From chemistry-request@server.ccl.net Mon Oct 18 16:45:54 1999 Received: from bobino.sefmedia.com (bobino.sefmedia.com [207.164.6.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA19649 for ; Mon, 18 Oct 1999 16:45:54 -0400 Received: from ppp-5800-01a-3122.mtl.total.net (ppp-5800-01a-3122.mtl.total.net [216.210.30.122]) by bobino.sefmedia.com (NTMail 4.30.0013/NT6102.00.ff403942) with ESMTP id tfcdaaaa for ; Mon, 18 Oct 1999 16:39:20 -0400 Reply-To: From: "Bill Hayden" To: Subject: APOLOGY Date: Mon, 18 Oct 1999 16:33:46 -0400 Message-ID: <000601bf19a8$141b5940$c40101c0@zman> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Our apologies for our recent posting announcing our new web site. The web site was not yet up when the CCL went out. IT IS NOW READY!!! Thanks, Bill ***************************************************************** Chemical Computing Group Inc. has just released the latest edition of its web site, “The Journal of the Chemical Computing Group” (http://www.chemcomp.com). Our new edition contains features on: *3D Bioinformatics & Comparative Modeling in MOE: Overiew of the MOE protien tools and presentation of CASP results; *Molecular Databases and MOE: Introduction to MOE's molecular database, Database Viewer and sundry database tools and applications; *MOE 1999.05: Facts & Features: Rundown of the newest features in MOE; This issue we are happy to have a "Guest Feature" by Dr. Jeff Madura of Duquesne University entitled: "Experiences Using MOE in Academia: Five different areas in which MOE is used to further research and education. In addition check out our departments: *About CCG *Products *Support & Training *In the News *Where We Will Be *Past JCCG Features *Japan There is also an announcement of our special offer to the academic community. http://www.chemcomp.com info@chemcomp.com William A. Hayden Vice President Chemical Computing Group hayden@chemcomp.com http://www.chemcomp.com 514 393 1055 -phone 514 874 9538 - fax William A. Hayden Vice President Chemical Computing Group hayden@chemcomp.com http://www.chemcomp.com 514 393 1055 -phone 514 874 9538 - fax From chemistry-request@server.ccl.net Tue Oct 19 00:10:24 1999 Received: from spamraaa.compuserve.com (as-img-rel-1.compuserve.com [149.174.217.142]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA21173 for ; Tue, 19 Oct 1999 00:10:23 -0400 Received: (from mailgate@localhost) by spamraaa.compuserve.com (8.9.3/8.9.3/SUN-REL-1.0) id AAA27912 for chemistry@ccl.net; Tue, 19 Oct 1999 00:02:00 -0400 (EDT) Sender: tony@acdlabs.com Received: from noteb-tony.acdlabs.com (ppp01.acdlabs.com [207.176.233.41]) by spamraaa.compuserve.com (8.9.3/8.9.3/SUN-REL-1.0) with SMTP id AAA27878; Tue, 19 Oct 1999 00:01:42 -0400 (EDT) Message-Id: <3.0.6.32.19991018233659.00833100@mail.acdlabs.com> X-Sender: tony@mail.acdlabs.com X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Mon, 18 Oct 1999 23:36:59 -0700 To: , From: Tony Williams Subject: Fw: CCL:Calculation of LogP, logD, pKa and solubility Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" There are a number of other companies that do produce modules for LogP and pKa prediction. LogD integrated prediction is a lot harder to come by. The ACD integrated suite certainly has one of the largest install bases and fastest development curves for these types of tools and there are many comparisons regarding ACD and other software results for LogP and pKa at the web site. From your letter the desktop interfaces seem strong compared to your needs and you may want to consider using the BATCH modules. There are three different versions of the batch software, compiled for three different operating systems. In addition, the modules that are available depend on the platform. Windows SGI Sun Solaris pKa pKa pKa LogP LogP LogP LogD LogD LogD The SGI and SOlaris compilations maybe more appropriate for your needs as these have already been used for the purposes you suggest below. Also...to clarify....the logD module you refer to for $19,900 is actually a compilation of SIX integrated programs. 1) Desktop LogP predictor with DB of 1000s of structures PLUS ability to train the database with your structures 2) Desktop pKa predictor with DB of 1000s of structures 3) Integrated LogD predictor using LogP and pKa tools 4) Batch LogP predictor 5) Batch pKa predictor 6) Batch LogD predictor Best wishes and good luck in your hunt! Tony Williams From: zheng@sciosinc.com To: chemistry@ccl.net Date: Friday, October 15, 1999 11:50 PM Subject: CCL:Calculation of LogP, logD, pKa and solubility. > > >Hi, > > I am looking for softwares for calculating physical and chemical > properties of small molecules, including logP, logD, pKa, solubility, > and etc. Specifically, I need executable programs that can read > in, e.g. an SD file of 1 or more molecules, and then write out their > corresponding calculated properties to an output file. I need to > directly access the executable programs from within my own > programs written in C++/Java without using any user-interface. > > While the ACD Labs in Toronto provides softwares to calculate > logP, logD, pKa, and etc., it is not apparent whether and how these > softwares can be accessed directly from a user's own programs. > ACD softwares are rather expensive, e.g. the logP module is $3,900 > whereas the logD module is $19,900, albeit such modules come > with a lot bells and whistles that I don't really need. > > Any suggestions? > > Thanks, > > Qiang Zheng > Sr. Scientist, PhD > Scios Inc. > 820 West Maude Avenue > Sunnyvale, CA 94086 > 408-616-8253 (tel) > 408-616-8206 (fax) > zheng@sciosinc.com > From chemistry-request@server.ccl.net Tue Oct 19 13:32:41 1999 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA25382 for ; Tue, 19 Oct 1999 13:32:41 -0400 Received: from ithi.schrodinger.com (vacek@ithi.schrodinger.com [192.156.98.12]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id KAA20364; Tue, 19 Oct 1999 10:25:39 -0700 Received: (from vacek@localhost) by ithi.schrodinger.com (8.8.5/8.8.5) id KAA10746; Tue, 19 Oct 1999 10:25:36 -0700 Date: Tue, 19 Oct 1999 10:25:35 -0700 (PDT) From: George Vacek To: angelo vargas cc: Computational Chemistry List Subject: Re: CCL:summary on Ni basis set In-Reply-To: <380B127E.7B94F8A0@tech.chem.ethz.ch> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 18 Oct 1999, angelo vargas wrote: > here are the answers (11) to my enquiry on a good gaussians Ni basis > set. > I thank the authors of the answers for their help. Angelo Sorry I didn't respond sooner. I only noticed your summary, not the original post. As several respondants pointed out, the real issue is most likely the initial guess, not the basis set itself. The Jaguar Quantum Chemistry package has a high quality initial guess specifically designed for systems containing transition metals. The success rate of this initial guess is phenomenal compared with the Huckel guess that's used in Gaussian, for instance. The method and some results are published in: G. Vacek, J.K. Perry and J.-M. Lanlois, Chem. Phys. Lett., 310 (1999) pp189-94. You should also be able to get an evaluation copy of the program to try it out for your systems. Information on that can be found at the Schrodinger web site. http://www.schrodinger.com/ Regards, George =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= George Vacek + Schrodinger, Inc. (503) 299-1150 + 1500 SW First, Suite 1180 vacek@schrodinger.com + Portland, OR 97201 http://www.schrodinger.com/~vacek/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=