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Alex Granovsky
gran@classic.chem.msu.su

did you try to visualize imaginary modes using ChemCraft or other software?

Kind regards,
Alex Granovsky


On Tue Apr 7 '15 3:13am, atthar wrote
-------------------------------------
>Hello,

>When I did semiempirical calculation using PM3 method, i got three imaginary frequency, they are -38,7; -32,25; and -19,32. I modeled about host-guest interaction complex between cyclodextrin as host and some molecule as guest (there are not transition state because it is not chemical reaction). Here is the input file :

> $SYSTEM MWORDS=50 $END
> $CONTRL RUNTYP=Optimize $END
> $STATPT  HSSEND=.T. OptTol=1e-5 NStep=500 $END
> $BASIS GBASIS=PM3 $END
> $CONTRL ICHARG=0  MULT=1 $END
> $DATA
>Molecule specification
>C1
>C  6.000000 -4.295559 -4.132164 -1.223340
>C  6.000000 -3.767370 -3.779221 2.640521
>C  6.000000 -3.464794 -4.148894 0.097546
>C  6.000000 -4.462500 -3.868317 1.264054
>C  6.000000 -3.303063 5.187438 -1.422124
>C  6.000000 -4.951800 -2.733811 -1.367374
>C  6.000000 -5.827226 -2.463995 -0.109289
>C  6.000000 0.288269 -5.151084 1.650169
>C  6.000000 0.569594 -4.275904 2.891279
>C  6.000000 1.220515 -4.803846 0.449955
>C  6.000000 0.751503 -5.627043 -0.793122
>C  6.000000 -1.547972 -5.675446 0.240543
>C  6.000000 -0.761436 -5.387151 -1.073151
>C  6.000000 4.054214 -1.581645 2.925748
>C  6.000000 6.039163 0.332060 0.325591
>C  6.000000 5.554116 0.772721 -1.084720
>C  6.000000 5.085488 -2.827024 -0.662724
>C  6.000000 4.504665 -2.524012 1.785259
>C  6.000000 4.811890 -1.771964 0.452968
>C  6.000000 3.634656 -4.419505 0.637006
>C  6.000000 -5.524756 2.853108 -0.195577
>C  6.000000 3.859978 -3.774773 -0.760642
>C  6.000000 -5.293134 2.094845 -1.533028
>C  6.000000 5.568312 2.325433 -1.121398
>C  6.000000 -4.713412 0.255341 2.256689
>C  6.000000 -6.031155 0.731840 -1.414530
>C  6.000000 -5.537891 0.843524 1.087779
>C  6.000000 -5.470634 -0.053894 -0.186572
>C  6.000000 -1.409754 6.246378 -0.161058
>C  6.000000 4.662296 2.879258 0.023883
>C  6.000000 5.124989 2.268356 1.386033
>C  6.000000 -2.979485 4.958826 1.092870
>C  6.000000 -1.798935 5.561258 -1.503221
>C  6.000000 -3.522734 4.255573 -0.191226
>C  6.000000 -2.935322 4.006739 2.313259
>C  6.000000 4.129948 2.532753 2.543491
>C  6.000000 3.092092 5.164606 -1.470114
>C  6.000000 0.955415 5.631788 -0.147989
>C  6.000000 1.852289 5.676393 1.125286
>C  6.000000 3.835053 5.185288 -0.100687
>C  6.000000 1.822155 6.060614 -1.371280
>C  6.000000 1.134809 5.130591 2.382088
>H  1.000000 -6.756542 -3.081057 -0.090667
>O  8.000000 -6.331839 -1.172134 0.063346
>H  1.000000 -5.226031 -3.031948 3.632552
>H  1.000000 -3.915846 -4.227256 -3.103197
>O  8.000000 -5.754508 -2.761081 -2.524289
>H  1.000000 -3.109493 -2.881391 2.714107
>O  8.000000 -4.675708 -3.803087 3.705383
>O  8.000000 -3.431830 -4.410988 -2.307523
>O  8.000000 -5.083464 -2.596036 1.082097
>O  8.000000 -2.927680 -5.459043 0.291748
>H  1.000000 -6.008339 -1.850824 -2.680418
>H  1.000000 -3.146191 -4.674701 2.821808
>H  1.000000 -2.674568 -3.359468 0.081919
>H  1.000000 -5.075048 -4.934039 -1.197785
>H  1.000000 1.272919 -4.513473 -2.289276
>H  1.000000 4.632033 5.150883 -2.600961
>O  8.000000 1.026835 5.915857 -2.534899
>H  1.000000 1.591239 6.102266 -3.275199
>O  8.000000 1.525978 -5.369371 -1.941399
>O  8.000000 -0.056119 -4.769122 4.042969
>H  1.000000 -4.163989 -1.934400 -1.452939
>O  8.000000 -1.079553 -4.905446 1.323834
>H  1.000000 -1.727964 -4.001276 -1.976430
>O  8.000000 2.529603 -5.251466 0.819772
>H  1.000000 -5.253105 -4.659364 1.286983
>H  1.000000 1.640997 -4.311428 3.158714
>O  8.000000 -0.883265 -4.062739 -1.531616
>O  8.000000 6.431090 0.303779 -2.081092
>H  1.000000 -0.994913 -4.693375 3.915241
>H  1.000000 0.404797 -6.233082 1.913279
>H  1.000000 1.187841 -3.708568 0.230037
>O  8.000000 -0.075944 6.605673 0.040905
>O  8.000000 1.942445 5.168030 3.524234
>H  1.000000 2.670034 4.563029 3.390106
>O  8.000000 4.063402 -2.219680 4.172516
>H  1.000000 -1.512907 -6.770518 0.464984
>H  1.000000 0.939229 -6.713720 -0.626189
>H  1.000000 -1.115440 -6.089936 -1.865969
>O  8.000000 5.268226 -2.136676 -1.885997
>O  8.000000 6.013526 -1.024213 0.657252
>H  1.000000 0.290983 -3.216604 2.712919
>H  1.000000 3.339735 -5.246511 -1.858341
>H  1.000000 3.056965 -1.139672 2.716762
>O  8.000000 3.409947 -3.425331 1.611631
>H  1.000000 5.424117 -2.801848 -2.546141
>H  1.000000 3.406426 -2.905917 4.150734
>H  1.000000 4.765866 -0.744431 3.077847
>H  1.000000 5.406142 -3.105918 2.102511
>H  1.000000 7.112437 0.582419 0.503437
>H  1.000000 4.467104 -5.110211 0.916805
>H  1.000000 3.945991 -1.123333 0.164566
>O  8.000000 4.529082 1.933923 3.745832
>H  1.000000 2.961032 -3.169277 -1.075707
>O  8.000000 4.154954 -4.757945 -1.723414
>O  8.000000 4.889383 4.291453 0.100047
>O  8.000000 5.037923 2.800569 -2.341514
>H  1.000000 4.522343 0.986022 3.622045
>H  1.000000 6.014940 -3.403734 -0.428738
>H  1.000000 6.284879 -0.642916 -2.114293
>H  1.000000 -6.601406 3.099539 -0.029110
>H  1.000000 4.514092 0.402075 -1.284483
>H  1.000000 6.613268 2.707542 -1.004024
>H  1.000000 -4.419515 -0.386328 -0.400990
>H  1.000000 -4.202243 1.921203 -1.721438
>H  1.000000 -7.132924 0.888813 -1.300858
>O  8.000000 -4.959121 2.123589 0.866211
>H  1.000000 -3.668641 0.044838 1.928523
>H  1.000000 5.568126 2.424399 -3.032147
>O  8.000000 -5.857796 2.808376 -2.608294
>O  8.000000 -4.718994 1.054326 3.404311
>O  8.000000 -5.806194 -0.056954 -2.568847
>H  1.000000 -5.154355 -0.692250 2.614484
>H  1.000000 -6.603080 0.986093 1.396138
>H  1.000000 -6.060509 0.472837 -3.314479
>H  1.000000 -4.384540 1.920291 3.176804
>H  1.000000 3.588778 2.614265 -0.185218
>H  1.000000 -3.933283 6.107063 -1.328775
>H  1.000000 -1.920605 7.230419 -0.027286
>H  1.000000 -1.189138 4.637226 -1.675706
>H  1.000000 -2.200876 3.191802 2.149608
>H  1.000000 -3.603077 5.857747 1.324369
>H  1.000000 -5.279877 3.563103 -2.732598
>H  1.000000 -3.921700 3.538828 2.507723
>O  8.000000 -3.710024 4.478562 -2.579002
>O  8.000000 -1.628486 6.455466 -2.578101
>H  1.000000 -3.000874 3.279699 -0.351573
>H  1.000000 -0.679421 6.533348 -2.687301
>H  1.000000 -3.477567 5.019807 -3.323695
>O  8.000000 -4.932740 4.100614 -0.001439
>H  1.000000 6.140163 2.655701 1.647919
>H  1.000000 3.105387 2.211147 2.264104
>O  8.000000 -2.677980 4.679017 3.512633
>H  1.000000 -1.803009 5.046746 3.460013
>H  1.000000 2.112508 7.136969 -1.270525
>H  1.000000 0.547241 4.600857 -0.302974
>H  1.000000 2.806214 4.120807 -1.759799
>O  8.000000 -1.625820 5.375854 0.925476
>H  1.000000 0.284509 5.783044 2.650222
>H  1.000000 4.346894 6.162553 0.076470
>H  1.000000 2.207487 6.720872 1.307690
>H  1.000000 0.745157 4.108000 2.204254
>O  8.000000 2.979389 4.825356 0.953204
>O  8.000000 3.901524 5.742606 -2.473059
>H  1.000000 4.088654 3.609019 2.806967
>O  8.000000 5.183004 0.847808 1.312869
>C  6.000000 -1.352761 -1.213186 3.924063
>C  6.000000 -0.725351 -0.430317 2.940965
>C  6.000000 0.534753 0.176202 3.166067
>C  6.000000 1.193191 0.030249 4.400827
>C  6.000000 0.557127 -0.722542 5.363585
>C  6.000000 -0.694944 -1.337738 5.128152
>N  7.000000 -1.090042 -0.096452 1.624615
>C  6.000000 -0.081934 0.732601 1.091818
>N  7.000000 0.900185 0.874873 2.004990
>S  16.000000 -0.069815 1.531448 -0.512875
>C  6.000000 1.542707 0.886962 -1.171981
>C  6.000000 1.537478 0.625539 -2.639904
>N  7.000000 1.712069 1.697800 -3.459226
>C  6.000000 1.750651 1.531052 -4.796941
>C  6.000000 1.616725 0.273856 -5.384161
>C  6.000000 1.433228 -0.833118 -4.550184
>C  6.000000 1.387094 -0.677813 -3.152899
>O  8.000000 1.169575 -2.098244 -5.067933
>C  6.000000 2.089217 -2.595296 -6.005220
>C  6.000000 3.256449 -3.377818 -5.291889
>F  9.000000 2.845114 -4.223825 -4.323836
>C  6.000000 1.165117 -1.818013 -2.231889
>O  8.000000 -1.207678 0.807467 -1.274857
>F  9.000000 3.974342 -4.138779 -6.144928
>F  9.000000 4.164942 -2.578566 -4.691288
>H  1.000000 1.646691 0.168914 -6.474894
>H  1.000000 1.890100 2.444981 -5.386203
>H  1.000000 -2.009797 -0.204809 1.257846
>H  1.000000 2.168639 0.500439 4.575667
>H  1.000000 1.029623 -0.859329 6.342861
>H  1.000000 -1.144685 -1.934887 5.929586
>H  1.000000 -2.318576 -1.703589 3.724897
>H  1.000000 0.143401 -1.781749 -1.824406
>H  1.000000 1.869046 -1.779497 -1.374209
>H  1.000000 1.288708 -2.802872 -2.712447
>H  1.000000 2.515241 -1.823680 -6.673725
>H  1.000000 1.477996 -3.298849 -6.595942
>H  1.000000 2.302078 1.662965 -0.902917
>H  1.000000 1.864868 -0.041459 -0.648239
> $END

>Are there any solution to fix this problem in order to i can get all positive frequency?

>Thank you very much.

>Regards,
>atthar
>