From chemistry-request@ccl.net Sat May 1 06:24:32 2004 Received: from gold.csi.cam.ac.uk (gold.csi.cam.ac.uk [131.111.8.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i41BOVkh025457 for ; Sat, 1 May 2004 06:24:31 -0500 Received: from snow.csi.cam.ac.uk ([131.111.8.15]) by gold.csi.cam.ac.uk with esmtp (Exim 4.20) id 1BJsd4-0006Wr-Ts for chemistry*at*ccl.net; Sat, 01 May 2004 12:25:58 +0100 Received: from prayer by snow.csi.cam.ac.uk with local (Exim 4.30) id 1BJsd4-0000O2-RM for chemistry*at*ccl.net; Sat, 01 May 2004 12:25:58 +0100 From: Andreas Bender To: chemistry*at*ccl.net Subject: Cheminformatics Programs, QSAR Datasets Links Available Date: 01 May 2004 12:25:58 +0100 X-Mailer: Prayer v1.0.11 X-Originating-IP: [131.111.121.25] Message-ID: Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset=ISO-8859-1 X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned X-Spam-Status: No, hits=3.5 required=7.5 tests=FROM_ENDS_IN_NUMS, FVGT_s_OBFU_Q1,MAILTO_TO_SPAM_ADDR,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL'lers, During my PhD I came across quite a number of cheminformatics-related programs (or libraries for your own programs) and lots of QSAR (Solubility, Toxicity, Caco-2 permeability, hERG affinity, etc.) datasets. I now compiled a list of both datasets and programs which I found useful at http://www.cheminformatics.org The datasets (which link to external websites or are drawn by hand) always contain molecular structures, in contrast to some other dataset collections. This facilitates the generation of descriptors one prefers. Please just contact me if you would like to include information - or if you find errors in the structures (for which I already apologize.) Right now, close to 20 datasets are available, ranging in size from ~20 to several thousand structures and covering a range of properties like Caco-2 permeability, standard QSAR datasets, aequeous solubility etc.. The linklist is classified by genre of the program or other resource and should (in principle ...) by up-to-date. It's using phplinks, so links can be checked for validity automatically and new resources can be submitted by users. So far classification is far from being perfect, but given the additional search facility one should usually find what one is looking for. There are close to 300 links in there right now, mainly to computer programs (classified by area like docking/alignment, file format tools, QM, MM/MD, etc.), but also to relevant university websites, databases and other resources. I hope some of you find these resources useful, Best wishes, Andreas -- Andreas Kieron Patrick Bender - http://www.andreasbender.de ab454*at*cam.ac.uk - Andreas.Bender*at*Alumni.TU-Berlin.DE From chemistry-request@ccl.net Sat May 1 14:16:34 2004 Received: from web21208.mail.yahoo.com (web21208.mail.yahoo.com [216.136.175.205]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i41JGXkh002659 for ; Sat, 1 May 2004 14:16:33 -0500 Message-ID: <20040501191758.91420.qmail..at..web21208.mail.yahoo.com> Received: from [4.239.219.153] by web21208.mail.yahoo.com via HTTP; Sat, 01 May 2004 12:17:58 PDT Date: Sat, 1 May 2004 12:17:58 -0700 (PDT) From: Konstantin Kudin Subject: Re: Question regarding Gaussian warnings and output file tags To: chemistry..at..ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Douglas Sievers wrote: > As all users of Gaussian know, the output files are usually full of > cryptic phrases, such as the following ... Those "cryptic" phrases are probably not meant for the end users, but rather for those developing and debugging new code. And in most cases there should be no harm in not knowing what those phrases mean if you're the end user. In any event, the message "EnCoef did X forward-backward iterations" relates to the constrained optimization within EDIIS which is a robust SCF convergence algorithm {J. Chem. Phys. 116, 8255 (2002)} http://dx.doi.org/10.1063/1.1470195 Regards, Konstantin __________________________________ Do you Yahoo!? Win a $20,000 Career Makeover at Yahoo! HotJobs http://hotjobs.sweepstakes.yahoo.com/careermakeover