From chemistry-request@ccl.net Tue Mar 15 03:05:40 2005 Received: from ppsw-5.csi.cam.ac.uk (ppsw-5.csi.cam.ac.uk [131.111.8.135]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2F85eNO025006 for ; Tue, 15 Mar 2005 03:05:40 -0500 Received: from hermes-1.csi.cam.ac.uk ([131.111.8.51]:39595) by ppsw-5.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.155]:25) with esmtpa (EXTERNAL:ab454) id 1DB73Z-0000bS-IA (Exim 4.44) (return-path ); Tue, 15 Mar 2005 08:05:37 +0000 Received: from prayer by hermes-1.csi.cam.ac.uk (hermes.cam.ac.uk) with local (PRAYER:ab454) id 1DB73Z-0005H8-JI (Exim 4.43) (return-path ); Tue, 15 Mar 2005 08:05:37 +0000 From: Andreas Bender To: CHMINF-L/at/LISTSERV.INDIANA.EDU, chemistry/at/ccl.net, boyd/at/CHEM.IUPUI.EDU Subject: Re: molecular similarity, access restrictions rectified Date: 15 Mar 2005 08:05:37 +0000 X-Mailer: Prayer v1.0.13 X-Originating-IP: [131.111.121.25] In-Reply-To: Message-ID: References: <423079CD.268012AA/at/chem.iupui.edu> Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Sender: ab454/at/hermes.cam.ac.uk X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned Dear all, Access to the similarity search at http://cheminformatics.org/simsearch is now open to everyone. During setup restrictions to local IP addresses were applied and I simply didn't delete the .htaccess file. Shame on me - the infinite enlightenment of a PhD obviously still has to dawn upon me. My sincerest apologies and thank you for everyone who replied so far. Please contact me in case of any further comments. For details see the attached mail below. Best wishes, Andreas -- Andreas Kieron Patrick Bender http://www.andreasbender.de On Mar 14 2005, Andreas Bender wrote: > > Hi, Is there a web server where one can submit SMILES or molfiles > > and have a Tanimoto similarity score computed? Thanks, Don > > Hi Don and everyone interested, > > I just set up a web form for similarity searching at the following > URL: http://cheminformatics.org/simsearch/ > > You can upload a query and a library (restricted to 1000 > structures for traffic reasons) and the script will score and rank > the library structures according to Tanimoto simimilarity to the > query. Circular fingerprints ("MOLPRINT 2D") are used for this > purpose; mol2 input format is required. (Might include the > conversion from other formats in the future if I have time.) > > The descriptor has been recently validated and published in J. > Chem. Inf. Comput. Sci. , 2004, 44, 170-178 ( DOI > http://dx.doi.org/10.1021/ci034207y ) and J. Chem. Inf. Comput. > Sci. , 2004, 44, 1708-1718 ( DOI > http://dx.doi.org/10.1021/ci0498719 ) on several datasets from the > MDDR. > > Source code / binaries for local installation can also be obtained > from me (for Linux and IRIX). Access to the web site as well as the > tools themselves are free (feel free to invite me for a pint if you > find the tool useful :-) ). And if you are looking for a postdoc in > virtual screening or other areas of ligand-based drug design from > early next year on - any location worldwide, interesting work more > important than pay, you are more than welcome to contact me. > > Best wishes, > Andreas > > P.S.: I tested the site on Windows and Linux with Netscape, IE and > Konqueror - if there are any strange error messages or otherwise > unexplicable behaviour please inform me. > > From chemistry-request@ccl.net Tue Mar 15 10:04:03 2005 Received: from mx1.ustc.edu.cn (ns.ustc.edu.cn [202.38.64.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2FF40Nt018009 for ; Tue, 15 Mar 2005 10:04:01 -0500 Received: from ustc.edu.cn (email.ustc.edu.cn [202.38.64.8]) by mx1.ustc.edu.cn (8.11.6/8.11.6) with SMTP id j2FDnMq03733 for ; Tue, 15 Mar 2005 21:49:23 +0800 Received: (eyou send program); Tue, 15 Mar 2005 21:57:42 +0800 Message-ID: <310895062.23318 () ustc.edu.cn> Received: from 202.38.82.38 by 202.38.64.8 with HTTP; Tue, 15 Mar 2005 21:57:42 +0800 X-WebMAIL-MUA: [202.38.82.38] From: "Huan Zhan" To: chemistry () ccl.net Date: Tue, 15 Mar 2005 21:57:42 +0800 Reply-To: "Huan Zhan" X-Priority: 3 Subject: A question about basis set including spin-orbit correction Content-Type: text/plain Hi, everyone: I am trying to do some calculation on transition metal clusters with Gaussian98. The basis set I have chosen include spin-orbit correction which is described as below: Basis Set Expn. C(n=4) C(n=5) (-4.276) (-0.2357) s 2.755 -3.199012 1.021876 2.283 3.442446 -1.150251 0.6654 0.587557 -0.275872 0.1015 0.006566 0.608271 0.03656 -0.000981 0.532979 (-2.749) p 5.594 -0.139059 1.683 0.722125 0.6177 0.415392 0.0833 0.014673 0.02520 -0.004374 (-0.5079) d 2.651 0.211233 1.457 0.319090 0.6517 0.439187 0.2210 0.249585 Potential n Exp. Coef. f 5 2 6.264100 -3.583704 2 17.344300 -41.529720 2 49.052200 -90.437640 2 167.699300 -254.952445 1 583.984700 -26.654188 s-f 7 2 2.663100 -27.865314 2 3.130400 89.866401 2 4.203600 -176.237830 2 6.233300 323.629535 2 8.938600 -149.800874 1 14.172400 18.868885 0 9.847400 3.267561 p-f 7 2 2.525500 -27.751392 2 3.002200 94.344560 2 4.046200 -187.945038 2 6.164900 377.220075 2 9.546400 -298.965025 1 14.713400 56.066181 0 99.159800 4.337621 d-f 7 2 3.039300 38.588593 2 3.620400 -126.887046 2 5.005900 263.188524 2 7.604500 -325.305981 2 12.028900 319.688475 1 36.319500 12.954285 0 30.562900 7.228974 spin-orbit operator p-f 7 2 2.525500 .143660 2 3.002200 1.210926 2 4.046200 -8.474302 2 6.164900 33.759634 2 9.546400 -43.680972 1 14.713400 1.097872 0 99.159800 -.150004 d-f 7 2 3.039300 .836538 2 3.620400 -2.772086 2 5.005900 5.791072 2 7.604500 -7.172794 2 12.028900 3.666091 1 36.319500 -.243119 0 30.562900 .010721 f 5 2 6.264100 -.029867 2 17.344300 .040639 2 49.052200 .641132 2 167.699300 1.784101 1 583.9 However, I have heard that Gaussian can't calculate the basis set that includes spin-orbit correction. I wonder is that true. If the program can do the calculation, could anyone give an example of input format. Thank you! From chemistry-request@ccl.net Tue Mar 15 10:32:44 2005 Received: from mprelay.uc.edu (mprelay.uc.edu [129.137.3.48]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2FFWhI1019731 for ; Tue, 15 Mar 2005 10:32:44 -0500 Received: from mirapoint.uc.edu (webmail.uc.edu [10.23.4.254]) by mprelay.uc.edu (MOS 3.4.7-GR) with ESMTP id CQJ41472; Tue, 15 Mar 2005 09:24:12 -0500 (EST) Received: from 10.39.6.152 by mirapoint.uc.edu (MOS 3.4.7-GR) with HTTP/1.1; Tue, 15 Mar 2005 09:24:12 -0500 Date: Tue, 15 Mar 2005 09:24:12 -0500 From: Chi-Yuan Chen Subject: Ensembles in Gaussian03? To: Computational Chemistry List X-Mailer: Webmail Mirapoint Direct 3.4.7-GR MIME-Version: 1.0 Message-Id: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Sirs: Does anyone know how to set up ensembles, like NVT or NVE, for dynamics calculations(BOMD or ADMP) in Gaussian03? I very appreciate your help! Chi-Yuan Chen Graduate Student OBR Center for Computer-Aided Molecular Design Department of Chemical and Materials Engineering University of Cincinnati Cincinnati, Ohio 45221-0171 Email: chenca ~~ email.uc.edu From chemistry-request@ccl.net Tue Mar 15 10:49:37 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2FFnZGE020651 for ; Tue, 15 Mar 2005 10:49:35 -0500 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j2FFnZjC020650 for chemistry ~~ ccl.net; Tue, 15 Mar 2005 10:49:35 -0500 Date: Tue, 15 Mar 2005 10:49:35 -0500 Message-Id: <200503151549.j2FFnZjC020650 ~~ server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request ~~ ccl.net using -f From: "Elie, , Cohen" To: chemistry ~~ ccl.net X-Web-Message-Number: 050315104849-20613 Subject: W: New release of Molecular Conceptor v2.2 Synergix Ltd. is pleased to announce the release of Molecular Conceptor v2.2. Molecular Conceptor is a computer-based course for teaching rational drug design and molecular modeling. The course contains more than 3000 slides, 1500 3D molecules and is the fruit of 7 years of intensive development. Click here to review the NEW table of contents: http://www.molecular-conceptor.com/toc.html I invite you to get more details from our website: http://www.molecular-conceptor.com Elie Cohen elie ~~ molecular-conceptor.com elie ~~ drugdesign.org Project Leader Molecular Conceptor From chemistry-request@ccl.net Tue Mar 15 12:32:13 2005 Received: from ppsw-4.csi.cam.ac.uk (ppsw-4.csi.cam.ac.uk [131.111.8.134]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2FHWCRV028709 for ; Tue, 15 Mar 2005 12:32:13 -0500 Received: from adsl-64-175-175-163.dsl.sndg02.pacbell.net ([64.175.175.163]:1427 helo=arcturus.cam.ac.uk) by ppsw-4.csi.cam.ac.uk (smtp.hermes.cam.ac.uk [131.111.8.154]:25) with esmtpsa (LOGIN:pm286) (TLSv1:RC4-SHA:128) id 1DBEgA-0004q2-DN (Exim 4.44) (return-path ); Tue, 15 Mar 2005 16:13:59 +0000 Message-Id: <6.0.1.1.0.20050315161143.01ba2688=at=pop.hermes.cam.ac.uk> X-Sender: pm286=at=pop.hermes.cam.ac.uk X-Mailer: QUALCOMM Windows Eudora Version 6.0.1.1 Date: Tue, 15 Mar 2005 16:13:51 +0000 To: Andreas Bender , CHMINF-L=at=LISTSERV.INDIANA.EDU, chemistry=at=ccl.net, boyd=at=CHEM.IUPUI.EDU From: Peter Murray-Rust Subject: Re: CCL:molecular similarity, access restrictions rectified Cc: yong Zhang In-Reply-To: References: <423079CD.268012AA=at=chem.iupui.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Sender: pm286=at=hermes.cam.ac.uk X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned At 08:05 15/03/2005, Andreas Bender wrote: >http://cheminformatics.org/simsearch Thanks Andreas, Two suggestions: - a list of test molecules so users who don't have mol2 files can test the system - (talk with YY) - a link to our webserver so people can convert molecules with Openbabel as part of the process. Webservices should make this transparent. Also you can clone our server (with attribution) P. Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 Fax: +44 1223 763076 From chemistry-request@ccl.net Tue Mar 15 14:14:47 2005 Received: from pm-mx6.mx.noos.fr (pm-mx6.mgn.net [195.46.220.208]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2FJEkUF003037 for ; Tue, 15 Mar 2005 14:14:46 -0500 Received: from ALB.cristal.org (m212.net195-132-128.noos.fr [195.132.128.212]) by pm-mx6.mx.noos.fr (Postfix) with ESMTP id EA8CC26D7A for ; Tue, 15 Mar 2005 18:57:58 +0100 (MET) Message-Id: <5.2.0.9.2.20050315184213.00bd41c8 |a| mail.noos.fr> X-Sender: xtal |a| mail.noos.fr (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Tue, 15 Mar 2005 18:57:44 +0100 To: From: Armel Le Bail Subject: Inorganic structure prediction with GRINSP Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi, A new software, GRINSP, for inorganic structure prediction of N-connected 3D nets is available : http://sdpd.univ-lemans.fr/grinsp/ Structure candidates are produced for N=3, 4, 5, 6 in binary compounds M2X3, MX2, M2X5, MX3 or in ternary compounds mixing tetrahedra and octahedra, or triangles like BO3 with octahedra or tetrahedra, etc. The current limitation is that polyhedra are exclusively connected by corners. The description is now published as an open access paper in the J. Appl. Cryst. : http://scripts.iucr.org/cgi-bin/paper?cg5019 More than 1000 hypothetical structures are available as CIF files in the PCOD (Predicted Crystallography Open Database): http://www.crystallography.net/pcod/ Much more to come... This database expects to receive the upload of small or medium-size hypothetical crystal sructures, inorganic or organic. Send preferably CIF files, thanks ! A. Le Bail From chemistry-request@ccl.net Tue Mar 15 17:25:18 2005 Received: from cascades-ss.cascades.com (host-37.norampac.com [207.164.26.37]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j2FMPHrX014368 for ; Tue, 15 Mar 2005 17:25:17 -0500 Received: from do_webmail-MTA by cascades-ss.cascades.com with Novell_GroupWise; Tue, 15 Mar 2005 16:24:27 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.2 Date: Tue, 15 Mar 2005 16:23:59 -0500 From: "Mathieu Roberge" To: Subject: First Applied Pulp & Paper Molecular Modelling Symposium Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j2FMPIrX014371 Hello everybody, The Cascades R&D Centre and the Norampac Technical and Development Centre have decided to organize the First Applied Pulp and Paper Molecular Modelling Symposium (FAPPMMS), in partnership with Domtar as well as McGill, UQTR and McMaster universities. This symposium will be held on 24 to 26 of August, 2005, at the McCord Museum in Montrial, Qc, Canada. More information on how to subit a paper and/or attend the symposium is available on the following web site : http://www.fappmms.org/ Mathieu Roberge, M. Sc. Chimiste Recherche et diveloppement Cascades Canada inc. Til.: (819) 363-5745 Cel.: (819) 350-7033 Fax : (819) 363-5755 471, boul. Marie-Victorin, Kingsey Falls, Quibec, Canada, J0A 1B0