From chemistry-request@ccl.net Wed Sep 17 07:10:02 2003 Received: from postoffice9.mail.cornell.edu (postoffice9.mail.cornell.edu [132.236.56.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8HB9UAg006877 for ; Wed, 17 Sep 2003 07:09:31 -0400 Received: from cornell.edu ([128.84.183.113]) by postoffice9.mail.cornell.edu (8.12.9/8.12.6) with ESMTP id h8HB9S9h014867; Wed, 17 Sep 2003 07:09:28 -0400 (EDT) Date: Wed, 17 Sep 2003 07:09:28 -0400 Subject: Re: CCL:CD's mac/pc Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v552) Cc: chemistry^at^ccl.net To: Joe Leonard From: Richard Gillilan In-Reply-To: <5.1.0.14.1.20030916190411.00a00b80^at^pop.theworld.com> Message-Id: <67752A85-E8FF-11D7-9B49-000393D59F68^at^cornell.edu> Content-Transfer-Encoding: 7bit X-Mailer: Apple Mail (2.552) X-Spam-Status: No, hits=-0.5 required=7.0 tests=IN_REP_TO,USER_AGENT_APPLEMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) MacOSX writes iso/hfs hybrid CD's that can be read in both windows and linux boxes (I do it frequently). Linux does read the hfs filesystem as well as iso. Linux can also mount and read an hfs firewire drive, but last I tried, writing hfs was dangerous and unstable. As far as I know, MacOS X cannot read ext2 or ext3 Linux filesystems, thought there is a SF project to do this underway (I think). I haven't really tried Mac-burned DVD-R's on Linux yet. Richard Gillilan MacCHESS, Cornell From chemistry-request@ccl.net Wed Sep 17 05:12:13 2003 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8H9BeAg027498 for ; Wed, 17 Sep 2003 05:11:40 -0400 Received: from [136.206.1.18] by hawk.dcu.ie with HTTP; Wed, 17 Sep 2003 10:11:38 +0100 Date: Wed, 17 Sep 2003 10:11:38 +0100 Message-ID: <3F335BC00001BFFF^at^hawk.dcu.ie> From: "Noel O'Boyle" Subject: Problem with TD-DFT convergence To: chemistry^at^ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h8H9CDAg027514 Dear CCLers, This is a Gaussan TD-DFT question... I am trying to find the 25 lowest energy singlet excitations of a Ru polypyridyl complex. The structure has been optimised with opt=tight and int=ultrafine at the b3lyp/lanl2dz level. Although I was able to find the 5 lowest energy excitations, I have been unable to find the 25 lowest ones. The procedure was running for a week and a half before I stopped it, and I have no idea whether it is converged to a solution or not. Does anybody know what I can do to calculate these other excitations, or what the problem might be? Rather than attach the log file (which is quite big), a search through the file for all lines containing either the word 'iteration' or 'converged' gives the following: (Note that it initially reads the 5 converged values from the checkpoint file, but these are 'lost' over the course of the iterations.) I hope someone can help - any comments are appreciated, Thanks, Noel O'Boyle Iteration 1 Dimension 40 NMult 40 Excitation Energies [eV] at current iteration: Iteration 2 Dimension 90 NMult 90 Root 1 has converged. Root 2 has converged. Root 3 has converged. Root 4 has converged. Root 5 has converged. Root 6 not converged, maximum delta is 0.007404730926991 Root 7 not converged, maximum delta is 0.008862238982638 Root 8 not converged, maximum delta is 0.001315772511908 Root 9 not converged, maximum delta is 0.005655129788134 Root 10 not converged, maximum delta is 0.014705549327562 Root 11 not converged, maximum delta is 0.456816622625382 Root 12 not converged, maximum delta is 0.636760077402860 Root 13 not converged, maximum delta is 0.093106988944881 Root 14 not converged, maximum delta is 0.335732118501267 Root 15 not converged, maximum delta is 0.386136511103660 Root 16 not converged, maximum delta is 0.386226800709465 Root 17 not converged, maximum delta is 0.242509992468454 Root 18 not converged, maximum delta is 0.138078107351396 Root 19 not converged, maximum delta is 0.251579277869682 Root 20 not converged, maximum delta is 0.239996792984087 Root 21 not converged, maximum delta is 0.332451371567408 Root 22 not converged, maximum delta is 0.337274071447587 Root 23 not converged, maximum delta is 0.326072596902637 Root 24 not converged, maximum delta is 0.278960047488199 Root 25 not converged, maximum delta is 0.214223630505890 Excitation Energies [eV] at current iteration: Iteration 3 Dimension 130 NMult 130 Root 1 has converged. Root 2 has converged. Root 3 has converged. Root 4 has converged. Root 5 not converged, maximum delta is 0.002158767019168 Root 6 not converged, maximum delta is 0.017181947567395 Root 7 not converged, maximum delta is 0.014341128744181 Root 8 not converged, maximum delta is 0.001647397607816 Root 9 not converged, maximum delta is 0.001619157343413 Root 10 not converged, maximum delta is 0.009697980621986 Root 11 not converged, maximum delta is 0.081738184777113 Root 12 not converged, maximum delta is 0.132374439166443 Root 13 not converged, maximum delta is 0.332192394033528 Root 14 not converged, maximum delta is 0.417416468609908 Root 15 not converged, maximum delta is 0.053618107079752 Root 16 not converged, maximum delta is 0.215872230002141 Root 17 not converged, maximum delta is 0.146306290974896 Root 18 not converged, maximum delta is 0.244610986847678 Root 19 not converged, maximum delta is 0.321666353225352 Root 20 not converged, maximum delta is 0.314370717122375 Root 21 not converged, maximum delta is 0.105751688021024 Root 22 not converged, maximum delta is 0.096207911903002 Root 23 not converged, maximum delta is 0.233457007292169 Root 24 not converged, maximum delta is 0.096038870017231 Root 25 not converged, maximum delta is 0.394570089131416 Excitation Energies [eV] at current iteration: Iteration 4 Dimension 172 NMult 172 Root 2 not converged, maximum delta is 0.290903979490721 Root 3 not converged, maximum delta is 0.576341599575198 Root 4 not converged, maximum delta is 0.308482227791113 Root 5 not converged, maximum delta is 0.575238378436560 Root 6 not converged, maximum delta is 0.447174235162662 Root 7 not converged, maximum delta is 0.336602626914336 Root 8 not converged, maximum delta is 0.265224583707960 Root 9 not converged, maximum delta is 0.342352656348814 Root 10 not converged, maximum delta is 0.239547842131490 Root 11 not converged, maximum delta is 0.586932158353003 Root 12 not converged, maximum delta is 0.459628597103568 Root 13 not converged, maximum delta is 0.556042091094838 Root 14 not converged, maximum delta is 0.204519085955933 Root 15 not converged, maximum delta is 0.365348179604350 Root 16 not converged, maximum delta is 0.556637148934694 Root 17 not converged, maximum delta is 0.532481800020476 Root 18 not converged, maximum delta is 0.530539631766062 Root 19 not converged, maximum delta is 0.366730247992840 Root 20 not converged, maximum delta is 0.344415395376246 Root 21 not converged, maximum delta is 0.378143327609117 Root 22 not converged, maximum delta is 0.342108559885387 Root 23 not converged, maximum delta is 0.362192552660216 Root 24 not converged, maximum delta is 0.157268459363396 Root 25 not converged, maximum delta is 0.259931803599812 Excitation Energies [eV] at current iteration: Davidson failed to converge within maximum sub-space dimensions. Iteration 1 Dimension 100 NMult 272 Excitation Energies [eV] at current iteration: Iteration 2 Dimension 150 NMult 322 Root 2 not converged, maximum delta is 0.587118276026880 Root 3 not converged, maximum delta is 0.308977929793348 Root 4 not converged, maximum delta is 0.569376799096250 Root 5 not converged, maximum delta is 0.437625270516922 Root 6 not converged, maximum delta is 0.335489144488478 Root 7 not converged, maximum delta is 0.265530004589138 Root 8 not converged, maximum delta is 0.346163792165183 Root 9 not converged, maximum delta is 0.215839471882740 Root 10 not converged, maximum delta is 0.593305710271232 Root 11 not converged, maximum delta is 0.460135235335970 Root 12 not converged, maximum delta is 0.550379110043221 Root 13 not converged, maximum delta is 0.193959997096984 Root 14 not converged, maximum delta is 0.560065027592586 Root 15 not converged, maximum delta is 0.566092706764073 Root 16 not converged, maximum delta is 0.479744762565912 Root 17 not converged, maximum delta is 0.522023209056983 Root 18 not converged, maximum delta is 0.298365239773616 Root 19 not converged, maximum delta is 0.274649703656626 Root 20 not converged, maximum delta is 0.353980246233410 Root 21 not converged, maximum delta is 0.391878186623623 Root 22 not converged, maximum delta is 0.355611135353684 Root 23 not converged, maximum delta is 0.176364589035954 Root 24 not converged, maximum delta is 0.151360502978312 Root 25 not converged, maximum delta is 0.347983624138517 Excitation Energies [eV] at current iteration: Iteration 3 Dimension 200 NMult 372 Root 1 not converged, maximum delta is 0.345189238391117 Root 2 not converged, maximum delta is 0.001192116737011 Root 3 not converged, maximum delta is 0.005253173913077 Root 4 not converged, maximum delta is 0.012168930591592 Root 5 not converged, maximum delta is 0.002400831182232 Root 6 not converged, maximum delta is 0.106399874776660 Root 7 not converged, maximum delta is 0.024358472026430 Root 8 not converged, maximum delta is 0.301271978405603 Root 9 not converged, maximum delta is 0.025684438807635 Root 10 not converged, maximum delta is 0.025086539567935 Root 11 not converged, maximum delta is 0.011848707262560 Root 12 not converged, maximum delta is 0.003673761535937 Root 13 not converged, maximum delta is 0.008230809017020 Root 14 not converged, maximum delta is 0.020262757670748 Root 15 not converged, maximum delta is 0.029178519147024 Root 16 not converged, maximum delta is 0.231476435545580 Root 17 not converged, maximum delta is 0.088486363471744 Root 18 not converged, maximum delta is 0.416160385684284 Root 19 not converged, maximum delta is 0.312713938164234 Root 20 not converged, maximum delta is 0.182329588940812 Root 21 not converged, maximum delta is 0.201277872377635 Root 22 not converged, maximum delta is 0.064733146130738 Root 23 not converged, maximum delta is 0.050225848914440 Root 24 not converged, maximum delta is 0.097916853798891 Root 25 not converged, maximum delta is 0.141161306332803 Excitation Energies [eV] at current iteration: Davidson failed to converge within maximum sub-space dimensions. Iteration 1 Dimension 100 NMult 472 Excitation Energies [eV] at current iteration: Iteration 2 Dimension 150 NMult 522 Root 3 not converged, maximum delta is 0.588552250615731 Root 4 not converged, maximum delta is 0.567318119392896 Root 5 not converged, maximum delta is 0.522092443499910 Root 6 not converged, maximum delta is 0.525299388357712 Root 7 not converged, maximum delta is 0.411398121841434 Root 8 not converged, maximum delta is 0.377518928656678 Root 9 not converged, maximum delta is 0.437856291511860 Root 10 not converged, maximum delta is 0.552128206220513 Root 11 not converged, maximum delta is 0.539201161800403 Root 12 not converged, maximum delta is 0.590552391159834 Root 13 not converged, maximum delta is 0.540989037498566 Root 14 not converged, maximum delta is 0.179824128533078 Root 15 not converged, maximum delta is 0.621476345474806 Root 16 not converged, maximum delta is 0.526982914277785 Root 17 not converged, maximum delta is 0.602404662132160 Root 18 not converged, maximum delta is 0.436836289835759 Root 19 not converged, maximum delta is 0.481712167168911 Root 20 not converged, maximum delta is 0.326744952805407 Root 21 not converged, maximum delta is 0.272122574410498 Root 22 not converged, maximum delta is 0.242517077189514 Root 23 not converged, maximum delta is 0.341541709728267 Root 24 not converged, maximum delta is 0.445699586881525 Root 25 not converged, maximum delta is 0.564378458711976 Excitation Energies [eV] at current iteration: Iteration 3 Dimension 200 NMult 572 Root 2 not converged, maximum delta is 0.089633263432261 Root 3 not converged, maximum delta is 0.585036725586833 Root 4 not converged, maximum delta is 0.308953526722961 Root 5 not converged, maximum delta is 0.509493530900974 Root 6 not converged, maximum delta is 0.335946478673661 Root 7 not converged, maximum delta is 0.267055400127177 Root 8 not converged, maximum delta is 0.417800109978038 Root 9 not converged, maximum delta is 0.372104686817731 Root 10 not converged, maximum delta is 0.265327495522961 Root 11 not converged, maximum delta is 0.598187299305444 Root 12 not converged, maximum delta is 0.460731070589520 Root 13 not converged, maximum delta is 0.585170017550264 Root 14 not converged, maximum delta is 0.175251798711131 Root 15 not converged, maximum delta is 0.372943545645259 Root 16 not converged, maximum delta is 0.550074800415477 Root 17 not converged, maximum delta is 0.562203041309712 Root 18 not converged, maximum delta is 0.379742807470175 Root 19 not converged, maximum delta is 0.224992917053478 Root 20 not converged, maximum delta is 0.444587551629744 Root 21 not converged, maximum delta is 0.387418708764680 Root 22 not converged, maximum delta is 0.533544435861576 Root 23 not converged, maximum delta is 0.297736829988022 Root 24 not converged, maximum delta is 0.485589203422645 Root 25 not converged, maximum delta is 0.350600818896965 Excitation Energies [eV] at current iteration: Davidson failed to converge within maximum sub-space dimensions. Iteration 1 Dimension 100 NMult 672 Excitation Energies [eV] at current iteration: Iteration 2 Dimension 150 NMult 722 Root 2 not converged, maximum delta is 0.581887273073917 Root 3 not converged, maximum delta is 0.308661342420630 Root 4 not converged, maximum delta is 0.508871395502774 Root 5 not converged, maximum delta is 0.335988962400266 Root 6 not converged, maximum delta is 0.266304116110136 Root 7 not converged, maximum delta is 0.041767984415869 Root 8 not converged, maximum delta is 0.381393044262043 Root 9 not converged, maximum delta is 0.213383222141579 Root 10 not converged, maximum delta is 0.592936564841640 Root 11 not converged, maximum delta is 0.460004554702390 Root 12 not converged, maximum delta is 0.552058735603580 Root 13 not converged, maximum delta is 0.198652833770926 Root 14 not converged, maximum delta is 0.552692922207801 Root 15 not converged, maximum delta is 0.559181603137438 Root 16 not converged, maximum delta is 0.426523065946128 Root 17 not converged, maximum delta is 0.428768504357267 Root 18 not converged, maximum delta is 0.453543094109068 Root 19 not converged, maximum delta is 0.272152073756206 Root 20 not converged, maximum delta is 0.543098232425314 Root 21 not converged, maximum delta is 0.157716099048814 Root 22 not converged, maximum delta is 0.388348585233426 Root 23 not converged, maximum delta is 0.158012394139449 Root 24 not converged, maximum delta is 0.303263711069559 Root 25 not converged, maximum delta is 0.292369179834727 Excitation Energies [eV] at current iteration: Iteration 3 Dimension 200 NMult 772 Root 1 not converged, maximum delta is 0.181405866563266 Root 2 not converged, maximum delta is 0.176827257465427 Root 3 not converged, maximum delta is 0.004308316698573 Root 4 not converged, maximum delta is 0.003567542958468 Root 5 not converged, maximum delta is 0.041128411380335 Root 6 not converged, maximum delta is 0.131293659372140 Root 7 not converged, maximum delta is 0.023916375070765 Root 8 not converged, maximum delta is 0.044830058300122 Root 9 not converged, maximum delta is 0.010572834660462 Root 10 not converged, maximum delta is 0.012930447738519 Root 11 not converged, maximum delta is 0.007822891117551 Root 12 not converged, maximum delta is 0.012094010412010 Root 13 not converged, maximum delta is 0.030024078783344 Root 14 not converged, maximum delta is 0.348311205710793 Root 15 not converged, maximum delta is 0.059773943104910 Root 16 not converged, maximum delta is 0.210782557030684 Root 17 not converged, maximum delta is 0.164025407331235 Root 18 not converged, maximum delta is 0.023175229667803 Root 19 not converged, maximum delta is 0.042383233256127 Root 20 not converged, maximum delta is 0.049318585524357 Root 21 not converged, maximum delta is 0.056731841176364 Root 22 not converged, maximum delta is 0.287806738858008 Root 23 not converged, maximum delta is 0.288155093822039 Root 24 not converged, maximum delta is 0.194079745166977 Root 25 not converged, maximum delta is 0.104596528333144 Excitation Energies [eV] at current iteration: Davidson failed to converge within maximum sub-space dimensions. Iteration 1 Dimension 100 NMult 872 Excitation Energies [eV] at current iteration: Iteration 2 Dimension 150 NMult 922 Root 2 not converged, maximum delta is 0.583599185746736 Root 3 not converged, maximum delta is 0.308429390254305 Root 4 not converged, maximum delta is 0.509354618374657 Root 5 not converged, maximum delta is 0.335737556128847 Root 6 not converged, maximum delta is 0.022089489428945 Root 7 not converged, maximum delta is 0.433935802272197 Root 8 not converged, maximum delta is 0.345691995296515 Root 9 not converged, maximum delta is 0.233764074918117 Root 10 not converged, maximum delta is 0.586511719789674 Root 11 not converged, maximum delta is 0.460265556115391 Root 12 not converged, maximum delta is 0.553323531585801 Root 13 not converged, maximum delta is 0.197566332669070 Root 14 not converged, maximum delta is 0.541477518403312 Root 15 not converged, maximum delta is 0.557348220565688 Root 16 not converged, maximum delta is 0.554298302140383 Root 17 not converged, maximum delta is 0.496666856579465 Root 18 not converged, maximum delta is 0.404970960289473 Root 19 not converged, maximum delta is 0.378781537296653 Root 20 not converged, maximum delta is 0.279960244909309 Root 21 not converged, maximum delta is 0.410070658134310 Root 22 not converged, maximum delta is 0.561405949949656 Root 23 not converged, maximum delta is 0.303354839968558 Root 24 not converged, maximum delta is 0.397636239654990 Root 25 not converged, maximum delta is 0.473109731563097 Excitation Energies [eV] at current iteration: Iteration 3 Dimension 200 NMult 972 Root 1 not converged, maximum delta is 0.218330704057326 Root 2 not converged, maximum delta is 0.002695936639569 Root 3 not converged, maximum delta is 0.001788850122021 Root 4 not converged, maximum delta is 0.004976531696294 Root 5 not converged, maximum delta is 0.020819125354371 Root 6 not converged, maximum delta is 0.254914037829198 Root 7 not converged, maximum delta is 0.082014459738905 Root 8 not converged, maximum delta is 0.010967514353033 Root 9 not converged, maximum delta is 0.008548377144971 Root 10 not converged, maximum delta is 0.002762561791817 Root 11 not converged, maximum delta is 0.003083422097156 Root 12 not converged, maximum delta is 0.008776559380756 Root 13 not converged, maximum delta is 0.027270871306355 Root 14 not converged, maximum delta is 0.224773417797189 Root 15 not converged, maximum delta is 0.024361084992639 Root 16 not converged, maximum delta is 0.081808110257112 Root 17 not converged, maximum delta is 0.081881291028735 Root 18 not converged, maximum delta is 0.111294918826776 Root 19 not converged, maximum delta is 0.033240509783126 Root 20 not converged, maximum delta is 0.230523554086190 Root 21 not converged, maximum delta is 0.074801342823570 Root 22 not converged, maximum delta is 0.015079601052521 Root 23 not converged, maximum delta is 0.310741280134031 Root 24 not converged, maximum delta is 0.236718852471043 Root 25 not converged, maximum delta is 0.197258919455273 Excitation Energies [eV] at current iteration: Davidson failed to converge within maximum sub-space dimensions. Iteration 1 Dimension 100 NMult 1072 Excitation Energies [eV] at current iteration: Iteration 2 Dimension 150 NMult 1122 Root 2 not converged, maximum delta is 0.586584530411784 Root 3 not converged, maximum delta is 0.309084479521523 Root 4 not converged, maximum delta is 0.509561383395724 Root 5 not converged, maximum delta is 0.335343880783976 Root 6 not converged, maximum delta is 0.265245481993981 Root 7 not converged, maximum delta is 0.026685700821496 Root 8 not converged, maximum delta is 0.402922347357617 Root 9 not converged, maximum delta is 0.211078091279468 Root 10 not converged, maximum delta is 0.594954336694342 Root 11 not converged, maximum delta is 0.459699400415110 Root 12 not converged, maximum delta is 0.553443792763570 Root 13 not converged, maximum delta is 0.200201359323608 Root 14 not converged, maximum delta is 0.145644675822141 Root 15 not converged, maximum delta is 0.620200296249340 Root 16 not converged, maximum delta is 0.599496758454960 Root 17 not converged, maximum delta is 0.537398206516393 Root 18 not converged, maximum delta is 0.432162029960974 Root 19 not converged, maximum delta is 0.440780556059644 Root 20 not converged, maximum delta is 0.423405450471889 Root 21 not converged, maximum delta is 0.304986763315337 Root 22 not converged, maximum delta is 0.413719527601908 Root 23 not converged, maximum delta is 0.390298396973302 Root 24 not converged, maximum delta is 0.328044111994579 Root 25 not converged, maximum delta is 0.112082832490994 Excitation Energies [eV] at current iteration: Iteration 3 Dimension 200 NMult 1172 Root 2 not converged, maximum delta is 0.150395677664102 Root 3 not converged, maximum delta is 0.587766742558254 Root 4 not converged, maximum delta is 0.307876272429912 Root 5 not converged, maximum delta is 0.575600143027928 Root 6 not converged, maximum delta is 0.444422026477227 Root 7 not converged, maximum delta is 0.340423188747392 Root 8 not converged, maximum delta is 0.402854215551012 Root 9 not converged, maximum delta is 0.472473063023581 Root 10 not converged, maximum delta is 0.366070759760080 Root 11 not converged, maximum delta is 0.228604496152837 Root 12 not converged, maximum delta is 0.124358842473744 Root 13 not converged, maximum delta is 0.578881944628628 Root 14 not converged, maximum delta is 0.459710966010147 Root 15 not converged, maximum delta is 0.554158080794235 Root 16 not converged, maximum delta is 0.307890572965475 Root 17 not converged, maximum delta is 0.550598479076015 Root 18 not converged, maximum delta is 0.556994697702795 Root 19 not converged, maximum delta is 0.423737726039941 Root 20 not converged, maximum delta is 0.219827192671648 Root 21 not converged, maximum delta is 0.545606560169041 Root 22 not converged, maximum delta is 0.455577431562578 Root 23 not converged, maximum delta is 0.329505472673824 Root 24 not converged, maximum delta is 0.421666291784864 Root 25 not converged, maximum delta is 0.463658403789784 Excitation Energies [eV] at current iteration: Davidson failed to converge within maximum sub-space dimensions. Iteration 1 Dimension 100 NMult 1272 Excitation Energies [eV] at current iteration: Iteration 2 Dimension 150 NMult 1322 Root 3 not converged, maximum delta is 0.588123640154355 Root 4 not converged, maximum delta is 0.566086638772088 Root 5 not converged, maximum delta is 0.514660672798769 Root 6 not converged, maximum delta is 0.526055232362510 Root 7 not converged, maximum delta is 0.284152350710605 Root 8 not converged, maximum delta is 0.372239190741094 Root 9 not converged, maximum delta is 0.445769270212038 Root 10 not converged, maximum delta is 0.550875381726046 Root 11 not converged, maximum delta is 0.510210725093454 Root 12 not converged, maximum delta is 0.459571592003844 Root 13 not converged, maximum delta is 0.462552399419544 Root 14 not converged, maximum delta is 0.529592326751841 Root 15 not converged, maximum delta is 0.183587506415252 Root 16 not converged, maximum delta is 0.587851609169667 Root 17 not converged, maximum delta is 0.606931635530917 Root 18 not converged, maximum delta is 0.552694434466230 Root 19 not converged, maximum delta is 0.580040763064580 Root 20 not converged, maximum delta is 0.413232993489777 Root 21 not converged, maximum delta is 0.334333430272328 Root 22 not converged, maximum delta is 0.490838876697391 Root 23 not converged, maximum delta is 0.451658024856894 Root 24 not converged, maximum delta is 0.225613597366480 Root 25 not converged, maximum delta is 0.300075599116072 Excitation Energies [eV] at current iteration: Iteration 3 Dimension 200 NMult 1372 Root 1 not converged, maximum delta is 0.100243559202180 Root 2 not converged, maximum delta is 0.240936726888692 Root 3 not converged, maximum delta is 0.007128473022068 Root 4 not converged, maximum delta is 0.144177672838647 Root 5 not converged, maximum delta is 0.002536232545531 Root 6 not converged, maximum delta is 0.006425949628116 Root 7 not converged, maximum delta is 0.006032711188097 Root 8 not converged, maximum delta is 0.025607515446386 Root 9 not converged, maximum delta is 0.197451418062306 Root 10 not converged, maximum delta is 0.126943804654475 Root 11 not converged, maximum delta is 0.107243836598266 Root 12 not converged, maximum delta is 0.006419091394665 Root 13 not converged, maximum delta is 0.009319926360212 Root 14 not converged, maximum delta is 0.042191686553070 Root 15 not converged, maximum delta is 0.063350300894030 Root 16 not converged, maximum delta is 0.069366547272618 Root 17 not converged, maximum delta is 0.255373366611558 Root 18 not converged, maximum delta is 0.053800138675653 Root 19 not converged, maximum delta is 0.230664878891450 Root 20 not converged, maximum delta is 0.091420886280723 Root 21 not converged, maximum delta is 0.059550436485785 Root 22 not converged, maximum delta is 0.151085034362463 Root 23 not converged, maximum delta is 0.075935913939861 Root 24 not converged, maximum delta is 0.095161551402368 Root 25 not converged, maximum delta is 0.222912779436169 Excitation Energies [eV] at current iteration: Davidson failed to converge within maximum sub-space dimensions. Iteration 1 Dimension 100 NMult 1472 Excitation Energies [eV] at current iteration: Iteration 2 Dimension 150 NMult 1522 Root 3 not converged, maximum delta is 0.588601903440314 Root 4 not converged, maximum delta is 0.577325659005518 Root 5 not converged, maximum delta is 0.515113235430137 Root 6 not converged, maximum delta is 0.523588869303326 Root 7 not converged, maximum delta is 0.336194797126803 Root 8 not converged, maximum delta is 0.414685787973506 Root 9 not converged, maximum delta is 0.407856210032304 Root 10 not converged, maximum delta is 0.551976073161088 Root 11 not converged, maximum delta is 0.544171997884324 Root 12 not converged, maximum delta is 0.589181878709498 Root 13 not converged, maximum delta is 0.555506003152135 Root 14 not converged, maximum delta is 0.361511049717195 Root 15 not converged, maximum delta is 0.176723717421532 Root 16 not converged, maximum delta is 0.638883960649365 Root 17 not converged, maximum delta is 0.506449529909286 Root 18 not converged, maximum delta is 0.597793263391498 Root 19 not converged, maximum delta is 0.602186235841212 Root 20 not converged, maximum delta is 0.511816161145268 Root 21 not converged, maximum delta is 0.498602603487390 Root 22 not converged, maximum delta is 0.359689520243446 Root 23 not converged, maximum delta is 0.462835518464986 Root 24 not converged, maximum delta is 0.482350225720142 Root 25 not converged, maximum delta is 0.369875442764343 Excitation Energies [eV] at current iteration: Iteration 3 Dimension 200 NMult 1572 Root 1 not converged, maximum delta is 0.209313383313156 Root 2 not converged, maximum delta is 0.114012613591681 Root 3 not converged, maximum delta is 0.006582480573241 Root 4 not converged, maximum delta is 0.006421959213350 Root 5 not converged, maximum delta is 0.007280224373062 Root 6 not converged, maximum delta is 0.013185653647332 Root 7 not converged, maximum delta is 0.098836023503527 Root 8 not converged, maximum delta is 0.002455652549050 Root 9 not converged, maximum delta is 0.016864778248155 Root 10 not converged, maximum delta is 0.028148833967553 Root 11 not converged, maximum delta is 0.205928381261202 Root 12 not converged, maximum delta is 0.009127103425115 Root 13 not converged, maximum delta is 0.009627454967351 Root 14 not converged, maximum delta is 0.128381908975369 Root 15 not converged, maximum delta is 0.055728591151375 Root 16 not converged, maximum delta is 0.040193538339092 Root 17 not converged, maximum delta is 0.264749562488032 Root 18 not converged, maximum delta is 0.219606811166269 Root 19 not converged, maximum delta is 0.005939057059282 Root 20 not converged, maximum delta is 0.033984134950821 Root 21 not converged, maximum delta is 0.017114279031628 Root 22 not converged, maximum delta is 0.083833442843491 Root 23 not converged, maximum delta is 0.322194488492002 Root 24 not converged, maximum delta is 0.123959209292249 Root 25 not converged, maximum delta is 0.079097796612535 Excitation Energies [eV] at current iteration: Davidson failed to converge within maximum sub-space dimensions. Iteration 1 Dimension 100 NMult 1672 Excitation Energies [eV] at current iteration: Iteration 2 Dimension 150 NMult 1722 Root 3 not converged, maximum delta is 0.573820501397100 Root 4 not converged, maximum delta is 0.558552342515331 Root 5 not converged, maximum delta is 0.511714827420041 Root 6 not converged, maximum delta is 0.522406509519858 Root 7 not converged, maximum delta is 0.410269496574303 Root 8 not converged, maximum delta is 0.427216522467352 Root 9 not converged, maximum delta is 0.414667634791406 Root 10 not converged, maximum delta is 0.550859772905827 Root 11 not converged, maximum delta is 0.540125755023022 Root 12 not converged, maximum delta is 0.589428884131059 Root 13 not converged, maximum delta is 0.595733766354582 Root 14 not converged, maximum delta is 0.203006103160209 Root 15 not converged, maximum delta is 0.652666695635527 Root 16 not converged, maximum delta is 0.527816745222751 Root 17 not converged, maximum delta is 0.601731064026786 Root 18 not converged, maximum delta is 0.436315621019287 Root 19 not converged, maximum delta is 0.501519228669445 Root 20 not converged, maximum delta is 0.214651003133256 Root 21 not converged, maximum delta is 0.401920255332239 Root 22 not converged, maximum delta is 0.449189319096195 Root 23 not converged, maximum delta is 0.288995831166521 Root 24 not converged, maximum delta is 0.524239746900891 Root 25 not converged, maximum delta is 0.277919509826868 Excitation Energies [eV] at current iteration: Iteration 3 Dimension 200 NMult 1772 Root 1 not converged, maximum delta is 0.241369448901602 Root 2 not converged, maximum delta is 0.105962430442568 Root 3 not converged, maximum delta is 0.199580924231327 Root 4 not converged, maximum delta is 0.007178821251777 Root 5 not converged, maximum delta is 0.004145468621631 Root 6 not converged, maximum delta is 0.031662888802268 Root 7 not converged, maximum delta is 0.017059403268735 Root 8 not converged, maximum delta is 0.374166712320064 Root 9 not converged, maximum delta is 0.232914058129990 Root 10 not converged, maximum delta is 0.021046704147476 Root 11 not converged, maximum delta is 0.032749660894162 Root 12 not converged, maximum delta is 0.025391698922333 Root 13 not converged, maximum delta is 0.009376854833756 Root 14 not converged, maximum delta is 0.009230759177771 Root 15 not converged, maximum delta is 0.020114010826708 Root 16 not converged, maximum delta is 0.402016671206729 Root 17 not converged, maximum delta is 0.035587071967003 Root 18 not converged, maximum delta is 0.020023407949102 Root 19 not converged, maximum delta is 0.330457018871506 Root 20 not converged, maximum delta is 0.221155039494110 Root 21 not converged, maximum delta is 0.095894666080936 Root 22 not converged, maximum delta is 0.116415607841244 Root 23 not converged, maximum delta is 0.176523744113582 Root 24 not converged, maximum delta is 0.103816030889263 Root 25 not converged, maximum delta is 0.096893228231398 Excitation Energies [eV] at current iteration: Davidson failed to converge within maximum sub-space dimensions. Iteration 1 Dimension 100 NMult 1872 Excitation Energies [eV] at current iteration: Iteration 2 Dimension 150 NMult 1922 Root 2 not converged, maximum delta is 0.586051085098425 Root 3 not converged, maximum delta is 0.087517927623592 Root 4 not converged, maximum delta is 0.418390962528301 Root 5 not converged, maximum delta is 0.509744237965259 Root 6 not converged, maximum delta is 0.339229293328190 Root 7 not converged, maximum delta is 0.269899418809393 Root 8 not converged, maximum delta is 0.469680062367851 Root 9 not converged, maximum delta is 0.369617679899222 Root 10 not converged, maximum delta is 0.243290671860621 Root 11 not converged, maximum delta is 0.588032062787054 Root 12 not converged, maximum delta is 0.453877415141163 Root 13 not converged, maximum delta is 0.528367337855512 Root 14 not converged, maximum delta is 0.196145502164243 Root 15 not converged, maximum delta is 0.557977283262927 Root 16 not converged, maximum delta is 0.561445690068388 Root 17 not converged, maximum delta is 0.282601061784331 Root 18 not converged, maximum delta is 0.464354101693589 Root 19 not converged, maximum delta is 0.431265130596868 Root 20 not converged, maximum delta is 0.385496152552425 Root 21 not converged, maximum delta is 0.213421190002003 Root 22 not converged, maximum delta is 0.191326011083794 Root 23 not converged, maximum delta is 0.421321869143319 Root 24 not converged, maximum delta is 0.268124737277276 Root 25 not converged, maximum delta is 0.293657784148104 Excitation Energies [eV] at current iteration: Iteration 3 Dimension 200 NMult 1972 Root 1 not converged, maximum delta is 0.189381876193812 Root 2 not converged, maximum delta is 0.080178273164704 Root 3 not converged, maximum delta is 0.297895374847438 Root 4 not converged, maximum delta is 0.178241068691483 Root 5 not converged, maximum delta is 0.088675661410775 Root 6 not converged, maximum delta is 0.006702600826592 Root 7 not converged, maximum delta is 0.004720493434296 Root 8 not converged, maximum delta is 0.005446869052103 Root 9 not converged, maximum delta is 0.006652640022947 Root 10 not converged, maximum delta is 0.073363787822794 Root 11 not converged, maximum delta is 0.220436535090187 Root 12 not converged, maximum delta is 0.198891357835688 Root 13 not converged, maximum delta is 0.012919452788206 Root 14 not converged, maximum delta is 0.323390512609015 Root 15 not converged, maximum delta is 0.012124975457431 Root 16 not converged, maximum delta is 0.012627845676860 Root 17 not converged, maximum delta is 0.031209083341800 Root 18 not converged, maximum delta is 0.022352270844933 Root 19 not converged, maximum delta is 0.278957839843263 Root 20 not converged, maximum delta is 0.205817983678623 Root 21 not converged, maximum delta is 0.231936919100410 Root 22 not converged, maximum delta is 0.080192959477193 Root 23 not converged, maximum delta is 0.034254901543349 Root 24 not converged, maximum delta is 0.156592791759142 Root 25 not converged, maximum delta is 0.193699223773827 Excitation Energies [eV] at current iteration: Davidson failed to converge within maximum sub-space dimensions. Iteration 1 Dimension 100 NMult 2072 Excitation Energies [eV] at current iteration: Iteration 2 Dimension 150 NMult 2122 Root 2 not converged, maximum delta is 0.584481491676484 Root 3 not converged, maximum delta is 0.305400356731222 Root 4 not converged, maximum delta is 0.510835146636999 Root 5 not converged, maximum delta is 0.335316624653222 Root 6 not converged, maximum delta is 0.409213742685700 Root 7 not converged, maximum delta is 0.463191012437971 Root 8 not converged, maximum delta is 0.360348675050301 Root 9 not converged, maximum delta is 0.225584595567685 Root 10 not converged, maximum delta is 0.596113837565974 Root 11 not converged, maximum delta is 0.459154474763375 Root 12 not converged, maximum delta is 0.548756053350721 Root 13 not converged, maximum delta is 0.208638071392165 Root 14 not converged, maximum delta is 0.579160802818297 Root 15 not converged, maximum delta is 0.599284124629985 Root 16 not converged, maximum delta is 0.426253335887128 Root 17 not converged, maximum delta is 0.547992955720691 Root 18 not converged, maximum delta is 0.453536478524960 Root 19 not converged, maximum delta is 0.452891008202275 Root 20 not converged, maximum delta is 0.386849797779731 Root 21 not converged, maximum delta is 0.210064228260051 Root 22 not converged, maximum delta is 0.265825127740316 Root 23 not converged, maximum delta is 0.373148082841801 Root 24 not converged, maximum delta is 0.330687722488405 Root 25 not converged, maximum delta is 0.314228903308054 Excitation Energies [eV] at current iteration: Iteration 3 Dimension 200 NMult 2172 Root 1 not converged, maximum delta is 0.193065342667670 Root 2 not converged, maximum delta is 0.039075573235853 Root 3 not converged, maximum delta is 0.013206740919040 Root 4 not converged, maximum delta is 0.012158590499959 Root 5 not converged, maximum delta is 0.013835304999627 Root 6 not converged, maximum delta is 0.123017006818450 Root 7 not converged, maximum delta is 0.027927561541132 Root 8 not converged, maximum delta is 0.180072046420179 Root 9 not converged, maximum delta is 0.054043976431832 Root 10 not converged, maximum delta is 0.036736083311368 Root 11 not converged, maximum delta is 0.004619067465196 Root 12 not converged, maximum delta is 0.007145827863146 Root 13 not converged, maximum delta is 0.016314095966503 Root 14 not converged, maximum delta is 0.225896822571059 Root 15 not converged, maximum delta is 0.037900675714083 Root 16 not converged, maximum delta is 0.041540559481953 Root 17 not converged, maximum delta is 0.038518809480861 Root 18 not converged, maximum delta is 0.307407373433307 Root 19 not converged, maximum delta is 0.050325090558870 Root 20 not converged, maximum delta is 0.034228805765775 Root 21 not converged, maximum delta is 0.181117646798461 Root 22 not converged, maximum delta is 0.230979287192232 Root 23 not converged, maximum delta is 0.098955200080336 Root 24 not converged, maximum delta is 0.289393067376068 Root 25 not converged, maximum delta is 0.317167128241639 NMult goes from 40 --> 2172 over the course of the job. If I knew I was getting closer to convergence I would leave it for as long as it takes, but it is difficult to believe that it is. From chemistry-request@ccl.net Wed Sep 17 11:23:11 2003 Received: from smtp.dmbr.UGent.be (dmbr242.fvms.ugent.be [157.193.189.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8HFN6Ag014384 for ; Wed, 17 Sep 2003 11:23:06 -0400 Received: from dmbr032.fvms.ugent.be (dmbr032.fvms.ugent.be [157.193.200.89]) by smtp.dmbr.UGent.be (Postfix) with ESMTP id 7FC6F68004 for ; Wed, 17 Sep 2003 17:23:05 +0200 (CEST) Subject: analyzing PDB files using CHARMM From: Dominique Vlieghe To: forum CCL Content-Type: text/plain Organization: Message-Id: <1063812081.30241.15.camel!at!dmbr032.fvms.ugent.be> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.2.4 Date: 17 Sep 2003 17:21:21 +0200 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=1.1 required=7.0 tests=RCVD_IN_OSIRUSOFT_COM,USER_AGENT_XIMIAN,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello all, I would like to use CHARMM to analyze the interaction energies of an existing protein structure (from the PDB). I roughly follow this procedure: * I use the CHARMm22 toppar files * I use a distance dependent dielectric constant (d.d.d.c.) (nbon rdielec eps 4.0) * I minimize 500 steps to remove incidental clashes. Evidently, I don't use explicit water. * I use the INTER command to calculate interaction energies e.g. between residues... I am especially not sure of the d.d.d.c. I have a history in using CHARMM19 force fields where it is quite common to use a d.d.d.c., but I'm not sure if this is the correct choice when using CHARMM22 force fields. Am I doing the right thing? Any comment would be appreciated... Regards, Dominique -- ------------------------------ Dominique Vlieghe, Ph.D., Bioinformatics Core, Department for Molecular Biomedical Research (DMBR) VIB - Ghent University (new) 'Fiers-Schell-Van Montagu' building (new) Technologiepark 927 (new) B-9052 Ghent (Zwijnaarde), Belgium (new) Tel : +32-(0)9-33-13.693 (new) Fax : +32-(0)9-33-13.609 (new) email:dominique.vlieghe!at!dmbr.ugent.be (new) www:http://www.dmbr.ugent.be/ ------------------------------ From chemistry-request@ccl.net Wed Sep 17 09:50:59 2003 Received: from mail.shcnc.ac.cn (server.shcnc.ac.cn [159.226.128.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8HDoRAg027782 for ; Wed, 17 Sep 2003 09:50:28 -0400 Received: from DATA4 (unknown [202.127.19.76]) by mail.shcnc.ac.cn (4U Message Server) with SMTP id 6335E4594 for ; Wed, 17 Sep 2003 21:48:23 +0800 (CST) Message-ID: <002601c37d22$96bc9fd0$4c137fca=at=simm.ac.cn> Reply-To: "Mingyue Zheng" From: "Mingyue Zheng" To: Subject: molecule substructure searching algorithms Date: Wed, 17 Sep 2003 21:50:00 +0800 Organization: SIMM MIME-Version: 1.0 Content-Type: text/plain; charset="GB18030" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Spam-Status: No, hits=3.0 required=7.0 tests=BASE64_ENC_TEXT,RCVD_IN_RFCI version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id h8HDoxAg028012 Hi all CCLers: I want to write a program calculatting pKa of molecule based on it's structure. The first problem harassing me is how to efficiently recognize and sign a specific functional group in a molecule. Is here anyone who could tell me where can I find some open source code for molecule substructure searching algorithms, or any free program dealing with it? Thank you in advance! Regards! (UTF-8) *********************************************************************** Mingyue Zheng Drug Design & Discovery Center SIMM,China Acadmy of Science 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park,Shanghai 201203,China Tel: 86-21-50806600 Fax: 86-21-50807088 myzheng=at=mail.shcnc.ac.cn myzheng=at=iris3.simm.ac.cn *********************************************************************** From chemistry-request@ccl.net Wed Sep 17 15:23:38 2003 Received: from mercury.chem.northwestern.edu (mercury.chem.northwestern.edu [129.105.116.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8HJN6Ag014056 for ; Wed, 17 Sep 2003 15:23:07 -0400 Received: from chem.northwestern.edu (cat207.cqe.northwestern.edu [129.105.122.207]) by mercury.chem.northwestern.edu (8.12.8/8.12.8) with ESMTP id h8HJN7xP007436 for ; Wed, 17 Sep 2003 14:23:07 -0500 (CDT) Date: Wed, 17 Sep 2003 14:23:06 -0500 Mime-Version: 1.0 (Apple Message framework v552) Content-Type: text/plain; charset=US-ASCII; format=flowed Subject: Re: Summary of relationships between IP, EA and electrochemistry From: Geoff Hutchison To: chemistry{at}ccl.net Content-Transfer-Encoding: 7bit Message-Id: <5D527324-E944-11D7-AEEE-000A95701B7A{at}chem.northwestern.edu> X-Mailer: Apple Mail (2.552) X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_APPLEMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Last week, I asked about the relationship between gas-phase IP and EA values and electrochemical values. In particular I was trying to remember a paper I had read, but could no longer find in my files. Thanks to Toomas Tamm, Christopher Cramer, Roger DeKock, and Brian Peterson for suggestions. The particular article I remembered was found it in a last desperate SciFinder search. It relates IP and EA to electrochemistry by a Kamlet-Taft expression and suggests when solvent effects might vary due to polarizability: M. Jonsson, A. Houmam, G. Jocys, and D. D. M. Wayner, J. Chem. Soc., Perkin Trans. 2, 1999, 425-429. "Solvent effects on redox properties of radical ions" Several posters suggested the following paper, which discusses oxidation potentials and compares semiempirical solvation methods to bare gas-phase methods: P. Winget, E.J. Weber, C.J. Cramer, and D.G. Truhlar, Phys. Chem. Chem. Phys., 2000, 2, 1231-1239, "Computational electrochemistry: aqueous one-electron oxidation potentials for substituted anilines." Other suggestions: Michael Laing, "The electronegativity of a metal and its E0: should they correlate?", South African Journal of Science, vol 98 (2002), pp 573-580. You might find what you are looking for in the quantum chemistry textbook by John Lowe, Academic Press, second edition. ---- Original post: I'm writing up a manuscript and am trying to find a reference I know I once had that related gas-phase IP and EA values to electrochemistry. It empirically corrected for solvent effects via a linear relationship (perhaps a linear free energy relationship?). In particular, I'm interested in organic pi-conjugated type molecules, but others could work too. If anyone has leads on this article or other articles relating gas-phase IP/EA data to electrochemical measurements, I'd appreciate it. I'll be glad to summarize to the list. -- -Geoff Hutchison Ratner/Marks Groups (847) 491-3295 Northwestern Chemistry http://www.chem.northwestern.edu/ From chemistry-request@ccl.net Wed Sep 17 15:10:53 2003 Received: from mercury.chem.northwestern.edu (mercury.chem.northwestern.edu [129.105.116.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8HJAMAg012842 for ; Wed, 17 Sep 2003 15:10:22 -0400 Received: from chem.northwestern.edu (cat207.cqe.northwestern.edu [129.105.122.207]) by mercury.chem.northwestern.edu (8.12.8/8.12.8) with ESMTP id h8HJAMxP006976; Wed, 17 Sep 2003 14:10:22 -0500 (CDT) Date: Wed, 17 Sep 2003 14:10:21 -0500 Subject: Re: CCL:molecule substructure searching algorithms Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v552) Cc: chemistry{at}ccl.net To: "Mingyue Zheng" From: Geoff Hutchison In-Reply-To: <002601c37d22$96bc9fd0$4c137fca{at}simm.ac.cn> Message-Id: <9594CCE6-E942-11D7-AEEE-000A95701B7A{at}chem.northwestern.edu> Content-Transfer-Encoding: 7bit X-Mailer: Apple Mail (2.552) X-Spam-Status: No, hits=-1.0 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,USER_AGENT_APPLEMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) > The first problem harassing me is how to efficiently recognize and > sign a specific > functional group in a molecule. > > Is here anyone who could tell me where can I find some open source > code for > molecule substructure searching algorithms, or any free program > dealing with it? There are several open source implementations of Daylight SMARTS. OpenBabel (C++) http://openbabel.sf.net/ JOELib (Java) http://joelib.sf.net/ It's quite easy to write SMARTS patterns for matching functional groups. http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html -Geoff -- -Geoff Hutchison Ratner/Marks Groups (847) 491-3295 Northwestern Chemistry http://www.chem.northwestern.edu/ From chemistry-request@ccl.net Wed Sep 17 16:06:25 2003 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8HK5qAg021227 for ; Wed, 17 Sep 2003 16:05:53 -0400 Received: from dialin-16.sci.kun.nl by wn1.sci.kun.nl via dialin-16.sci.kun.nl [131.174.9.16] with ESMTP id h8HK5l6v028987 (8.12.9/3.58); Wed, 17 Sep 2003 22:05:48 +0200 (MEST) From: "E.L. Willighagen (Egon)" Reply-To: egonw~at~sci.kun.nl To: Geoff Hutchison , "Mingyue Zheng" Subject: Re: CCL:molecule substructure searching algorithms Date: Wed, 17 Sep 2003 22:07:14 +0200 User-Agent: KMail/1.5.1 Cc: chemistry~at~ccl.net References: <9594CCE6-E942-11D7-AEEE-000A95701B7A~at~chem.northwestern.edu> In-Reply-To: <9594CCE6-E942-11D7-AEEE-000A95701B7A~at~chem.northwestern.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200309172207.14473.egonw~at~sci.kun.nl> X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_KMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On Wednesday 17 September 2003 21:10, Geoff Hutchison wrote: > > The first problem harassing me is how to efficiently recognize and > > sign a specific functional group in a molecule. > > > > Is here anyone who could tell me where can I find some open source > > code for molecule substructure searching algorithms, or any free program > > dealing with it? CDK (Java, http://cdk.sf.net/) does substructure searching. Egon -- PhD Molecular Representation in Chemometrics Laboratory of Analytical Chemistry http://www-cac.sci.kun.nl/people/egonw.html