From owner-chemistry@ccl.net Sat Jul 7 15:17:01 2007 From: "Chialuka Iheonunekwu neljunior4success2004]^[yahoo.co.uk" To: CCL Subject: CCL: Cygwin segmentation fault Message-Id: <-34683-070706172932-3778-QFVkWDEHn2hdPvFzobcALA=server.ccl.net> X-Original-From: Chialuka Iheonunekwu Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 6 Jul 2007 21:29:08 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Chialuka Iheonunekwu [neljunior4success2004]_[yahoo.co.uk] Hi everybody, I keep getting an error message: "segmentation fault" whenenever I try to run autogrid4 on cygwin. I've tried to set the stack size to unliimited using the command "ulimit -s unlimited" but it's still not working. Can anyone tell me what to do please? Thanks, Chialuka. ___________________________________________________________ Yahoo! Answers - Got a question? Someone out there knows the answer. Try it now. http://uk.answers.yahoo.com/ From owner-chemistry@ccl.net Sat Jul 7 15:53:01 2007 From: "Mike F Falcetta mffalcetta-$-gcc.edu" To: CCL Subject: CCL:G: oligiovalent link atom in oniom Message-Id: <-34684-070707145530-27405-7dxA4puO+Ixm15Y2TXMHTQ-*-server.ccl.net> X-Original-From: "Mike F Falcetta" Date: Sat, 7 Jul 2007 14:55:25 -0400 Sent to CCL by: "Mike F Falcetta" [mffalcetta##gcc.edu] I am doing an oniom calculation in gaussian 03 and have a situation where the link atom is an oxygen connected to TWO of my high level atoms (it is a trivalent O in a crystal). Can anyone help me with the syntax for telling he program that this link atom is connected to two different atoms? Here is an example of an input line O 11.885 9.873 5.994 L O 11 You can see that right now the link atom is designated as an O and connected to atom 11 (an atom in my high level model), but I also want it to be connected to atom 13 in the high level model. The program asks me if the atom is oligiovalent, but I can't figure out how to tell it that this link atom is connected to two atoms in the high-level model. I am, of course not using an H but an O as a link atom (which is perfectly fine). Thanks in advance Mike From owner-chemistry@ccl.net Sat Jul 7 16:28:00 2007 From: "Keerthi Jayasundera jaya0046(_)d.umn.edu" To: CCL Subject: CCL:G: oniom calculation Message-Id: <-34685-070707144716-26503-EB+uiOpNuFoxdqAKjHQr8g%a%server.ccl.net> X-Original-From: "Keerthi Jayasundera" Date: Sat, 7 Jul 2007 14:47:12 -0400 Sent to CCL by: "Keerthi Jayasundera" [jaya0046^d.umn.edu] I am a beginner to oniom I am trying an oniom calculation for a peptide chain with a triazole ring in the middle. I always get an error message in the middle of the calculation. As a start I used a 3-layer oniom as given in the gaussian tutorial. So I got a message saying that same parameter is missing to a N atom in the high layer. Anyway I found that could come with the "Amber" So I changed it to UFF in the low layer. Now I get some other error which does not give any understandable message. I think I have not used commands correctly. Please someone help me to solve the problem Here is my input file. %chk=quick.chk %mem=6MW %nproc=1 opt=rcfc oniom(rhf/6-31g:ram1:amber) geom=connectivity Title Card Required 0 1 0 1 0 1 0 1 0 1 0 1 C-CM- 0 -0.979628 -1.159218 0.000009 H C-CM- 0 0.422122 -1.159218 0.000009 H H-H4- 0 1.066495 -2.031924 0.000034 M H-H4 2 N- 0 -0.310937 1.003031 -0.000095 H N-N2- 0 0.846120 0.211578 0.000009 H N-N3--0.516300 0 -1.419355 0.161290 0.000000 H C-CT-0.039700 0 -2.859630 0.320067 0.000068 H H-H1-0.110500 0 -3.277620 -0.150672 -0.889757 M H-H1 7 C-CT-0.056000 0 -3.483217 -0.326921 1.232208 M H-H1 7 C-C-0.536600 0 -3.248651 1.791511 0.000147 M H-H1 7 H-HC--0.017300 0 -3.250175 -1.391678 1.241385 M H-HC--0.017300 0 -3.081256 0.140223 2.131266 M C-CT-0.013600 0 -4.981165 -0.140179 1.195083 M O-O--0.581900 0 -2.355867 2.678364 0.000146 M H-HC--0.042500 0 -5.215008 0.924407 1.186354 M H-HC--0.042500 0 -5.383929 -0.607494 0.296474 M C-C-0.805400 0 -5.605570 -0.788016 2.428839 M O-O2--0.818800 0 -5.734708 -0.067706 3.454547 M O-O2--0.818800 0 -5.947450 -1.997018 2.333810 M N-N--0.415700 0 -4.667286 2.176705 0.000223 M H-H-0.271900 0 -5.358580 1.538797 0.339614 M C-CT--0.087500 0 -5.063971 3.480727 -0.491479 M H-H1-0.096900 0 -4.580882 4.256153 0.103028 M C-CT-0.298500 0 -4.660558 3.663221 -1.950786 L H-H1 22 C-C-0.597300 0 -6.571867 3.665676 -0.399129 L H-H1 22 H-HC--0.029700 0 -3.578481 3.570399 -2.043492 L C-CT--0.319200 0 -5.336934 2.594335 -2.802621 L C-CT--0.319200 0 -5.094761 5.044582 -2.429256 L O-O--0.567900 0 -7.292069 2.741987 0.060956 L H-HC-0.079100 0 -6.419114 2.686824 -2.710783 L H-HC-0.079100 0 -5.048915 2.724325 -3.845812 L H-HC-0.079100 0 -5.026906 1.606779 -2.460984 L H-HC-0.079100 0 -4.611580 5.808946 -1.820665 L H-HC-0.079100 0 -4.806645 5.175545 -3.472299 L H-HC-0.079100 0 -6.176850 5.137991 -2.337278 L N-N--0.516300 0 -7.186941 4.923315 -0.847381 L H-H-0.293600 0 -6.651063 5.581231 -1.376513 L C-CT-0.039700 0 -8.569717 5.209666 -0.522518 L H-H1-0.110500 0 -9.210774 4.437288 -0.947463 L C-CT-0.056000 0 -8.783229 5.244046 0.987069 L C-C-0.536600 0 -8.996294 6.558691 -1.083453 L H-HC--0.017300 0 -8.518191 4.276855 1.414148 L H-HC--0.017300 0 -8.154675 6.018939 1.425887 L C-CT-0.013600 0 -10.233003 5.544569 1.283615 L O-O--0.581900 0 -8.175766 7.258267 -1.732221 L H-HC--0.042500 0 -10.498670 6.511888 0.857216 L H-HC--0.042500 0 -10.862188 4.769803 0.845477 L C-C-0.805400 0 -10.446796 5.578994 2.795182 L O-O2--0.818800 0 -10.298521 6.688991 3.372697 L O-O2--0.818800 0 -10.756343 4.494968 3.357912 L N-N--0.415700 0 -10.366797 7.044417 -0.867366 L H-H-0.271900 0 -10.957507 6.593282 -0.198382 L C-CT--0.002400 0 -10.861782 8.176899 -1.623723 L H-H1-0.097800 0 -10.239071 9.048695 -1.422967 L C-CT--0.034300 0 -10.832645 7.891714 -3.121536 L C-C-0.597300 0 -12.297546 8.506169 -1.240775 L H-HC-0.029500 0 -9.808555 7.685743 -3.432851 L H-HC-0.029500 0 -11.459040 7.026711 -3.339479 L C-CA-0.011800 0 -11.331632 9.017578 -3.995345 L O-O--0.567900 0 -12.888752 7.820305 -0.366912 L C-CA--0.125600 0 -11.350562 8.867789 -5.387180 L C-CA--0.125600 0 -11.775340 10.211216 -3.413663 L H-HA-0.133000 0 -11.005104 7.938457 -5.840061 L C-CA--0.170400 0 -11.813199 9.911636 -6.197334 L C-CA--0.170400 0 -12.237977 11.255063 -4.223817 L H-HA-0.133000 0 -11.760602 10.327838 -2.330020 L H-HA-0.143000 0 -11.827938 9.795014 -7.280977 L C-CA--0.107200 0 -12.256907 11.105274 -5.615652 L H-HA-0.143000 0 -12.583435 12.184395 -3.770936 L H-HA-0.129700 0 -12.617104 11.917984 -6.246414 L N-N--0.347900 0 -12.993637 9.625381 -1.891714 L H-H-0.274700 0 -12.550033 10.125419 -2.635473 L C-CT--0.263700 0 -14.322568 10.004049 -1.455647 L H-H1-0.156000 0 -15.001717 9.161287 -1.584520 L C-CT--0.000700 0 -14.323143 10.410005 0.014326 L C-C-0.734100 0 -14.849615 11.181352 -2.263524 L H-HC-0.032700 0 -13.982173 9.572662 0.623175 L H-HC-0.032700 0 -13.654477 11.258795 0.157651 L C-CT-0.039000 0 -15.736543 10.800370 0.433298 L O-O2--0.589400 0 -14.141789 11.688069 -3.172254 L H-HC-0.028500 0 -16.078044 11.638013 -0.174841 L H-HC-0.028500 0 -16.405741 9.951881 0.290683 L C-CT-0.048600 0 -15.737119 11.206327 1.903273 L H-H1-0.068700 0 -15.396149 10.368984 2.512121 L H-H1-0.068700 0 -15.068452 12.055116 2.046597 L N-N2--0.529500 0 -17.095392 11.592620 2.346300 L H-H-0.345600 0 -17.850021 11.554247 1.676106 L C-CA-0.807600 0 -17.367676 11.987984 3.586642 L N-N2--0.862700 0 -16.427662 12.064208 4.524438 L N-N2--0.862700 0 -18.624431 12.312365 3.876888 L H-H-0.447800 0 -15.474243 11.817145 4.300713 L H-H-0.447800 0 -16.671555 12.368807 5.456015 L H-H-0.447800 0 -19.335864 12.253370 3.162407 L H-H-0.447800 0 -18.861600 12.616204 4.810447 L O-OH- 0 -16.149152 11.711677 -1.989919 L H-HO- 0 -16.493627 12.138214 -2.777956 L C-CT- 0 -1.971529 -2.337238 0.000148 H H-H1- 0 -2.312409 -2.516359 0.998454 M H-H1 97 H-H1- 0 -2.807007 -2.100096 -0.624865 M H-H1 97 N-N- 0 -1.302226 -3.541423 -0.512564 H H-H- 0 -1.939344 -4.059457 -1.083284 M H-H 100 C-C-0.597300 0 -0.864453 -4.376461 0.615251 M H-H 100 C-CT--0.024900 0 -0.037047 -5.628013 0.359323 M O-O--0.567900 0 -1.173802 -4.056507 1.792326 M N-N--0.415700 0 0.287099 -6.301875 1.600469 M H-H1-0.084300 0 0.882942 -5.339427 -0.149046 M C-CT-0.211700 0 -0.840250 -6.536712 -0.565206 M H-H-0.271900 0 -0.030927 -5.926491 2.471070 M H-H1-0.035200 0 -0.257411 -7.428659 -0.795052 M H-H1-0.035200 0 -1.768812 -6.826793 -0.073551 M O-OH--0.654600 0 -1.140564 -5.838678 -1.776594 M H-HO-0.427500 0 -1.646188 -6.410710 -2.358593 L H-HO 111 C-C-0.597300 0 1.083440 -7.537316 1.579817 M C-CT--0.059700 0 1.182562 -8.399803 2.829927 L H-H2 113 O-O--0.567900 0 1.683197 -7.881810 0.528539 L H-H1 113 N-N--0.415700 0 2.011332 -9.565021 2.595383 L H-H1-0.086900 0 0.179485 -8.717971 3.114015 L C-CT-0.130300 0 1.787312 -7.563573 3.952701 L H-H-0.271900 0 2.427990 -9.709793 1.697922 L H-HC-0.018700 0 1.840278 -8.160662 4.863074 L C-CT--0.320400 0 3.190484 -7.117729 3.555261 L C-CT--0.043000 0 0.915074 -6.337240 4.199546 L H-HC-0.088200 0 3.138271 -6.520160 2.645160 L H-HC-0.088200 0 3.623208 -6.519964 4.357462 L H-HC-0.088200 0 3.814318 -7.993944 3.378686 L H-HC-0.023600 0 0.862007 -5.739377 3.289687 L H-HC-0.023600 0 -0.088004 -6.655407 4.483633 L C-CT--0.066000 0 1.519823 -5.501009 5.322319 L H-HC-0.018600 0 2.522801 -5.182068 5.038746 L H-HC-0.018600 0 0.896743 -4.624314 5.499167 L H-HC-0.018600 0 1.572790 -6.098098 6.232692 L C-C-0.536600 0 2.239625 -10.534308 3.676709 L C-CT-0.039700 0 3.284848 -11.628043 3.510163 L O-O--0.581900 0 1.570859 -10.459764 4.740083 L N-N--0.516300 0 3.349503 -12.471304 4.686740 L H-H1-0.110500 0 4.255202 -11.160138 3.344097 L C-CT-0.056000 0 2.917005 -12.439652 2.272582 L H-H-0.293600 0 2.749247 -12.289694 5.465655 L H-HC--0.017300 0 3.668607 -13.211525 2.107031 L H-HC--0.017300 0 1.943386 -12.906989 2.420098 L C-CT-0.013600 0 2.860022 -11.527101 1.070874 L H-HC--0.042500 0 2.108260 -10.755186 1.235505 L H-HC--0.042500 0 3.833481 -11.059722 0.922437 L C-C-0.805400 0 2.491696 -12.339774 -0.168330 L O-O2--0.818800 0 1.266381 -12.454522 -0.438582 L O-O2--0.818800 0 3.439166 -12.838062 -0.832867 L C-C-0.597300 0 4.297472 -13.593752 4.735361 L C-CT--0.024900 0 4.292558 -14.543002 5.925061 L O-O--0.567900 0 5.113049 -13.769784 3.793332 L N-N3--0.415700 0 5.300035 -15.573477 5.774352 L H-H1-0.084300 0 3.307903 -15.004749 5.998170 L C-CT-0.211700 0 4.537363 -13.715592 7.182473 L H-H-0.271900 0 5.883024 -15.587765 4.961997 L H-H1-0.035200 0 4.505016 -14.364945 8.057342 L H-H1-0.035200 0 5.515908 -13.239521 7.119974 L O-OH--0.654600 0 3.525587 -12.711534 7.296830 L H-HO-0.427500 0 3.679694 -12.190672 8.088381 L H-H-0.271900 0 5.412337 -16.270352 6.482698 L 1 2 2.0 6 1.0 97 1.0 2 3 1.0 5 1.0 3 4 5 2.0 6 1.0 5 6 7 1.0 7 8 1.0 9 1.0 10 1.0 8 9 11 1.0 12 1.0 13 1.0 10 14 2.0 20 1.0 11 12 13 15 1.0 16 1.0 17 1.0 14 15 16 17 18 1.5 19 1.5 18 19 20 21 1.0 22 1.0 21 22 23 1.0 24 1.0 25 1.0 23 24 26 1.0 27 1.0 28 1.0 25 29 2.0 36 1.0 26 27 30 1.0 31 1.0 32 1.0 28 33 1.0 34 1.0 35 1.0 29 30 31 32 33 34 35 36 37 1.0 38 1.0 37 38 39 1.0 40 1.0 41 1.0 39 40 42 1.0 43 1.0 44 1.0 41 45 2.0 51 1.0 42 43 44 46 1.0 47 1.0 48 1.0 45 46 47 48 49 1.5 50 1.5 49 50 51 52 1.0 53 1.0 52 53 54 1.0 55 1.0 56 1.0 54 55 57 1.0 58 1.0 59 1.0 56 60 2.0 71 1.0 57 58 59 61 1.5 62 1.5 60 61 63 1.0 64 1.5 62 65 1.5 66 1.0 63 64 67 1.0 68 1.5 65 68 1.5 69 1.0 66 67 68 70 1.0 69 70 71 72 1.0 73 1.0 72 73 74 1.0 75 1.0 76 1.0 74 75 77 1.0 78 1.0 79 1.0 76 80 2.0 95 1.0 77 78 79 81 1.0 82 1.0 83 1.0 80 81 82 83 84 1.0 85 1.0 86 1.0 84 85 86 87 1.0 88 1.5 87 88 89 1.5 90 1.5 89 91 1.0 92 1.0 90 93 1.0 94 1.0 91 92 93 94 95 96 1.0 96 97 98 1.0 99 1.0 100 1.0 98 99 100 101 1.0 102 1.0 101 102 103 1.0 104 2.0 103 105 1.0 106 1.0 107 1.0 104 105 108 1.0 113 1.0 106 107 109 1.0 110 1.0 111 1.0 108 109 110 111 112 1.0 112 113 114 1.0 115 2.0 114 116 1.0 117 1.0 118 1.0 115 116 119 1.0 132 1.0 117 118 120 1.0 121 1.0 122 1.0 119 120 121 123 1.0 124 1.0 125 1.0 122 126 1.0 127 1.0 128 1.0 123 124 125 126 127 128 129 1.0 130 1.0 131 1.0 129 130 131 132 133 1.0 134 2.0 133 135 1.0 136 1.0 137 1.0 134 135 138 1.0 147 1.0 136 137 139 1.0 140 1.0 141 1.0 138 139 140 141 142 1.0 143 1.0 144 1.0 142 143 144 145 1.5 146 1.5 145 146 147 148 1.0 149 2.0 148 150 1.0 151 1.0 152 1.0 149 150 153 1.0 158 1.0 151 152 154 1.0 155 1.0 156 1.0 153 154 155 156 157 1.0 157 158