From owner-chemistry@ccl.net Thu Mar 22 04:23:00 2007 From: "Tomasz Grabarkiewicz grabar[A]man.poznan.pl" To: CCL Subject: CCL: Amber in Gaussian, Help? Message-Id: <-33871-070322041235-13976-ZCu3eBnH8A98O2NDtLFodA###server.ccl.net> X-Original-From: "Tomasz Grabarkiewicz" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="ISO-8859-1"; reply-type=response Date: Thu, 22 Mar 2007 08:28:08 +0100 MIME-Version: 1.0 Sent to CCL by: "Tomasz Grabarkiewicz" [grabar{=}man.poznan.pl] Thomas, Since you are you using a forcefield method, you need to define some additional parameters. Your log file implies that you simply forgot to add parameters for the harmonic bends and stretches. Include them at the end of your input file in the following form: HrmStr1 * * F 1.08 HrmBnd2 * * * F 120.0 Replace the asterisks with the specific atom types and F with the appropriate force constants. Hope this helps Cheers Tomasz From owner-chemistry@ccl.net Thu Mar 22 06:09:01 2007 From: "Frank Neese neese!^!thch.uni-bonn.de" To: CCL Subject: CCL: vibrational spectra Message-Id: <-33872-070322060059-14866-ttpvJCbchIGac3BQn+J/7g,server.ccl.net> X-Original-From: Frank Neese Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Thu, 22 Mar 2007 11:00:15 +0100 Mime-Version: 1.0 Sent to CCL by: Frank Neese [neese:thch.uni-bonn.de] Dear Dr. Misra, this takes just a few minutes with the ORCA program. here are parts of the input and output. # # # ! PM3 VeryTightSCF Opt NumFreq %freq centraldiff true end * xyz 0 1 Sb 0.823587 7.162675 1.894190 O 0.304908 5.418973 0.827952 O -0.598827 6.779650 -0.530297 O -0.698673 4.842312 -2.550191 O 1.433721 8.796461 3.077093 O 0.410855 9.960199 1.625043 O 1.570693 12.339685 2.493383 C 2.276037 7.698595 0.410971 C 1.936908 8.505594 -0.651107 C 2.945617 8.817734 -1.564661 C 4.232635 8.320912 -1.380045 C 4.533477 7.509805 -0.286935 C 3.538287 7.187972 0.632992 C -1.221718 7.398059 2.490239 C -2.082088 8.201570 1.776369 C -3.402432 8.287309 2.222417 C -3.807120 7.573054 3.346131 C -2.906305 6.764621 4.037691 C -1.585886 6.670769 3.605244 C 1.755140 5.902562 3.334554 C 2.402080 4.759077 2.904446 C 3.011903 3.939237 3.852199 C 2.964392 4.280022 5.200824 C 2.308289 5.437275 5.610983 C 1.694015 6.259773 4.669072 C -0.344894 5.593027 -0.282111 C -0.741915 4.400180 -1.198511 C 0.281366 3.279829 -1.073384 C 0.060587 2.210424 -0.203286 C 1.002599 1.195453 -0.081701 C 2.175536 1.237278 -0.826682 C 2.405642 2.302999 -1.689127 C 1.467848 3.322613 -1.810677 C -2.148336 3.915843 -0.854189 C -2.916009 3.285774 -1.837768 C -4.197689 2.832771 -1.547311 C -4.725490 2.996457 -0.271336 C -3.963344 3.612171 0.714511 C -2.681370 4.068471 0.427128 C 1.084402 9.976174 2.664210 C 1.492327 11.269605 3.427442 C 2.895075 11.123633 4.001358 C 3.996107 11.156043 3.139957 C 5.285406 11.026441 3.642914 C 5.491135 10.856340 5.007607 C 4.400429 10.815653 5.867933 C 3.109312 10.948958 5.368818 C 0.450370 11.572377 4.502472 C -0.146297 10.545592 5.239197 C -1.091954 10.835643 6.215906 C -1.450102 12.153839 6.474904 C -0.850210 13.181934 5.757389 C 0.097075 12.895304 4.780367 H -1.263032 5.603232 -2.607585 H 0.746330 12.358886 2.023097 H 0.914494 8.888147 -0.770666 H 2.719206 9.455807 -2.425306 H 5.019014 8.570394 -2.100507 H 5.549396 7.125782 -0.149024 H 3.747399 6.553120 1.504082 H -1.740064 8.749355 0.888006 H -4.117419 8.917397 1.683017 H -4.844419 7.644447 3.690493 H -3.233930 6.204026 4.919103 H -0.855716 6.040305 4.130069 H 2.420201 4.488976 1.840908 H 3.526335 3.026639 3.533513 H 3.446410 3.635003 5.943130 H 2.276754 5.704070 6.672418 H 1.188911 7.183479 4.980949 H -0.860251 2.172949 0.392933 H 0.817010 0.361115 0.602258 H 2.914444 0.435085 -0.734527 H 3.328647 2.341450 -2.276633 H 1.668229 4.157967 -2.491958 H -2.506719 3.140685 -2.845328 H -4.790894 2.343807 -2.327000 H -5.735341 2.640430 -0.043812 H -4.371544 3.741013 1.722286 H -2.093945 4.550135 1.219439 H 3.847908 11.287329 2.061571 H 6.140763 11.058138 2.960401 H 6.507020 10.754454 5.402019 H 4.555376 10.679770 6.943059 H 2.256409 10.912755 6.058477 H 0.132199 9.499138 5.056224 H -1.555408 10.021013 6.781841 H -2.197573 12.380563 7.241814 H -1.120721 14.223061 5.962236 H 0.570422 13.722353 4.236416 * you will find that the geometry converges smoothly: ***********************HURRAY******************** *** THE OPTIMIZATION HAS CONVERGED *** ************************************************* with the result --------------------------------- CARTESIAN COORDINATES (ANGSTROEM) --------------------------------- Sb 0.823394 7.164838 1.891720 O 0.305010 5.420365 0.826549 O -0.606453 6.779031 -0.528658 O -0.705929 4.842484 -2.548923 O 1.433089 8.798042 3.075563 O 0.402606 9.962123 1.629095 O 1.560145 12.342314 2.496855 C 2.281447 7.696470 0.412275 C 1.948231 8.505730 -0.649941 C 2.960412 8.814386 -1.560851 C 4.244844 8.311873 -1.373715 C 4.539593 7.498288 -0.280778 C 3.540993 7.180234 0.636752 C -1.223239 7.405456 2.481181 C -2.076231 8.220445 1.771510 C -3.397929 8.309196 2.212965 C -3.811159 7.586474 3.328118 C -2.917476 6.767060 4.016007 C -1.595943 6.669657 3.587775 C 1.748530 5.904821 3.336269 C 2.393032 4.758683 2.909538 C 2.999135 3.939137 3.859919 C 2.950531 4.282849 5.207781 C 2.297133 5.442850 5.614485 C 1.686773 6.265204 4.669896 C -0.348674 5.593019 -0.281488 C -0.744713 4.399438 -1.197376 C 0.281626 3.281744 -1.075105 C 0.065977 2.212227 -0.203805 C 1.010335 1.199113 -0.084999 C 2.180538 1.242792 -0.834196 C 2.405205 2.308261 -1.698406 C 1.465153 3.326149 -1.816940 C -2.149051 3.910885 -0.850258 C -2.915718 3.276686 -1.831891 C -4.195307 2.819163 -1.539023 C -4.721658 2.982030 -0.262405 C -3.960195 3.601452 0.721740 C -2.680507 4.062402 0.431906 C 1.079347 9.977732 2.666208 C 1.488007 11.270714 3.429704 C 2.893607 11.126712 3.997147 C 3.990691 11.163352 3.130891 C 5.282547 11.035911 3.627816 C 5.494802 10.863814 4.991252 C 4.408072 10.818991 5.856392 C 3.114415 10.950072 5.363327 C 0.450131 11.569455 4.509824 C -0.141861 10.539979 5.246542 C -1.083808 10.826243 6.227942 C -1.442611 12.143287 6.491850 C -0.847033 13.174056 5.774584 C 0.096305 12.891218 4.792642 H -1.273301 5.601277 -2.604681 H 0.733322 12.361093 2.030880 H 0.927725 8.892593 -0.771645 H 2.738764 9.454191 -2.421454 H 5.033903 8.558475 -2.092244 H 5.553622 7.110117 -0.140613 H 3.745138 6.543027 1.507317 H -1.727548 8.774786 0.889846 H -4.107325 8.948050 1.676501 H -4.849275 7.660907 3.669365 H -3.251978 6.199331 4.890239 H -0.871220 6.030786 4.109956 H 2.412794 4.486760 1.846502 H 3.511489 3.024444 3.543884 H 3.429243 3.637834 5.952219 H 2.265068 5.712166 6.675274 H 1.184648 7.191460 4.978977 H -0.852967 2.173024 0.395201 H 0.828929 0.364946 0.600293 H 2.921201 0.441956 -0.744433 H 3.326081 2.348305 -2.289151 H 1.661218 4.160764 -2.500391 H -2.507225 3.131625 -2.839762 H -4.787806 2.326932 -2.317206 H -5.729904 2.622636 -0.033074 H -4.367272 3.729787 1.730029 H -2.093199 4.545990 1.223175 H 3.837339 11.296491 2.053454 H 6.134753 11.070904 2.941534 H 6.512688 10.763602 5.380914 H 4.568178 10.681485 6.930565 H 2.264728 10.910817 6.056774 H 0.137206 9.494368 5.059643 H -1.543730 10.009541 6.793770 H -2.187033 12.367035 7.262594 H -1.118185 14.214272 5.983175 H 0.566770 13.720313 4.249309 and then: ----------------------- VIBRATIONAL FREQUENCIES ----------------------- 0: 0.00 cm**-1 1: 0.00 cm**-1 2: 0.00 cm**-1 3: 0.00 cm**-1 4: 0.00 cm**-1 5: 0.00 cm**-1 6: 8.05 cm**-1 7: 9.46 cm**-1 8: 9.76 cm**-1 9: 11.65 cm**-1 10: 15.40 cm**-1 11: 18.77 cm**-1 12: 20.71 cm**-1 13: 32.32 cm**-1 14: 32.62 cm**-1 15: 37.00 cm**-1 16: 38.10 cm**-1 17: 38.96 cm**-1 18: 43.78 cm**-1 19: 47.29 cm**-1 20: 54.82 cm**-1 21: 57.04 cm**-1 22: 63.89 cm**-1 23: 64.72 cm**-1 24: 73.60 cm**-1 25: 81.46 cm**-1 26: 89.17 cm**-1 27: 95.58 cm**-1 28: 123.49 cm**-1 29: 125.99 cm**-1 30: 140.30 cm**-1 31: 147.68 cm**-1 32: 154.20 cm**-1 33: 159.46 cm**-1 34: 167.05 cm**-1 35: 180.26 cm**-1 36: 188.90 cm**-1 37: 196.41 cm**-1 38: 203.28 cm**-1 39: 211.26 cm**-1 40: 213.93 cm**-1 41: 217.42 cm**-1 42: 223.36 cm**-1 43: 224.60 cm**-1 44: 235.33 cm**-1 45: 252.13 cm**-1 46: 262.98 cm**-1 47: 291.72 cm**-1 48: 292.85 cm**-1 49: 293.57 cm**-1 50: 310.82 cm**-1 51: 316.93 cm**-1 52: 319.29 cm**-1 53: 342.84 cm**-1 54: 345.66 cm**-1 55: 355.94 cm**-1 56: 356.76 cm**-1 57: 357.40 cm**-1 58: 357.86 cm**-1 59: 359.95 cm**-1 60: 362.70 cm**-1 61: 370.74 cm**-1 62: 372.07 cm**-1 63: 378.09 cm**-1 64: 380.84 cm**-1 65: 385.22 cm**-1 66: 431.34 cm**-1 67: 433.07 cm**-1 68: 434.26 cm**-1 69: 438.97 cm**-1 70: 441.09 cm**-1 71: 489.14 cm**-1 72: 495.18 cm**-1 73: 512.06 cm**-1 74: 516.52 cm**-1 75: 560.79 cm**-1 76: 566.88 cm**-1 77: 619.57 cm**-1 78: 620.56 cm**-1 79: 621.57 cm**-1 80: 622.38 cm**-1 81: 625.38 cm**-1 82: 628.25 cm**-1 83: 629.48 cm**-1 84: 629.59 cm**-1 85: 629.82 cm**-1 86: 630.20 cm**-1 87: 631.44 cm**-1 88: 641.86 cm**-1 89: 644.33 cm**-1 90: 645.20 cm**-1 91: 662.86 cm**-1 92: 664.28 cm**-1 93: 665.11 cm**-1 94: 668.24 cm**-1 95: 678.70 cm**-1 96: 693.11 cm**-1 97: 695.37 cm**-1 98: 721.06 cm**-1 99: 722.25 cm**-1 100: 760.94 cm**-1 101: 762.71 cm**-1 102: 763.54 cm**-1 103: 775.47 cm**-1 104: 775.69 cm**-1 105: 778.29 cm**-1 106: 779.89 cm**-1 107: 789.37 cm**-1 108: 791.70 cm**-1 109: 840.99 cm**-1 110: 843.94 cm**-1 111: 846.53 cm**-1 112: 847.12 cm**-1 113: 848.24 cm**-1 114: 849.35 cm**-1 115: 852.24 cm**-1 116: 927.30 cm**-1 117: 927.57 cm**-1 118: 929.10 cm**-1 119: 933.82 cm**-1 120: 936.26 cm**-1 121: 937.03 cm**-1 122: 937.66 cm**-1 123: 954.83 cm**-1 124: 955.02 cm**-1 125: 958.68 cm**-1 126: 967.22 cm**-1 127: 976.47 cm**-1 128: 976.75 cm**-1 129: 977.05 cm**-1 130: 977.82 cm**-1 131: 978.11 cm**-1 132: 981.47 cm**-1 133: 982.40 cm**-1 134: 987.04 cm**-1 135: 994.67 cm**-1 136: 995.02 cm**-1 137: 1015.44 cm**-1 138: 1015.73 cm**-1 139: 1017.05 cm**-1 140: 1017.10 cm**-1 141: 1017.37 cm**-1 142: 1018.45 cm**-1 143: 1018.86 cm**-1 144: 1055.60 cm**-1 145: 1055.84 cm**-1 146: 1060.44 cm**-1 147: 1062.08 cm**-1 148: 1062.67 cm**-1 149: 1064.00 cm**-1 150: 1075.47 cm**-1 151: 1093.59 cm**-1 152: 1095.01 cm**-1 153: 1102.32 cm**-1 154: 1108.18 cm**-1 155: 1109.49 cm**-1 156: 1110.45 cm**-1 157: 1111.25 cm**-1 158: 1121.16 cm**-1 159: 1123.42 cm**-1 160: 1138.38 cm**-1 161: 1139.59 cm**-1 162: 1140.27 cm**-1 163: 1141.00 cm**-1 164: 1148.82 cm**-1 165: 1149.30 cm**-1 166: 1151.20 cm**-1 167: 1152.86 cm**-1 168: 1153.80 cm**-1 169: 1154.11 cm**-1 170: 1155.42 cm**-1 171: 1155.73 cm**-1 172: 1173.27 cm**-1 173: 1174.39 cm**-1 174: 1175.47 cm**-1 175: 1176.59 cm**-1 176: 1201.91 cm**-1 177: 1202.49 cm**-1 178: 1211.60 cm**-1 179: 1229.70 cm**-1 180: 1231.06 cm**-1 181: 1233.61 cm**-1 182: 1233.68 cm**-1 183: 1247.48 cm**-1 184: 1248.46 cm**-1 185: 1252.57 cm**-1 186: 1253.41 cm**-1 187: 1257.78 cm**-1 188: 1301.68 cm**-1 189: 1303.92 cm**-1 190: 1306.79 cm**-1 191: 1306.80 cm**-1 192: 1309.95 cm**-1 193: 1311.18 cm**-1 194: 1311.75 cm**-1 195: 1314.35 cm**-1 196: 1316.65 cm**-1 197: 1336.36 cm**-1 198: 1337.05 cm**-1 199: 1418.01 cm**-1 200: 1420.39 cm**-1 201: 1531.63 cm**-1 202: 1533.45 cm**-1 203: 1534.61 cm**-1 204: 1537.14 cm**-1 205: 1537.89 cm**-1 206: 1538.36 cm**-1 207: 1540.69 cm**-1 208: 1541.07 cm**-1 209: 1541.37 cm**-1 210: 1548.38 cm**-1 211: 1558.82 cm**-1 212: 1572.10 cm**-1 213: 1583.87 cm**-1 214: 1584.57 cm**-1 215: 1589.89 cm**-1 216: 1590.06 cm**-1 217: 1747.14 cm**-1 218: 1751.50 cm**-1 219: 1763.81 cm**-1 220: 1777.00 cm**-1 221: 1777.98 cm**-1 222: 1778.77 cm**-1 223: 1778.94 cm**-1 224: 1794.74 cm**-1 225: 1795.17 cm**-1 226: 1795.32 cm**-1 227: 1796.85 cm**-1 228: 1797.14 cm**-1 229: 1800.62 cm**-1 230: 1802.63 cm**-1 231: 1833.75 cm**-1 232: 1839.95 cm**-1 233: 3029.38 cm**-1 234: 3031.92 cm**-1 235: 3032.12 cm**-1 236: 3035.16 cm**-1 237: 3035.28 cm**-1 238: 3036.43 cm**-1 239: 3036.93 cm**-1 240: 3037.61 cm**-1 241: 3039.11 cm**-1 242: 3041.64 cm**-1 243: 3042.26 cm**-1 244: 3044.55 cm**-1 245: 3049.63 cm**-1 246: 3050.15 cm**-1 247: 3054.89 cm**-1 248: 3055.03 cm**-1 249: 3055.71 cm**-1 250: 3058.12 cm**-1 251: 3058.23 cm**-1 252: 3059.42 cm**-1 253: 3059.57 cm**-1 254: 3065.39 cm**-1 255: 3065.68 cm**-1 256: 3066.44 cm**-1 257: 3066.62 cm**-1 258: 3066.77 cm**-1 259: 3067.06 cm**-1 260: 3067.29 cm**-1 261: 3076.43 cm**-1 262: 3076.62 cm**-1 263: 3076.87 cm**-1 264: 3078.57 cm**-1 265: 3078.61 cm**-1 266: 3079.63 cm**-1 267: 3079.81 cm**-1 268: 3877.28 cm**-1 269: 3880.37 cm**-1 ----------- IR SPECTRUM ----------- Mode freq (cm**-1) T**2 TX TY TZ ------------------------------------------------------------------- 15: 37.00 34.408379 ( 1.542075 -5.631600 0.561660) 16: 38.10 175.455502 ( 1.998590 -6.118373 11.576988) 17: 38.96 312.658922 ( 5.743729 -14.767931 7.847084) 18: 43.78 92.080053 ( -7.917766 1.963509 -5.053084) 19: 47.29 399.073719 ( 10.549013 4.661375 -16.311457) 20: 54.82 263.656849 ( -6.106697 -0.491829 -15.037394) 21: 57.04 1007.924553 ( 2.171118 -30.479617 8.614161) 22: 63.89 866.348952 (-12.938448 -20.623195 -16.541746) 23: 64.72 866.166292 ( 8.889036 13.280696 24.713851) 24: 73.60 478.892280 ( 18.165891 -10.961550 -5.360702) 25: 81.46 148.888111 ( 3.215816 -2.148073 11.572918) 26: 89.17 157.032908 ( 2.367409 -12.038223 -2.551367) 27: 95.58 109.843954 ( 4.656209 -9.099596 -2.315388) 28: 123.49 48.498781 ( -5.699887 1.324332 3.775740) 29: 125.99 31.499855 ( 2.585565 -1.154508 4.845804) 30: 140.30 56.177705 ( -4.648882 3.659596 4.601408) 31: 147.68 29.860567 ( 1.419144 5.248579 -0.546820) 32: 154.20 25.511272 ( 0.915673 4.868550 -0.984905) 33: 159.46 42.187235 ( -4.106377 -0.733562 -4.978634) 34: 167.05 40.542784 ( -2.836866 -5.193173 -2.350729) 35: 180.26 0.203118 ( -0.145653 0.157241 -0.396458) 36: 188.90 67.527610 ( 7.525126 -0.422600 -3.274371) 37: 196.41 477.922878 (-15.119570 -14.067450 -7.171355) 38: 203.28 27.878390 ( 2.638754 -2.766531 3.641658) 39: 211.26 90.667691 ( 8.061119 -4.979842 0.941932) 40: 213.93 124.399922 ( -0.871438 10.263173 4.278761) 41: 217.42 24.929366 ( 4.570325 1.853030 0.779601) 42: 223.36 1053.759670 ( -5.941580 -25.127652 -19.673800) 43: 224.60 74.327909 ( 3.241681 7.584657 -2.508464) 44: 235.33 145.236323 ( 4.611346 10.115494 4.652805) 45: 252.13 114.552027 ( 9.898910 -4.067785 -0.129344) 46: 262.98 303.426580 ( 4.341933 14.308494 8.935390) 47: 291.72 201.583196 ( -4.494205 12.987939 3.563532) 48: 292.85 593.989799 ( 16.524931 -0.875257 17.892747) 49: 293.57 1605.261943 ( 14.147463 -27.245241 25.745059) 50: 310.82 2083.932822 ( 36.227422 4.990217 -27.324063) 51: 316.93 179.620473 ( 13.206297 2.034882 1.036075) 52: 319.29 124.491562 ( -7.510575 8.172325 1.138389) 53: 342.84 58.378048 ( -7.270860 -2.203428 -0.810897) 54: 345.66 95.277912 ( 5.608593 -5.922428 -5.361571) 55: 355.94 3.116651 ( 1.028414 1.308507 0.588919) 56: 356.76 6.885943 ( -1.545566 1.968191 0.789552) 57: 357.40 5.448810 ( -1.749417 1.418252 0.613932) 58: 357.86 3.756003 ( -1.824992 -0.649023 0.064616) 59: 359.95 0.620830 ( -0.720928 0.144884 0.283022) 60: 362.70 22.979907 ( 0.966135 3.961468 2.520568) 61: 370.74 8.080053 ( -1.810262 1.155637 -1.862124) 62: 372.07 195.169295 ( 8.818802 5.625020 9.260517) 63: 378.09 139.465822 ( 8.291079 -2.203304 8.115989) 64: 380.84 246.577722 ( -1.452396 14.681788 5.377114) 65: 385.22 201.095472 ( -0.815558 13.024388 5.549383) 66: 431.34 167.375081 ( -4.149541 2.829806 -11.922608) 67: 433.07 41.814643 ( -0.322825 1.671966 -6.238185) 68: 434.26 115.990776 ( -1.664327 -10.640349 -0.061273) 69: 438.97 58.161684 ( 2.322002 6.864751 2.375959) 70: 441.09 2.386149 ( 0.266877 1.284166 0.815993) 71: 489.14 13.411251 ( -3.532766 0.345668 0.900740) 72: 495.18 8.015699 ( -2.686396 0.877624 0.169564) 73: 512.06 8.532850 ( -2.484788 -0.536039 1.439216) 74: 516.52 76.847690 ( -3.014481 -6.934855 -4.434904) 75: 560.79 321.970654 ( 6.836066 9.943002 13.280646) 76: 566.88 376.049906 ( 2.830909 18.035246 6.539553) 77: 619.57 42.380957 ( 1.967375 5.531192 2.813593) 78: 620.56 55.423943 ( -2.281746 3.220598 -6.312315) 79: 621.57 1.715538 ( 0.905855 -0.126527 -0.937526) 80: 622.38 5.050731 ( 1.374030 -0.708162 1.631343) 81: 625.38 1.110408 ( 0.174013 -0.949098 -0.423486) 82: 628.25 64.298573 ( -1.914960 -6.871123 -3.663218) 83: 629.48 2.866883 ( 0.480309 -1.137029 1.159030) 84: 629.59 27.440137 ( 1.824967 4.077054 2.736286) 85: 629.82 28.440842 ( 1.904046 3.867994 3.139119) 86: 630.20 3.504577 ( -0.648335 0.846660 -1.538638) 87: 631.44 78.891285 ( 3.116649 6.861643 4.700600) 88: 641.86 209.993887 ( 10.876440 9.549451 0.710576) 89: 644.33 203.580376 ( -5.109662 -12.103600 -5.565483) 90: 645.20 495.310539 ( 3.729295 16.906871 13.984298) 91: 662.86 478.120022 (-20.435006 7.776552 -0.236173) 92: 664.28 188.978817 ( 5.831926 5.945700 -10.936915) 93: 665.11 119.509335 ( 10.270210 -3.169899 -1.995961) 94: 668.24 166.990459 ( -1.023312 -7.908473 10.168547) 95: 678.70 67.180385 ( -4.115071 4.941391 -5.082246) 96: 693.11 124.038626 ( 2.462683 5.805990 9.179559) 97: 695.37 84.751006 ( 4.096259 -7.930908 2.252193) 98: 721.06 138.804006 ( -0.789379 -5.948242 -10.138999) 99: 722.25 95.098302 ( -6.217500 -7.424027 1.151010) 100: 760.94 1658.600514 ( 27.698139 28.817230 7.809025) 101: 762.71 7.455904 ( 1.245052 1.313075 -2.044892) 102: 763.54 479.425222 ( 3.934373 -14.345554 -16.067078) 103: 775.47 2290.471511 ( 23.423101 33.084582 25.440918) 104: 775.69 3204.970527 ( 6.340944 48.747351 28.079508) 105: 778.29 1985.039021 (-20.562412 -21.248082 -33.327845) 106: 779.89 1696.565574 ( 0.778007 40.464403 7.654566) 107: 789.37 1713.220799 ( 3.352934 -41.248427 -0.738852) 108: 791.70 3915.896385 ( 19.063566 40.802177 43.447200) 109: 840.99 0.946914 ( 0.864643 -0.405961 0.185745) 110: 843.94 3.612986 ( 0.951061 -0.532026 -1.557375) 111: 846.53 1.199886 ( -0.425124 -0.805203 0.608936) 112: 847.12 3.314705 ( -0.381309 0.980269 1.486062) 113: 848.24 0.428504 ( 0.160480 -0.460738 -0.436429) 114: 849.35 3.122167 ( -0.608395 -1.578140 -0.511369) 115: 852.24 2.473556 ( -1.072954 1.031008 -0.509262) 116: 927.30 133.322435 ( -9.335549 6.046610 -3.099754) 117: 927.57 177.848073 (-11.513951 4.364485 -5.121356) 118: 929.10 114.195727 ( 7.527835 7.570884 0.457314) 119: 933.82 1.883536 ( -1.063235 0.698914 -0.514380) 120: 936.26 30.580220 ( 0.918859 5.036833 2.089554) 121: 937.03 69.299212 ( 3.869820 -6.158626 -4.049078) 122: 937.66 160.811359 ( -8.588181 2.276927 9.048210) 123: 954.83 47.684488 ( -6.536887 2.057179 -0.849473) 124: 955.02 0.393047 ( -0.562628 0.198231 0.192877) 125: 958.68 1044.845324 (-25.946404 -5.182852 18.567915) 126: 967.22 305.335162 ( 10.754732 -10.116204 9.345230) 127: 976.47 74.988724 ( 4.005379 -6.399967 4.241001) 128: 976.75 16.787400 ( -2.050215 -0.095059 -3.546122) 129: 977.05 11.485602 ( -1.056410 -2.973568 -1.235918) 130: 977.82 4.785830 ( -1.084694 0.351431 -1.867020) 131: 978.11 5.790231 ( -0.469446 2.339386 -0.311648) 132: 981.47 106.356752 ( -5.357645 6.215251 -6.246843) 133: 982.40 10.105590 ( -0.259864 3.023417 -0.947107) 134: 987.04 40.587235 ( 2.887508 -4.219905 3.800254) 135: 994.67 1221.562820 ( 4.223159 34.488366 3.778939) 136: 995.02 4008.190018 ( 19.126576 45.509073 39.639480) 137: 1015.44 400.700336 ( -8.329900 -11.571447 -14.050435) 138: 1015.73 133.804897 ( -0.610424 11.327854 2.260975) 139: 1017.05 1073.880929 ( 9.880853 28.478733 12.853459) 140: 1017.10 720.947196 ( 6.052145 19.774548 17.125595) 141: 1017.37 72.590938 ( 0.765414 7.053956 4.716650) 142: 1018.45 0.193888 ( 0.141900 0.343903 0.235549) 143: 1018.86 31.807432 ( 2.493224 -3.291146 -3.841825) 144: 1055.60 730.583088 ( -3.034285 -24.992774 -9.835519) 145: 1055.84 974.559943 ( -8.185165 -21.149706 -21.453506) 146: 1060.44 1831.051685 (-25.347689 -14.389913 31.328529) 147: 1062.08 1531.715787 (-35.735831 12.165867 10.327530) 148: 1062.67 692.559485 (-22.661222 -12.531573 -4.689157) 149: 1064.00 445.364662 ( -2.260705 -15.712208 -13.906128) 150: 1075.47 1746.088387 (-18.634712 25.295463 -27.549509) 151: 1093.59 517.317115 (-21.366955 3.648132 -6.889229) 152: 1095.01 1042.663702 ( -7.226758 22.419582 -22.086195) 153: 1102.32 1094.003437 ( 11.543752 -18.168429 -25.112814) 154: 1108.18 7630.725647 (-19.356775 -62.747689 -57.608753) 155: 1109.49 5384.862726 ( 28.282167 65.353392 17.717672) 156: 1110.45 2564.339171 ( 39.672619 30.816702 -6.383836) 157: 1111.25 4368.650424 (-18.695233 39.639499 49.475740) 158: 1121.16 13463.584687 (-50.408639 -73.268458 -74.527088) 159: 1123.42 12967.146653 ( 4.207022 105.378051 42.952463) 160: 1138.38 430.792961 ( 16.543346 -7.668671 9.914744) 161: 1139.59 1165.886239 ( 33.958938 -3.431213 -0.950545) 162: 1140.27 6795.945270 (-78.590599 -19.624148 -15.308685) 163: 1141.00 10276.064226 ( 91.425555 -30.981955 -30.944315) 164: 1148.82 0.665706 ( 0.216797 0.599310 -0.509443) 165: 1149.30 0.496104 ( 0.661250 0.213639 0.114938) 166: 1151.20 1.740496 ( 0.218602 -0.126595 1.294868) 167: 1152.86 11.508995 ( -1.719282 2.416761 -1.646915) 168: 1153.80 56.156598 ( 0.878106 6.526155 -3.576986) 169: 1154.11 53.996483 ( 3.821161 -3.347450 5.309406) 170: 1155.42 519.700532 ( 19.960527 9.491967 5.583946) 171: 1155.73 460.818920 (-14.929995 10.110009 11.649115) 172: 1173.27 173.339242 ( 10.202246 5.323171 6.396661) 173: 1174.39 188.009742 ( -8.048520 10.457369 3.724849) 174: 1175.47 89.996967 ( 7.195046 2.308712 -5.735690) 175: 1176.59 64.626335 ( 4.259265 5.730367 -3.694306) 176: 1201.91 34.301979 ( 0.983020 -2.320891 5.286692) 177: 1202.49 73.065622 ( -4.826695 5.756393 -4.078306) 178: 1211.60 55.138347 ( -0.632830 5.584649 4.852790) 179: 1229.70 760.409758 (-10.317964 -24.645699 -6.821942) 180: 1231.06 921.517460 ( 0.723888 18.325599 24.190202) 181: 1233.61 50.862396 ( -2.281777 -4.781095 -4.774623) 182: 1233.68 124.607264 ( 2.135451 10.280250 3.789929) 183: 1247.48 7292.741389 (-11.128470 -60.028621 -59.711499) 184: 1248.46 5460.641470 ( 31.173239 63.972201 19.910503) 185: 1252.57 2869.390117 ( 13.182961 25.839532 -45.032413) 186: 1253.41 29859.454861 (-151.270437 -9.847377 82.944192) 187: 1257.78 19530.970303 ( 65.809474 -82.002046 92.063825) 188: 1301.68 8667.496868 (-58.229951 -58.507842 -43.053479) 189: 1303.92 4898.436530 ( 19.902370 -59.868319 -30.300438) 190: 1306.79 789.057064 (-18.208071 -16.704113 -13.360234) 191: 1306.80 291.760490 ( -3.595120 -15.124110 -7.077916) 192: 1309.95 393.994008 (-17.920491 -4.063279 7.505982) 193: 1311.18 19.455362 ( 0.077865 0.103735 -4.408916) 194: 1311.75 355.716875 (-14.398948 3.215171 11.749462) 195: 1314.35 14297.839582 (-23.226722 102.468026 57.084697) 196: 1316.65 13823.230503 ( 74.214674 73.954271 53.349587) 197: 1336.36 27244.814905 (-24.895395 129.734895 98.964091) 198: 1337.05 26389.761622 (-108.477427 -102.105583 -64.783172) 199: 1418.01 3419.311868 ( 43.382212 33.727674 19.993489) 200: 1420.39 2760.173708 (-27.045582 39.695346 21.283556) 201: 1531.63 1573.137166 (-11.617556 25.785638 27.807740) 202: 1533.45 1305.426855 ( -4.991806 -22.924724 27.476640) 203: 1534.61 942.036216 (-24.732630 10.600386 -14.763639) 204: 1537.14 1399.997940 (-36.043288 4.983960 8.720061) 205: 1537.89 1293.741634 ( 2.107720 -33.415702 -13.141158) 206: 1538.36 709.539892 ( 11.215133 11.985903 20.978532) 207: 1540.69 1081.242188 ( 7.718530 -19.877595 25.030935) 208: 1541.07 873.301642 ( -9.556109 -11.304451 25.577174) 209: 1541.37 2102.566472 ( 22.610006 13.888881 -37.395897) 210: 1548.38 543.136094 ( 10.348775 -12.714161 16.564693) 211: 1558.82 1062.974097 (-11.406682 -25.936904 -16.128816) 212: 1572.10 5.483480 ( -1.537950 1.161790 1.329824) 213: 1583.87 417.956727 ( 6.804851 -11.112978 -15.752855) 214: 1584.57 412.838361 (-16.392527 -11.945776 -1.192415) 215: 1589.89 307.452279 ( 12.491944 -12.303903 0.132569) 216: 1590.06 579.046383 (-23.567464 3.888577 -2.915474) 217: 1747.14 162.604718 ( 10.595207 1.748062 -6.876815) 218: 1751.50 25.674498 ( 4.500584 -2.015829 1.164336) 219: 1763.81 13.102342 ( 1.809836 -2.049759 2.371777) 220: 1777.00 0.454657 ( 0.360689 0.447523 0.352539) 221: 1777.98 1.037754 ( 0.161662 0.633809 0.780965) 222: 1778.77 0.716321 ( 0.355193 0.309896 -0.702939) 223: 1778.94 0.906620 ( -0.332806 -0.593563 0.665991) 224: 1794.74 4.514409 ( -1.888273 -0.834727 0.502059) 225: 1795.17 14.618488 ( 2.280084 1.881472 2.424824) 226: 1795.32 28.376446 ( 0.429287 -4.904904 -2.033243) 227: 1796.85 278.423617 ( -4.787761 -10.328042 -12.199693) 228: 1797.14 236.753125 ( 3.196655 14.510355 3.998014) 229: 1800.62 24.398204 ( 2.109719 2.140590 -3.919843) 230: 1802.63 92.710272 ( -5.229949 5.636442 -5.795552) 231: 1833.75 822.302581 ( -7.381220 -22.486095 -16.192459) 232: 1839.95 1078.662495 ( 11.358722 -20.774872 22.760637) 233: 3029.38 5285.643150 (-18.849264 -23.790853 66.063180) 234: 3031.92 5268.733120 (-60.952901 39.410871 0.510165) 235: 3032.12 7376.394470 (-10.904597 -47.263446 -70.877718) 236: 3035.16 483.385713 ( -2.873888 -14.093323 -16.628432) 237: 3035.28 12453.415946 (-58.601387 -91.487527 -25.481874) 238: 3036.43 3457.925754 ( -5.226858 -54.042958 -22.582391) 239: 3036.93 11939.597871 (-17.216064 -76.151206 -76.447360) 240: 3037.61 2546.155527 ( 45.904356 -14.047957 15.543504) 241: 3039.11 3189.792223 ( 7.678753 27.720211 -48.604721) 242: 3041.64 1743.230219 (-20.814752 35.466834 -7.216646) 243: 3042.26 16505.407714 ( 5.770049 122.604892 37.949372) 244: 3044.55 15280.955254 ( 47.473837 72.680106 88.004501) 245: 3049.63 6175.674022 ( 1.506646 41.184799 66.912005) 246: 3050.15 5300.255436 (-31.486712 -65.575452 -2.949998) 247: 3054.89 465.864068 (-18.786460 -1.305965 10.546442) 248: 3055.03 313.141213 (-14.421186 -2.483982 9.949896) 249: 3055.71 90.292230 ( 1.891447 -2.841783 8.867859) 250: 3058.12 7633.264037 ( -1.565395 -77.181970 -40.911577) 251: 3058.23 6563.679207 (-40.605962 -52.122397 -46.883800) 252: 3059.42 6582.778899 (-11.145158 -60.003512 -53.461602) 253: 3059.57 6302.030395 (-28.793583 -66.754375 -31.887511) 254: 3065.39 11127.836339 ( 10.173441 104.996816 0.077917) 255: 3065.68 9567.018252 ( -9.214434 -32.536466 -91.779577) 256: 3066.44 9321.404211 (-31.807394 66.179356 62.689606) 257: 3066.62 2518.471445 (-21.325998 34.603217 -29.432816) 258: 3066.77 17750.336945 (-60.619452 76.814746 -90.416335) 259: 3067.06 9616.743508 ( 49.888231 42.311922 -73.058944) 260: 3067.29 11825.963357 ( 39.484785 16.376916 -99.993559) 261: 3076.43 132975.475875 (309.018455 36.738617 -190.087728) 262: 3076.62 20807.950750 (-80.037186 80.902030 -88.638937) 263: 3076.87 64129.781414 (110.716360 -149.817923 171.540837) 264: 3078.57 185170.358244 ( 36.017930 -329.989570 -273.824671) 265: 3078.61 131696.491194 (334.361765 133.794964 44.694614) 266: 3079.63 171210.952838 (-43.981904 367.260888 185.461545) 267: 3079.81 143063.780489 (-275.504254 -197.383880 -167.930910) 268: 3877.28 20984.680613 (-12.574462 -144.029017 -9.066742) 269: 3880.37 20810.853553 ( 46.707968 52.339284 126.054824) Hope that helps, best regards, Frank From owner-chemistry@ccl.net Thu Mar 22 06:40:00 2007 From: "Herbert Fruchtl herbert.fruchtl^_^st-andrews.ac.uk" To: CCL Subject: CCL: vibrational spectra Message-Id: <-33873-070322062442-22696-NoVL6820ztFLVAa9994j6w:-:server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 22 Mar 2007 09:55:02 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl ~~ st-andrews.ac.uk] A frequency calculation is fairly heavy on memory. Have a look in the output if there is something about "memory required" and "memory available" (the actual message may vary between MOPAC versions). Increase it with the MEMORY keyword. HTH, Herbert neeraj misra misraneeraj]^[gmail.com wrote: > Sent to CCL by: "neeraj misra" [misraneeraj%x%gmail.com] > I have been trying to calculate the vibrational spectra of a 90 atom molecule by semi empirical PM3 but no success so far .The structure gets optimized but fails to run for the frequency calculations.Please can anyone help me in this.I am attaching the input file of the molecule. > > > > > 90 > Sb 1.05300 7.25300 1.82800 > O 0.35200 5.48400 0.83900 > O -0.53400 6.88100 -0.65400 > O -1.16600 4.93500 -2.33900 > O 1.62800 8.87000 3.04200 > O 0.86700 10.24900 1.46600 > O 1.98300 12.35200 2.77000 > C 2.35700 7.63000 0.22500 > C 2.01900 8.43400 -0.85500 > C 2.87200 8.48700 -1.94300 > C 4.05000 7.76000 -1.94500 > C 4.38200 6.98100 -0.85900 > C 3.53400 6.90200 0.22100 > C -0.96200 7.60000 2.34700 > C -1.83900 8.33600 1.56800 > C -3.17800 8.34700 1.91000 > C -3.63500 7.65500 3.01700 > C -2.74900 6.96600 3.81800 > C -1.41200 6.93300 3.48700 > C 2.10200 5.99100 3.15400 > C 2.23800 4.63600 2.85400 > C 3.05600 3.83600 3.63500 > C 3.73600 4.35700 4.70400 > C 3.60200 5.69600 5.00500 > C 2.78800 6.51600 4.24200 > C -0.32200 5.74500 -0.24100 > C -0.88900 4.52700 -0.99200 > C 0.20300 3.45600 -1.06300 > C 0.16300 2.32000 -0.27100 > C 1.21800 1.40200 -0.32800 > C 2.28700 1.61900 -1.14700 > C 2.33700 2.75900 -1.91700 > C 1.29500 3.66700 -1.87600 > C -2.18600 4.06900 -0.33400 > C -2.94000 3.09700 -0.99400 > C -4.18800 2.73100 -0.51900 > C -4.69600 3.32800 0.61900 > C -3.95100 4.25300 1.29800 > C -2.71100 4.62900 0.81900 > C 1.33400 10.05700 2.57400 > C 1.57600 11.23200 3.55200 > C 2.71200 10.91700 4.51300 > C 3.95100 10.54700 3.98200 > C 5.00400 10.22200 4.81400 > C 4.84000 10.25700 6.18800 > C 3.63000 10.63500 6.72600 > C 2.57000 10.97100 5.89000 > C 0.25800 11.49900 4.28600 > C -0.47700 10.45400 4.82400 > C -1.62300 10.70100 5.56000 > C -2.05600 11.99200 5.75400 > C -1.33700 13.03800 5.22400 > C -0.18200 12.79700 4.49300 > H -1.70400 5.55500 -2.33300 > H 1.38800 12.54600 2.24000 > H 1.23200 8.93000 -0.84700 > H 2.65400 9.01300 -2.67900 > H 4.61800 7.79900 -2.68000 > H 5.18300 6.50700 -0.85600 > H 3.75100 6.36100 0.94500 > H -1.53400 8.81300 0.83000 > H -3.78000 8.82800 1.38800 > H -4.54300 7.65400 3.22100 > H -3.05300 6.52600 4.57800 > H -0.81000 6.46700 4.02200 > H 1.78000 4.26900 2.13200 > H 3.14400 2.93200 3.43100 > H 4.28500 3.81400 5.22200 > H 4.06300 6.05200 5.72900 > H 2.70100 7.41600 4.45800 > H -0.56100 2.16900 0.29500 > H 1.19000 0.63700 0.19800 > H 2.98000 1.00000 -1.18500 > H 3.07000 2.91800 -2.46700 > H 1.33100 4.43200 -2.40400 > H -2.60000 2.69200 -1.75900 > H -4.68300 2.08300 -0.96700 > H -5.54500 3.10000 0.92300 > H -4.28000 4.62800 2.08300 > H -2.21900 5.27100 1.28000 > H 4.06700 10.51900 3.05900 > H 5.82400 9.97900 4.45000 > H 5.54700 10.02500 6.74600 > H 3.52200 10.66600 7.65000 > H 1.75900 11.23600 6.25800 > H -0.19800 9.57900 4.68900 > H -2.10100 9.99300 5.92300 > H -2.83100 12.15600 6.24000 > H -1.62700 13.91300 5.35700 > H 0.29900 13.51100 4.14100> > > -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews From owner-chemistry@ccl.net Thu Mar 22 07:25:02 2007 From: "neeraj misra neerajmisra*_*hotmail.com" To: CCL Subject: CCL: vibrational spectra Message-Id: <-33874-070321224732-13387-1SMmjSR6vkaPLadYLEu52Q(a)server.ccl.net> X-Original-From: "neeraj misra" Date: Wed, 21 Mar 2007 22:47:29 -0400 Sent to CCL by: "neeraj misra" [neerajmisra]![hotmail.com] I am unable to find the reason as to why vibrational spectra of a molecule cannot be calculated inspite of the structure being optimized.I am enclosing the input coordinates of the molecule (90 atoms).I have been employing semi empirical methods using PM3.But no success so far. Any help?? 90 Sb 1.05300 7.25300 1.82800 O 0.35200 5.48400 0.83900 O -0.53400 6.88100 -0.65400 O -1.16600 4.93500 -2.33900 O 1.62800 8.87000 3.04200 O 0.86700 10.24900 1.46600 O 1.98300 12.35200 2.77000 C 2.35700 7.63000 0.22500 C 2.01900 8.43400 -0.85500 C 2.87200 8.48700 -1.94300 C 4.05000 7.76000 -1.94500 C 4.38200 6.98100 -0.85900 C 3.53400 6.90200 0.22100 C -0.96200 7.60000 2.34700 C -1.83900 8.33600 1.56800 C -3.17800 8.34700 1.91000 C -3.63500 7.65500 3.01700 C -2.74900 6.96600 3.81800 C -1.41200 6.93300 3.48700 C 2.10200 5.99100 3.15400 C 2.23800 4.63600 2.85400 C 3.05600 3.83600 3.63500 C 3.73600 4.35700 4.70400 C 3.60200 5.69600 5.00500 C 2.78800 6.51600 4.24200 C -0.32200 5.74500 -0.24100 C -0.88900 4.52700 -0.99200 C 0.20300 3.45600 -1.06300 C 0.16300 2.32000 -0.27100 C 1.21800 1.40200 -0.32800 C 2.28700 1.61900 -1.14700 C 2.33700 2.75900 -1.91700 C 1.29500 3.66700 -1.87600 C -2.18600 4.06900 -0.33400 C -2.94000 3.09700 -0.99400 C -4.18800 2.73100 -0.51900 C -4.69600 3.32800 0.61900 C -3.95100 4.25300 1.29800 C -2.71100 4.62900 0.81900 C 1.33400 10.05700 2.57400 C 1.57600 11.23200 3.55200 C 2.71200 10.91700 4.51300 C 3.95100 10.54700 3.98200 C 5.00400 10.22200 4.81400 C 4.84000 10.25700 6.18800 C 3.63000 10.63500 6.72600 C 2.57000 10.97100 5.89000 C 0.25800 11.49900 4.28600 C -0.47700 10.45400 4.82400 C -1.62300 10.70100 5.56000 C -2.05600 11.99200 5.75400 C -1.33700 13.03800 5.22400 C -0.18200 12.79700 4.49300 H -1.70400 5.55500 -2.33300 H 1.38800 12.54600 2.24000 H 1.23200 8.93000 -0.84700 H 2.65400 9.01300 -2.67900 H 4.61800 7.79900 -2.68000 H 5.18300 6.50700 -0.85600 H 3.75100 6.36100 0.94500 H -1.53400 8.81300 0.83000 H -3.78000 8.82800 1.38800 H -4.54300 7.65400 3.22100 H -3.05300 6.52600 4.57800 H -0.81000 6.46700 4.02200 H 1.78000 4.26900 2.13200 H 3.14400 2.93200 3.43100 H 4.28500 3.81400 5.22200 H 4.06300 6.05200 5.72900 H 2.70100 7.41600 4.45800 H -0.56100 2.16900 0.29500 H 1.19000 0.63700 0.19800 H 2.98000 1.00000 -1.18500 H 3.07000 2.91800 -2.46700 H 1.33100 4.43200 -2.40400 H -2.60000 2.69200 -1.75900 H -4.68300 2.08300 -0.96700 H -5.54500 3.10000 0.92300 H -4.28000 4.62800 2.08300 H -2.21900 5.27100 1.28000 H 4.06700 10.51900 3.05900 H 5.82400 9.97900 4.45000 H 5.54700 10.02500 6.74600 H 3.52200 10.66600 7.65000 H 1.75900 11.23600 6.25800 H -0.19800 9.57900 4.68900 H -2.10100 9.99300 5.92300 H -2.83100 12.15600 6.24000 H -1.62700 13.91300 5.35700 H 0.29900 13.51100 4.14100 From owner-chemistry@ccl.net Thu Mar 22 08:18:01 2007 From: "Jin Zhao jiz38^unixs1.cis.pitt.edu" To: CCL Subject: CCL: code for solving a 3d schrodinger equation Message-Id: <-33875-070322062442-12345-4QDIMzy0U5mzk0ei7W94hQ]*[server.ccl.net> X-Original-From: Jin Zhao Date: Wed, 21 Mar 2007 16:52:40 -0400 (EDT) Sent to CCL by: Jin Zhao [jiz38,+,unixs1.cis.pitt.edu] Dear all, I want to solve a single-electron 3d schrodinger equation numerically, get the eigenvalues and wavefunctions while I have the determined effective potential in the format of a 3d grid. Does anybody know if there is any free code for this or any other information? Thanks a lot! best Jin ==================================== Jin Zhao G-01 Allen Hall Laboratory of Ultrafast Dynamics 412-624-6226 Dept. of Physics & Astronomy Univ. of Pittsburgh Pittsburgh, PA 15260, USA ==================================== From owner-chemistry@ccl.net Thu Mar 22 09:01:01 2007 From: "Rajarshi Guha rguha|*|indiana.edu" To: CCL Subject: CCL: General Molecule/Fragment Database Message-Id: <-33876-070322001211-21208-mDOhVA78g9bRXxIRDFDMQw[a]server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 21 Mar 2007 09:29:19 -0400 Mime-Version: 1.0 Sent to CCL by: Rajarshi Guha [rguha]|[indiana.edu] At Indiana University we host a database of 3D structures. The original structures are taken from PubChem (we have about 8.5M out of the 10M currently in PubChem). The structures were optimized using MMFF94 and a single low energy conformation is stored in the database. You can access it via a web form or via web services, using CID, SMARTS and in a few weeks 3D similarity to a query structure. The form is located here: http://rguha.ath.cx/~rguha/p3d/ The data can be downloaded in SD format, which you could then convert to PDB using Openbabel ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- The Heineken Uncertainty Principle: You can never be sure how many beers you had last night. From owner-chemistry@ccl.net Thu Mar 22 11:29:01 2007 From: "David Gallagher gallagher.da-.-gmail.com" To: CCL Subject: CCL: vibrational spectra Message-Id: <-33877-070322110736-26088-eXfyFkFbrDCD+FW6uDLh3g|,|server.ccl.net> X-Original-From: David Gallagher Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Thu, 22 Mar 2007 08:07:42 -0700 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da,,gmail.com] The vibrational spectrum of your molecule works fine with PM3 in MOPAC2007, so it could be a bug in the version you are using or perhaps, a memory issue as older versions of MOPAC did not dynamically allocate memory. Take a look to see if the MOPAC output file provides any clues as many errors are reported here. If you want to try the new version of MOPAC, it is available at MOPAC2007.com. Regards David Gallagher CAChe Research At 07:47 PM 3/21/2007, neeraj misra neerajmisra*_*hotmail.com wrote: >Sent to CCL by: "neeraj misra" [neerajmisra]![hotmail.com] >I am unable to find the reason as to why vibrational spectra of a >molecule cannot be calculated inspite of the structure being >optimized.I am enclosing the input coordinates of the molecule (90 >atoms).I have been employing semi empirical methods using PM3.But no >success so far. Any help?? From owner-chemistry@ccl.net Thu Mar 22 12:52:00 2007 From: "Steve Gwaltney drg51,,ra.msstate.edu" To: CCL Subject: CCL: ccsd(t) disc requirements Message-Id: <-33878-070322000249-20013-7wWqb9xkktPyXWqf4AqiQw-,-server.ccl.net> X-Original-From: Steve Gwaltney Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 21 Mar 2007 22:24:18 -0500 (CDT) MIME-Version: 1.0 Sent to CCL by: Steve Gwaltney [drg51,,ra.msstate.edu] You really need to give us more information for us to help you. What is the molecule? What it its symmetry? How many basis functions and electrons do you have? From these answers we may be able to provide some advice. Another poster mentioned that you should probably consider another program and suggested Molpro. ACES II also has a very strong CC code. Other possibilites are Psi and NWChem, depending on your computational resouces. But again, we need to know more about what you are trying to do to be able to help you. Steve Gwaltney Dr. Steven Gwaltney Phone: 662-325-7602 Assistant Professor Fax: 662-325-1618 Department of Chemistry, Mail: Box 9573 Center for Environmental Health Sciences, Mississippi State University and HPCC Center for Computational Sciences Mississippi State, MS 39762 On Wed, 21 Mar 2007, Julia Subbotina ysubboti() ucalgary.ca wrote: > > Sent to CCL by: "Julia Subbotina" [ysubboti%a%ucalgary.ca] > Dear CCLers > I have a problem with running CCSD(T)\ Ahlrichs pVDZ single point energy job. I am limited with my disc space (~110GB), but this job seems to need even more (Transformation cannot fit in the specified MaxDisk.). The input line is: > %mem=3GB > ccsd(t)/gen MaxDisk=100GB > And later I am expected to make a single point calculation for the bigger system than one I am struggling with now. I need a suggestion how i can handle this kind of problem. Any tips are welcome. > > Thank you in advance, > Julia > From owner-chemistry@ccl.net Thu Mar 22 13:45:00 2007 From: "Gustavo Seabra gustavo.seabra]~[gmail.com" To: CCL Subject: CCL:G: Amber in Gaussian, Help? Message-Id: <-33879-070322114139-653-E4KLh9dbzytx+5RfeBYifw-,-server.ccl.net> X-Original-From: Gustavo Seabra Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 22 Mar 2007 10:36:01 -0400 MIME-Version: 1.0 Sent to CCL by: Gustavo Seabra [gustavo.seabra-$-gmail.com] Hi Thomas, It seems to me that the Amber force field as implemented in Gaussian just doesn't have all the parameters you need, which is not surprising since the Amber force fields were *not* designed for polymers, but mainly for biological molecules. In that case, what you would need to do is to create the missing parameters yourself. (If you were using the Amber program, I'd recommend you to use Antechamber for that.) But you have to be careful there, for you want those parameters to be compatible with the other parameters used for the rest of the system. And there you have a problem: Gaussian does *not* make it clear which parameter set it is using. Actually, it is a common mistake to just cite "Amber parameters", since that only defines an equation model. There are a number of different parameter sets (ff94, ff99, ff99SB, ff03, glycam, etc, see http://amber.scripps.edu/#ff), developed for different systems or using different methods, and they don't necessarily work well together. So, if you are going to develop your own parameters, you should find out in details which Amber force field is implemented in Gaussian, so you can follow a similar procedure to develop your own parameters. Also, notice that unless you are using UFF, Gaussian does *NOT* automatically assign atomic charges to the atoms. But, the atom charges are part of the parameter set. So, you need to add them yourself in the input, atom-by-atom. In order to use a balanced force field, you should try to find out the charges belonging to that same force field (again, we're back to the point of finding out which is the force field used by Gaussian). HTH, Gustavo Seabra. tlazza##po-box.mcgill.ca wrote: > > Sent to CCL by: tlazza|-|po-box.mcgill.ca > Dear CCL people, > > I have a question concerning the use of AMBER in Gaussian 03. I am > modeling a polymer of styrene and maleic anhydride. Gaussian runs > fine when optimizing the styrene part of the polymer but fails when > adding maleic anhydride (5 member ring with 4 carbons and 1 oxygen, > and 2 C=O bonds) > > I believe it has something to do with missing parameters. Could > anyone enlighten me on this problem and maybe suggest how to solve it. > > I would greatly apreciate any help. > > The output file for maleic anhydride fails with amber and reads as such: > > # opt amber geom=connectivity > ----------------------------- > 1/6=10,10=10,14=-1,18=4000020,38=1,56=2,57=2,64=3/1,3; > 2/9=110,17=6,18=5,40=1/2; > 3/5=2,7=1,11=9,16=1,25=1,30=1/1; > 4/20=11,22=1001,24=3/2; > 7/44=-1/16; > 1/6=10,10=10,14=-1,18=4000020,64=3/3(1); > 99//99; > 2/9=110/2; > 3/5=2,7=1,11=9,16=1,25=1,30=1/1; > 4/16=2,20=11,22=1001,24=3/2; > 7/44=-1/16; > 1/6=10,10=10,14=-1,18=4000020,64=3/3(-4); > 2/9=110/2; > 99//99; > ----- > test7 > ----- > Symbolic Z-matrix: > Charge = 0 Multiplicity = 1 > C-CT- > H-HC- 1 B1 > H-HC- 1 B2 2 A1 > C-CT- 1 B3 3 A2 2 D1 0 > H-HC- 4 B4 1 A3 3 D2 0 > H-HC- 4 B5 1 A4 3 D3 0 > C-CA- 1 B6 4 A5 5 D4 0 > C-CA- 4 B7 1 A6 7 D5 0 > O-O2- 7 B8 1 A7 4 D6 0 > O-O2- 8 B9 4 A8 1 D7 0 > O-O2- 7 B10 1 A9 4 D8 0 > Variables: > B1 1.07 B2 > 1.07 B3 1.51674 > B4 1.07 B5 > 1.07 B6 1.53548 > B7 1.52063 B8 > 1.3013 B9 1.3013 > B10 1.33149 A1 > 108.27071 A2 112.26108 > A3 111.65225 A4 > 112.62779 A5 100.98759 > A6 99.96086 A7 > 125.11583 A8 126.18119 > A9 109.75626 D1 > -123.43758 D2 -43.6756 > D3 78.18336 D4 > 79.94422 D5 -34.62622 > D6 -149.9875 D7 > -150.53131 D8 30.81761 > I= 7 IAn= 6 Valence= 6. > JB= 1 J= 9 IAn= 8 IBT= 2 Dist= 1.30D+00 > JB= 2 J= 11 IAn= 8 IBT= 1 Dist= 1.33D+00 > JB= 3 J= 1 IAn= 6 IBT= 1 Dist= 1.54D+00 > I= 8 IAn= 6 Valence= 6. > JB= 1 J= 10 IAn= 8 IBT= 2 Dist= 1.30D+00 > JB= 2 J= 11 IAn= 8 IBT= 1 Dist= 1.45D+00 > JB= 3 J= 4 IAn= 6 IBT= 1 Dist= 1.52D+00 > Include all MM classes > Bondstretch undefined between atoms 7 9 > Bondstretch undefined between atoms 7 11 > Bondstretch undefined between atoms 8 10 > Bondstretch undefined between atoms 8 11 > Angle bend undefined between atoms 1 7 9 > Angle bend undefined between atoms 1 7 11 > Angle bend undefined between atoms 4 8 10 > Angle bend undefined between atoms 4 8 11 > Angle bend undefined between atoms 7 11 8 > Angle bend undefined between atoms 9 7 11 > Angle bend undefined between atoms 10 8 11 > MM function not complete > Error termination via Lnk1e in C:\G03W\l101.exe at Tue Mar 20 21:20:34 > 2007. Job cpu time: 0 days 0 hours 0 minutes 3.0 seconds. > File lengths (MBytes): RWF= 12 Int= 0 D2E= 0 Chk= 1 > Scr= 1 > > > Thomas D. Lazzara From owner-chemistry@ccl.net Thu Mar 22 14:51:00 2007 From: "Boyd, D. boyd===chem.iupui.edu" To: CCL Subject: CCL: computational chemistry books Message-Id: <-33880-070322143149-8943-xWYC+K4Jj3yW7JW3WRfmHQ:+:server.ccl.net> X-Original-From: "Boyd, D." Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 22 Mar 2007 13:34:41 -0500 MIME-Version: 1.0 Sent to CCL by: "Boyd, D." [boyd|,|chem.iupui.edu] The website (http://chem.iupui.edu/rcc/rcc.html) for Reviews in Computational Chemistry has been updated to include information on the latest volume. The website has been redesigned to make it a little easier to use the online subject indexes and author indexes. Don Donald B. Boyd, Ph.D. Editor Emeritus From owner-chemistry@ccl.net Thu Mar 22 16:07:00 2007 From: "ysubboti:ucalgary.ca" To: CCL Subject: CCL:G: ccsd(t) disc requirements Message-Id: <-33881-070322152411-29020-HX2su8UDB0Lv7A0T9JAJIA!=!server.ccl.net> X-Original-From: ysubboti#%#ucalgary.ca Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 22 Mar 2007 12:31:10 -0600 (MDT) MIME-Version: 1.0 Sent to CCL by: ysubboti/./ucalgary.ca Hi everybody, Thank you for your attention and replays. Looks like my answer was not sent to everybody. >You really need to give us more information for us to help you. What is >the molecule? What it its symmetry? How many basis functions and >electrons do you have? From these answers we may be able to provide some >advice. Well, the system is quite big - 73 atoms. Actually I didn't specify any symmetry, so by default it is C1. 644 basis functions, 1085 primitive gaussians, 674 cartesian basis functions 129 alpha electrons 129 beta electrons. Gaussian asks for the disc space what is almost 11 times more than i have on one machine. Even if it is possible to redirect saving files to other machines I still would have less resources. So I think this is just a bad luck. By the way is there any utility in gaussian to estimate memory requirements for any kind of job (not only for freq) before you start it? My best, Julia > > Sent to CCL by: Steve Gwaltney [drg51,,ra.msstate.edu] > > You really need to give us more information for us to help you. What is > the molecule? What it its symmetry? How many basis functions and > electrons do you have? From these answers we may be able to provide some > advice. > > Another poster mentioned that you should probably consider another > program > and suggested Molpro. ACES II also has a very strong CC code. Other > possibilites are Psi and NWChem, depending on your computational > resouces. > But again, we need to know more about what you are trying to do to be > able > to help you. > > Steve Gwaltney > > Dr. Steven Gwaltney Phone: 662-325-7602 > Assistant Professor Fax: 662-325-1618 > Department of Chemistry, Mail: Box 9573 > Center for Environmental Health Sciences, Mississippi State University > and HPCC Center for Computational Sciences Mississippi State, MS 39762 > > On Wed, 21 Mar 2007, Julia Subbotina ysubboti() ucalgary.ca wrote: > >> >> Sent to CCL by: "Julia Subbotina" [ysubboti%a%ucalgary.ca] >> Dear CCLers >> I have a problem with running CCSD(T)\ Ahlrichs pVDZ single point energy >> job. I am limited with my disc space (~110GB), but this job seems to >> need even more (Transformation cannot fit in the specified MaxDisk.). >> The input line is: >> %mem=3GB >> ccsd(t)/gen MaxDisk=100GB >> And later I am expected to make a single point calculation for the >> bigger system than one I am struggling with now. I need a suggestion how >> i can handle this kind of problem. Any tips are welcome. >> >> Thank you in advance, >> Julia> > > > > From owner-chemistry@ccl.net Thu Mar 22 19:27:01 2007 From: "John Block John.Block-,-oregonstate.edu" To: CCL Subject: CCL: Symposium & Special Memorial Issue of JCAMD in honor of Phil Magee Message-Id: <-33882-070322192616-17747-CMGcOcsWundp9yrs2HKt4g_+_server.ccl.net> X-Original-From: "John Block" Date: Thu, 22 Mar 2007 19:26:12 -0400 Sent to CCL by: "John Block" [John.Block _ oregonstate.edu] The Editors of the Journal of Computer-Aided Molecular Design have graciously offered to publish a special issue of the Journal in honor of Phil Magee, who passed away in 2005. Papers presented at the Memorial Symposium that John Block, Lowell Hall and I are organizing for the ACS meeting in Boston this fall will automatically be considered for inclusion, but people who cannot make it to the meeting are welcome to submit papers as well. To do so, go to the Journal website at www.editorialmanager.com/jcam/ and follow the instructions you find there. Be sure to select "Special Issue: Magee Memorial" as the article type as you make your electronic submission. Please send me an e-mail after you have submitted the manuscript so that I can know to look for it. The deadline for submitting abstracts for presentation at the ACS meeting is April 2, which is only a week and a half away - you still have time, but not much. The full Symposium title is: "QSAR Reborn: Modern QSAR Techniques and Applications - A Symposium in Memory of Dr. Phillip Magee. Phil was a long-standing member of the QSAR community and one of the pioneers in utilizing QSAR, utilizing his knowledge of physical organic chemistry to model bioactivities of agrochemicals, transdermal properties of molecules and molecular toxicities. Whereas it is common to apply this technique to bioactivities in humans, he showed its application to agrochemicals. After retiring from the Ortho Chemical Division of Standard Oil, Phil used QSAR to study transdermal properties of molecules. Until his stroke, Phil was utilizing both his knowledge of physical organic chemistry and qsar descriptors to model bioactivities. Thus, it is appropriate that a symposium in his honor be broad in scope and that it include speakers who develop qsar methodologies and who apply qsar methodologies to solve difficult problems. Phil was the first President of the International QSAR Group and served for a number of years ion that position. People who knew or worked with Phil are particularly encouraged to participate. Appropriate topics include but are not limited to: QSAR descriptor development (physico-chemical, topological, quantum mechanical, structural, geometrical and stereochemical), analysis techniques (2D, 3D and topological QSAR, neural networks, classification methods, etc.) and real-world applications (drug and agrochemical design; toxicity prediction; and environmental property modelling). Abstracts for talks must be submitted electronically. To do so, go to: http://oasys.acs.org/acs/234nm/comp/papers/index.cgi and select "QSAR Reborn" as your topic of choice. Again, the deadline for submission is 2 April 2007. The symposium is being sponsored by the COMP and AGRO Divisions of the American Chemical Society and by the QSAR and Modelling Society. Some money from commercial sponsorships is already in hand and more is anticipated, so we will probably be able to help with expenses in a few cases. If you need such support, please contact myself (bclark at tripos.com) or one of the other organizers (john.block at oregonstate.edu or halllh at comcast.net) as soon as possible. I apologize in advance for overlapping notifications due to postings made in the hope of ensuring a broad participation. Best regards, John Block College of Pharmacy Oregon State University From owner-chemistry@ccl.net Thu Mar 22 20:02:00 2007 From: "ysubboti[#]ucalgary.ca" To: CCL Subject: CCL:G: [Fwd: Re: CCL:G: ccsd(t) disc requirements] Message-Id: <-33883-070322193306-20329-XZqFtf6H7YXnhN6v3mL74w++server.ccl.net> X-Original-From: ysubboti[#]ucalgary.ca Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 22 Mar 2007 17:32:48 -0600 (MDT) MIME-Version: 1.0 Sent to CCL by: ysubboti-$-ucalgary.ca Hello again! I am impressed!!! Well yes, this is what I thought about - to forget it))) I was just trying actually. Obviously I have expected difficulties, but this is so much. My problem was to estimate correctly the energy of complex of ion and neutral organic molecule. I have done already B3LYP and MP2, but you know sometimes you wanna more and more... And never knows would the result be better or not at all. Never..until you try it. So anyway thank you a lot for answers. Julia > Julia, > > You can crudely estimate memory requirements for CCSD like this: > > basis set rank = occupied orbitals + virtual orbitals (+ core orbitals) > > that is > > r = o + v > > two-electron integrals in orbital form are ~r^4 in number without symmetry > T2 cluster amplitudes are ~o^2*v^2 in number, again without symmetry > > Although I don't know the algorithm in Gaussian, obviously, in NWChem the iterative solution of CCSD requires 2*d copies of T2, where d is the number of DIIS vectors kept (default is 5). > > There are 8 bytes to a double so your memory requirement should be around > > 8*( r^4+10*o^2*v^2 ) > > With r = 644, your two-electron integrals are 172,005,949,696 in number which is ~1.4 terabytes. There is no way you can run this on a single machine since disk IO will make this calculation take eons even if you have that size disk array. > > If your target system is larger than this, you have no hope of running it on any machine. Even your current system is beyond the reach of all but a very few people with connections to the US-DOE. I have run CCSD with 650-750 basis functions (in D2h symmetry!) but only because I can run on 500+ processors at Pacific Northwest National Lab. CCSD(T) has basically the same memory cost as CCSD so you're going to need about that many processors to run in-core. Alternatively, a serious multiprocessor machine with very fast hard disks, like an 16-64 processor SGI running SCSI RAID, will work, assuming you can run for a month straight or so. > > 73 atoms would probably be the largest CCSD(T) calculation ever done. Is there some reason you need to use CCSD(T)? Is B3LYP or MP2 not sufficient? Unless you have some good friends at a supercomputing center, you're going to have to rethink your calculation. > > Best of luck, > > Jeff > > On 3/22/07, ysubboti:ucalgary.ca wrote: >> >> Sent to CCL by: ysubboti/./ucalgary.ca >> >> >> Hi everybody, >> Thank you for your attention and replays. Looks like my answer was not sent to everybody. >> >> >You really need to give us more information for us to help you. What >> is >> >the molecule? What it its symmetry? How many basis functions and electrons do you have? From these answers we may be able to provide >> some >> >advice. >> >> Well, the system is quite big - 73 atoms. Actually I didn't specify any symmetry, so by default it is C1. >> 644 basis functions, 1085 primitive gaussians, 674 cartesian basis functions >> 129 alpha electrons 129 beta electrons. >> >> Gaussian asks for the disc space what is almost 11 times more than i have >> on one machine. Even if it is possible to redirect saving files to other >> machines I still would have less resources. So I think this is just a bad >> luck. >> >> By the way is there any utility in gaussian to estimate memory requirements for any kind of job (not only for freq) before you start it? >> >> >> My best, >> Julia >> > >> > Sent to CCL by: Steve Gwaltney [drg51,,ra.msstate.edu] >> > >> > You really need to give us more information for us to help you. What >> is >> > the molecule? What it its symmetry? How many basis functions and electrons do you have? From these answers we may be able to provide >> some >> > advice. >> > >> > Another poster mentioned that you should probably consider another program >> > and suggested Molpro. ACES II also has a very strong CC code. Other possibilites are Psi and NWChem, depending on your computational resouces. >> > But again, we need to know more about what you are trying to do to be able >> > to help you. >> > >> > Steve Gwaltney >> > >> > Dr. Steven Gwaltney Phone: 662-325-7602 >> > Assistant Professor Fax: 662-325-1618 >> > Department of Chemistry, Mail: Box 9573 >> > Center for Environmental Health Sciences, Mississippi State >> University >> > and HPCC Center for Computational Sciences Mississippi State, MS >> 39762 >> > >> > On Wed, 21 Mar 2007, Julia Subbotina ysubboti() ucalgary.ca wrote: >> > >> >> >> >> Sent to CCL by: "Julia Subbotina" [ysubboti%a%ucalgary.ca] Dear CCLers >> >> I have a problem with running CCSD(T)\ Ahlrichs pVDZ single point >> energy >> >> job. I am limited with my disc space (~110GB), but this job seems to need even more (Transformation cannot fit in the specified >> MaxDisk.). >> >> The input line is: >> >> %mem=3GB >> >> ccsd(t)/gen MaxDisk=100GB >> >> And later I am expected to make a single point calculation for the bigger system than one I am struggling with now. I need a suggestion >> how >> >> i can handle this kind of problem. Any tips are welcome. >> >> >> >> Thank you in advance, >> >> Julia>> >> >> >> > > > -- > Jeff Hammond > The University of Chicago > > > From owner-chemistry@ccl.net Thu Mar 22 22:21:01 2007 From: "Joe Kwiatkowski jk905]![imperial.ac.uk" To: CCL Subject: CCL:G: Gaussian: Output overlap matrix Message-Id: <-33884-070322084559-10354-gvYzmRPICXn7A6GVaHdnhA\a/server.ccl.net> X-Original-From: Joe Kwiatkowski Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 22 Mar 2007 11:53:23 +0000 MIME-Version: 1.0 Sent to CCL by: Joe Kwiatkowski [jk905++imperial.ac.uk] Dear CCL's Does anybody know how to convince Gaussian to spit out the overlap matrix (in the atomic orbital basis set)? Many thanks, Joe Kwiatkowski Imperial College London From owner-chemistry@ccl.net Thu Mar 22 22:57:00 2007 From: "John Block blockj(0)onid.orst.edu" To: CCL Subject: CCL: Symposium & Special Memorial Issue of JCAMD in honor of Phil Magee Message-Id: <-33885-070322180416-10793-PX4v3C/TQ73VJoZ2nhSmPw~!~server.ccl.net> X-Original-From: "John Block" Date: Thu, 22 Mar 2007 18:04:12 -0400 Sent to CCL by: "John Block" [blockj .. onid.orst.edu] The Editors of the Journal of Computer-Aided Molecular Design have graciously offered to publish a special issue of the Journal in honor of Phil Magee, who passed away in 2005. Papers presented at the Memorial Symposium that John Block, Lowell Hall and I are organizing for the ACS meeting in Boston this fall will automatically be considered for inclusion, but people who cannot make it to the meeting are welcome to submit papers as well. To do so, go to the Journal website at www.editorialmanager.com/jcam/ and follow the instructions you find there. Be sure to select "Special Issue: Magee Memorial" as the article type as you make your electronic submission. Please send me an e-mail after you have submitted the manuscript so that I can know to look for it. The deadline for submitting abstracts for presentation at the ACS meeting is April 2, which is only a week and a half away - you still have time, but not much. The full Symposium title is: "QSAR Reborn: Modern QSAR Techniques and Applications - A Symposium in Memory of Dr. Phillip Magee. Phil was a long-standing member of the QSAR community and one of the pioneers in utilizing QSAR, utilizing his knowledge of physical organic chemistry to model bioactivities of agrochemicals, transdermal properties of molecules and molecular toxicities. Whereas it is common to apply this technique to bioactivities in humans, he showed its application to agrochemicals. After retiring from the Ortho Chemical Division of Standard Oil, Phil used QSAR to study transdermal properties of molecules. Until his stroke, Phil was utilizing both his knowledge of physical organic chemistry and qsar descriptors to model bioactivities. Thus, it is appropriate that a symposium in his honor be broad in scope and that it include speakers who develop qsar methodologies and who apply qsar methodologies to solve difficult problems. Phil was the first President of the International QSAR Group and served for a number of years ion that position. People who knew or worked with Phil are particularly encouraged to participate. Appropriate topics include but are not limited to: QSAR descriptor development (physico-chemical, topological, quantum mechanical, structural, geometrical and stereochemical), analysis techniques (2D, 3D and topological QSAR, neural networks, classification methods, etc.) and real-world applications (drug and agrochemical design; toxicity prediction; and environmental property modelling). Abstracts for talks must be submitted electronically. To do so, go to: http://oasys.acs.org/acs/234nm/comp/papers/index.cgi and select "QSAR Reborn" as your topic of choice. Again, the deadline for submission is 2 April 2007. The symposium is being sponsored by the COMP and AGRO Divisions of the American Chemical Society and by the QSAR and Modelling Society. Some money from commercial sponsorships is already in hand and more is anticipated, so we will probably be able to help with expenses in a few cases. If you need such support, please contact myself (bclark at tripos.com) or one of the other organizers (john.block at oregonstate.edu or halllh at comcast.net) as soon as possible. We apologize in advance for overlapping notifications due to postings made in the hope of ensuring a broad participation. John Block, Bob Clark, Lowell Hall and Lamont Kier