200,
> ntb=0, cut=99.0,
> ibelly=1,
> /
> Moveable atoms
> RES 8 8 12 12 27 64 66 66 68 69 80 80
> RES 83 84 91 91 95 95 98 98 103 115 123 123
> RES 130 132 136 136 138 138 150 150 154 154
> RES 156 156 161 161 174 174 239 239 245 245 251 251
> RES 257 257 265 265 314 315 348 348 371 371 394 394 404 404
> RES 477 477 515 515 538 538 569 569 578 578 595 596 667 667
> RES 677 677 679 680 683 683 698 698 771 771 779 779 798 798
> RES 820 820 826 826 849 849 886 886 894 894 900 900 903 903 913 913
> RES 921 922 960 960 963 963 990 990 1004 1004 1009 1009 1026 1026
> RES 1029 1029 1036 1036 1047 1047 1051 1051 1056 1056 1092 1092 1113 1113
> RES 1116 1116 1119 1119 1126 1127 1133 1133 1138 1138 1170 1171 1173 1173
> RES 1177 1177 1188 1188 1195 1195 1204 1204 1210 1210 1213 1213 1217 1217
> RES 1231 1231 1244 1244 1246 1246 1265 1266 1269 1269 1271 1271 1274 1274
> RES 1284 1284 1288 1288 1294 1294 1301 1301 1310 1310 1318 1318 1324 1324
> RES 1330 1330 1332 1332 1336 1336 1340 1340 1344 1344 1355 1355 1363 1364
> RES 1382 1382 1385 1385 1393 1393 1399 1400 1402 1402 1409 1409 1415 1415
> RES 1443 1443 1447 1448 1450 1451 1469 1469 1475 1475 1480 1480 1482 1482
> RES 1488 1488 1493 1493 1500 1500 1505 1505 1507 1507 1511 1511 1528 1528
> RES 1530 1530 1538 1538 1550 1550 1559 1559 1566 1566 1569 1569 1574 1575
> RES 1596 1596 1604 1604 1612 1612 1635 1635 1662 1662 1673 1673 1692 1692
> RES 1694 1694 1700 1700 1706 1706 1722 1722 1733 1733 1745 1745 1747 1747
> RES 1752 1752 1783 1784 1811 1811 1826 1826 1834 1834 1845 1845 1851 1851
> RES 1856 1856 1858 1858 1868 1868 1871 1871 1873 1873 1875 1875 1887 1887
> RES 1905 1906 1920 1920 1924 1924 1932 1932 1942 1942 1945 1945 1949 1950
> RES 1958 1958 1963 1963 1965 1965 1967 1967 1973 1973
> END
> END
> nmropt=1,
> ifqnt=1,
>
These variables must go inside the &cntrl namelist (between &cntrl and /).
You should move the GROUP input to the end of the input file (I don't
know that this is required, but it is the only way I have ever written
input files).
&qmmm
> qmmask='.1962-1998,541-547,778-783',
> qmcharge=-2,
> qm_theory='DFTB',
> qmshake=0,
> qm_ewald=1, qm_pme=1,
> writepdb=1,
> lnk_dis=1.09,
> lnk_method=1,
> lnk_atomic_no=1,
> /
> &end
>
&end and / are synonyms. The &end here does nothing (and may be
interpreted as a title for your GROUP input.
> &wt
> type='END',
> &end
>
I don't see where you defined any distance restraints. You turned nmropt
on, but then didn't tell it what to do, so it should not actually apply any
distance restraints.
In your input file, make sure all namelists (i.e., blocks of input
variables beginning with "&name") are terminated with _either_ "/" or
"&end" (but _not_ both). All input variables must be in the correct
namelist. The free-format part of the input (i.e., GROUP input and DISANG
identifier) should come at the end.
HTH,
Jason
P.S. This is a big reason why I prefer masks instead of GROUP input :)
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 22 2013 - 05:00:03 PDT
