From chemistry-request@server.ccl.net Mon Nov 25 20:46:39 2002 Received: from web20610.mail.yahoo.com ([216.136.226.168]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gAQ1kdO05763 for ; Mon, 25 Nov 2002 20:46:39 -0500 Message-ID: <20021126014639.17206.qmail@web20610.mail.yahoo.com> Received: from [206.111.112.115] by web20610.mail.yahoo.com via HTTP; Mon, 25 Nov 2002 17:46:39 PST Date: Mon, 25 Nov 2002 17:46:39 -0800 (PST) From: Sengen Sun Subject: Looking for a physical reference of wave-character for fullerene To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii I am looking for a reference of physics that deals with the wave character of fullerene molecules. I got the clue about this research somewhere (ACS web site?). But I lost it. The content of the paper is about the wave character of molecules when passing through something like a “grating”. At a high temperature, the waves can be even observed using fullerene molecules. As I remember, the author(s) mentioned that the difficulty for fullerene is that the fullerene molecules are too big. The intermolecular interactions become significant in the gas phase for big molecules, and the waves can be destroyed if the intermolecular interactions are present. The paper is very important to me as I am trying to learn the physicists’ view on the wave character. Thank you very much if any body can help. Sengen __________________________________________________ Do you Yahoo!? Yahoo! Mail Plus – Powerful. Affordable. Sign up now. http://mailplus.yahoo.com From chemistry-request@server.ccl.net Mon Nov 25 20:52:48 2002 Received: from smtp01.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQ1qkO06132 for ; Mon, 25 Nov 2002 20:52:48 -0500 Received: from PC12 (unknown [202.127.19.236]) by smtp01.sohu.com (Postfix) with ESMTP id 5775E538F7 for ; Tue, 26 Nov 2002 09:26:42 +0800 (CST) Date: Tue, 26 Nov 2002 9:53:7 +0800 From: "Liu zhiguo" Reply-To: zgliu@sohu.com To: "CHEMISTRY@ccl.net" Subject: Autodock X-mailer: Foxmail 4.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: <20021126012642.5775E538F7@smtp01.sohu.com> Dear CCLers, I have a question about "grid center" in the grid parameter file.There are two choices for this parameter:"xyz-coordinate" or "auto".According to what I know,xyz-coordinate is determined by the ligand position.Howeve,I don't know what "auto" means exactly.There is no help about this in autodock manual.Could anybody tell me what it means?Any help is appreciated! Best Regards! _______________________________________ Liu zhi-guo,Ph.D candidate, Shanghai Institute of Materia Medica` Phone:021-64311833-615 Email:zgliu@sohu.com _______________________________________ From chemistry-request@server.ccl.net Tue Nov 26 02:45:47 2002 Received: from gip2.u-picardie.fr ([193.49.184.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQ7jki27875 for ; Tue, 26 Nov 2002 02:45:47 -0500 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id 5830C91EF; Tue, 26 Nov 2002 08:45:47 +0100 (CET) To: gunter@chemeng.uct.ac.za, chemistry@ccl.net Subject: Re:SCF convergence with Lanthanide ECP/Basis set Message-ID: <1038296747.3de326ab4d9ca@webmail.u-picardie.fr> Date: Tue, 26 Nov 2002 08:45:47 +0100 (CET) From: FyD References: <1038256842.3de28aca5d309@webmail.u-picardie.fr> <3DE304FC.BCBA044@chemeng.uct.ac.za> In-Reply-To: <3DE304FC.BCBA044@chemeng.uct.ac.za> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 Dear Gunter, Dear All, > What method are you using - Hartree-Fock, MP2 or DFT? I use HF method as a first step. ----- Dear All, I am using the Cundari & Stevens ECP with the corresponding BASIS SET to optimize some Lanthanide derivatives. The SCF procedure DOES converge but demands a looot of steps with GAMESS or Gaussian98 (close or more than 200; the convergence is very slow). Is it a known problem for such calculations (such molecules and particular ECP/basis sets) and is there a way to decrease this number of SCF steps ? As in GAMESS the maximum number of SCF step is 200 how could I do if the SCF demand more than these 200 steps ? Should I modify the GAMESS source code and should I recompile GAMESS ? Thanks, regards, Francois From chemistry-request@server.ccl.net Tue Nov 26 04:40:39 2002 Received: from huygens.rijnh.nl ([192.42.124.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQ9eci02200 for ; Tue, 26 Nov 2002 04:40:38 -0500 Received: from pccoldmol1.rijnh.nl.huygens.rijnh.nl (pccoldmol1.rijnh.nl [192.42.124.141]) by huygens.rijnh.nl (SGI-8.9.3/8.9.3) with ESMTP id KAA76704; Tue, 26 Nov 2002 10:41:46 +0100 (MET) Sender: jochen@pccoldmol1.rijnh.nl To: Sengen Sun Cc: chemistry@ccl.net Subject: Re: CCL:Looking for a physical reference of wave-character for fullerene References: <20021126014639.17206.qmail@web20610.mail.yahoo.com> User-Agent: Emacs/Gnus X-Attribution: Jochen In-Reply-To: <20021126014639.17206.qmail@web20610.mail.yahoo.com> From: jochen@nowhere.net Organization: private Date: 26 Nov 2002 10:40:48 +0100 Message-ID: <877kf04qjj.fsf@pccoldmol1.rijnh.nl> Lines: 14 MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id gAQ9edi02205 On Mon, 25 Nov 2002 17:46:39 -0800 (PST) Sengen Sun wrote: Sengen> I am looking for a reference of physics that deals with the Sengen> wave character of fullerene molecules. I got the clue about Sengen> this research somewhere (ACS web site?). But I lost it. Anton Zeilinger. Sorry, don't have the ref. for a paper. Cheers Jochen -- Einigkeit und Recht und Freiheit http://www.Jochen-Kuepper.de Liberté, Égalité, Fraternité GnuPG key: CC1B0B4D Sex, drugs and rock-n-roll From chemistry-request@server.ccl.net Tue Nov 26 05:34:00 2002 Received: from kelly.bath.ac.uk ([138.38.32.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQAY0i04758 for ; Tue, 26 Nov 2002 05:34:00 -0500 Received: from mmdf by kelly.bath.ac.uk with pleasure id 18Gd2W-0007Op-01 for chemistry@ccl.net; Tue, 26 Nov 2002 10:34:00 +0000 Received: from midge.bath.ac.uk ([138.38.32.34] ident=mmdf) by kelly.bath.ac.uk with smtp id 18Gd2V-0002KF-01 for chemistry@ccl.net; Tue, 26 Nov 2002 10:33:59 +0000 Received: from prpcn144 ( prpc-n144.bath.ac.uk [138.38.128.144] ) by bath.ac.uk id aa07335 for ; 26 Nov 2002 10:33 +0000 From: James Robinson To: Chemistry Subject: Dielectric Constant of 4 Date: Tue, 26 Nov 2002 10:36:11 -0000 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id gAQAY2i04759 When building homology models of proteins, is there a particular reason why force-field dielectric constants are set to 4. Does this apply just modelling GPCR models or to a wide range of enzymes and proteins? Thanks in advance. James From chemistry-request@server.ccl.net Tue Nov 26 04:20:58 2002 Received: from laplinux.dcfe.unimi.it ([159.149.31.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQ9Kvi01204 for ; Tue, 26 Nov 2002 04:20:58 -0500 Received: from laplinux.dcfe.unimi.it (localhost [127.0.0.1]) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/SuSE Linux 0.6) with ESMTP id gAQ9JSGY004372 for ; Tue, 26 Nov 2002 10:19:28 +0100 Received: from localhost (acontini@localhost) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/Submit) with ESMTP id gAQ9JSfa004369 for ; Tue, 26 Nov 2002 10:19:28 +0100 X-Authentication-Warning: laplinux.dcfe.unimi.it: acontini owned process doing -bs Date: Tue, 26 Nov 2002 10:19:28 +0100 (CET) From: Alessandro Contini X-X-Sender: acontini@laplinux.dcfe.unimi.it To: CCL Subject: Number of tesserae in gaussian PCM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id gAQ9Kwi01205 Hi, I'm trying to perform a single point calculation using MP2/6-31G** basis and a PCM model for a complex, but the job ends with an error message: TESSERA: too many vertices in a tessera I tried to increase the number of tesserae by specifying TSNUM=100 at the end of the input file, but the program seems not to recognize this option. Does anybody knows how to fix this? Thanks a lot Alessandro Dott. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm From chemistry-request@server.ccl.net Tue Nov 26 04:17:08 2002 Received: from wrzx35.rz.uni-wuerzburg.de ([132.187.3.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQ9H7i00998 for ; Tue, 26 Nov 2002 04:17:07 -0500 Received: from wrzx34.rz.uni-wuerzburg.de (wrzx34.rz.uni-wuerzburg.de [132.187.3.34]) by wrzx35.rz.uni-wuerzburg.de (8.8.8/8.8.8/uniwue-MM-1.05) with ESMTP id KAA02263 for ; Tue, 26 Nov 2002 10:17:07 +0100 (MET) Received: from localhost (localhost [127.0.0.1]) by virusscan.rz.uni-wuerzburg.de (Postfix) with ESMTP id A67F0622FF for ; Tue, 26 Nov 2002 10:17:07 +0100 (CET) Received: from wrzx07.rz.uni-wuerzburg.de (wrzx07.rz.uni-wuerzburg.de [132.187.1.7]) by wrzx34.rz.uni-wuerzburg.de (Postfix) with ESMTP id 99F74CE7 for ; Tue, 26 Nov 2002 10:17:07 +0100 (CET) Received: from spamchecker (localhost [127.0.0.1]) by spamcheck.rz.uni-wuerzburg.de (Postfix) with ESMTP id BD0974320 for ; Tue, 26 Nov 2002 10:17:06 +0100 (CET) Received: from wocx51.chemie.uni-wuerzburg.de (wocx51.chemie.uni-wuerzburg.de [132.187.64.51]) by wrzx07.rz.uni-wuerzburg.de (Postfix) with ESMTP id 823394204 for ; Tue, 26 Nov 2002 10:17:04 +0100 (CET) Received: from chemie.uni-wuerzburg.de (wocd73.chemie.uni-wuerzburg.de [132.187.64.173]) by wocx51.chemie.uni-wuerzburg.de (SGI-8.9.3/8.9.3/uniwue-M-1.0) with ESMTP id KAA35238 for ; Tue, 26 Nov 2002 10:17:04 +0100 (MEZ) Message-ID: <3DE33D2B.E4893122@chemie.uni-wuerzburg.de> Date: Tue, 26 Nov 2002 10:21:47 +0100 From: Bernd Engels X-Mailer: Mozilla 4.78 [de] (Windows NT 5.0; U) X-Accept-Language: de MIME-Version: 1.0 To: ccl Subject: list about already computed molecules Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=-11.4 required=8.0 tests=CARRIAGE_RETURNS,LOCAL_CLIENT,LOCAL_SENDER,NICE_HELO, SPAM_PHRASE_00_01,SUBJECT_IS_LIST,USER_AGENT_MOZILLA_XM, X_ACCEPT_LANG version=2.43-string_20021002 X-Spam-Level: X-Virus-Scanned: by AMaViS snapshot-20020422 Dear all, I would like to make a listing about lists in the internet which contain the results of computation. I know their are some around but I not sure if I know all of them. Any help? Bernd -- Prof. Dr. Bernd Engels Institut für Organische Chemie Bayerische Julius-Maximilians-Universität Würzburg Am Hubland D- 97074 Würzburg Tel.: ++49 (0)931 - 888 - 5394 Fax: ++49 (0)931 - 888 - 4606 e-mail: bernd@chemie.uni-wuerzburg.de From chemistry-request@server.ccl.net Tue Nov 26 09:43:29 2002 Received: from laplinux.dcfe.unimi.it ([159.149.31.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQEhTi14056 for ; Tue, 26 Nov 2002 09:43:29 -0500 Received: from laplinux.dcfe.unimi.it (localhost [127.0.0.1]) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/SuSE Linux 0.6) with ESMTP id gAQEg6GY009621 for ; Tue, 26 Nov 2002 15:42:06 +0100 Received: from localhost (acontini@localhost) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/Submit) with ESMTP id gAQEg5S0009606 for ; Tue, 26 Nov 2002 15:42:05 +0100 X-Authentication-Warning: laplinux.dcfe.unimi.it: acontini owned process doing -bs Date: Tue, 26 Nov 2002 15:42:04 +0100 (CET) From: Alessandro Contini X-X-Sender: acontini@laplinux.dcfe.unimi.it To: CCL Subject: Re: CCL:Number of tesserae in gaussian PCM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id gAQEhVi14057 Thanks to Mark Russell and Z. J. Wu for the working solutions. Best Reguards Alessandro Dott. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm From chemistry-request@server.ccl.net Tue Nov 26 10:35:59 2002 Received: from soul.helsinki.fi ([128.214.3.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQFZui15797 for ; Tue, 26 Nov 2002 10:35:59 -0500 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id RAA09781; Tue, 26 Nov 2002 17:35:55 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Tue, 26 Nov 2002 17:35:55 +0200 (EET) From: Mikael Johansson X-Sender: To: James Robinson cc: Chemistry Subject: Re: CCL:Dielectric Constant of 4 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello James and All! On Tue, 26 Nov 2002, James Robinson wrote: > When building homology models of proteins, is there a particular reason > why force-field dielectric constants are set to 4. Does this apply just > modelling GPCR models or to a wide range of enzymes and proteins? I guess the epsilon=4 convention has arisen as a reasonable guess for the dielectric constant in a protein environment. It is probably very hard to make reliable measurements of epsilon in a protein, but epsilon=4 should not be ridiculously wrong. Lacking a good reason for not using epsilon=4 makes it a good "standard". The topic is discussed for example in T. Simonson, D. Perahia, Proc. Natl. Acad. Sci. USA 92 (1995) 1082-1086 Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ From chemistry-request@server.ccl.net Tue Nov 26 09:27:13 2002 Received: from Snoopy.UCIS.Dal.Ca ([129.173.1.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQERCi13634 for ; Tue, 26 Nov 2002 09:27:12 -0500 Received: from chem1.chem.dal.ca (CHEM1.Chem.Dal.Ca [129.173.17.47]) by Snoopy.UCIS.Dal.Ca (8.10.1/8.10.1) with ESMTP id gAQERC112389; Tue, 26 Nov 2002 10:27:13 -0400 (AST) Message-Id: <200211261427.gAQERC112389@Snoopy.UCIS.Dal.Ca> Received: from CHEM1/SpoolDir by chem1.chem.dal.ca (Mercury 1.40); 26 Nov 102 10:27:11 -0400 Received: from SpoolDir by CHEM1 (Mercury 1.40); 26 Nov 102 10:23:22 -0400 From: "ZHIJIAN WU" Organization: Chemistry, Dalhousie University To: chemistry@ccl.net Date: Tue, 26 Nov 2002 10:23:16 -0400 MIME-Version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Subject: Re: CCL:Number of tesserae in gaussian PCM CC: alessandro.contini@unimi.it Priority: normal In-reply-to: X-mailer: Pegasus Mail for Win32 (v3.01b) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by server.ccl.net id gAQERDi13635 Hi, Alessandro, If you put keywords like scrf=(...pcm, read, solvent=...) in your calculation, the tsnum should be changed as you defined. Furthermore, my experience from Gaussian company is that they suggest to use tsare, which is easier to manage than tsnum. Regards, Wu -------------------- Z. J. Wu, Ph D Department of Chemistry Dalhousie University Halifax, NS Canada B3H 4J3 Date sent: Tue, 26 Nov 2002 10:19:28 +0100 (CET) From: Alessandro Contini To: CCL Subject: CCL:Number of tesserae in gaussian PCM > Hi, > I'm trying to perform a single point calculation using MP2/6-31G** basis > and a PCM model for a complex, but the job ends with an error message: > > TESSERA: too many vertices in a tessera > > I tried to increase the number of tesserae by specifying TSNUM=100 at the > end of the input file, but the program seems not to recognize this option. > Does anybody knows how to fix this? > Thanks a lot > > Alessandro > > Dott. Alessandro Contini > Istituto di Chimica Organica "Alessandro Marchesini" > Facoltà di Farmacia Università degli Studi di Milano > Via Venezian, 21 20133 Milano > Tel. +390250314480 Fax +390250314476 > http://users.unimi.it/istchimorg/pagconthtm.htm > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Tue Nov 26 09:22:08 2002 Received: from mefteh.dsi.univ-paris5.fr ([193.51.86.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQEM7i13536 for ; Tue, 26 Nov 2002 09:22:08 -0500 Received: (from root@localhost) by mefteh.dsi.univ-paris5.fr (8.11.6) id gAQAjeX12642; Tue, 26 Nov 2002 11:45:40 +0100 (MET) Received: from alpha.univ-paris5.fr (alpha.univ-paris5.fr [193.51.86.2]) by mefteh.dsi.univ-paris5.fr (8.11.6) with ESMTP id gAQAjcT12633; Tue, 26 Nov 2002 11:45:38 +0100 (MET) Received: from biomedicale.univ-paris5.fr (pcumr11.biomedicale.univ-paris5.fr [172.20.101.12]) by alpha.univ-paris5.fr (8.9.3/jtpda-5.3.1) with ESMTP id LAA18953 ; Tue, 26 Nov 2002 11:45:38 +0100 (MET) Sender: rog@univ-paris5.fr Message-ID: <3DE3CE92.F09160FA@biomedicale.univ-paris5.fr> Date: Tue, 26 Nov 2002 11:42:10 -0800 From: Roger Attias Organization: Universite Rene Descartes-CNRS Paris France X-Mailer: Mozilla 4.08 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@ccl.net Subject: stable and unstable complexes Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS perl-11
Dear all,
I am comparing two Ni complexes:
-complex A: tetrahedric, 4- coordinated, which could not be crystallized.
-complex B : pyramidal, 5-coordinated (with an additional water molecule), which can be crystalized.

In other related structures, we find 4- as well as 5- coordinated crystals.
Using these 4 and 5 coordinated crystals, together with molecular dynamics on A and B models,  I measure different geometrical parameters (related to bonded and non bonded energy) in order to analyze the differences in behaviour of A and B.

I would appreciate references of papers dealing with this kind of studies ... or further refinements.

Thanks
Roger

* Dr. Roger ATTIAS
* Universite Rene Descartes
* 45 Rue des Saints Peres 75006 Paris (France)
* E-mail:Roger.Attias@biomedicale.univ-paris5.fr

From chemistry-request@server.ccl.net Tue Nov 26 12:40:17 2002 Received: from dalton.quimica.unlp.edu.ar ([163.10.18.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQHeEi22499 for ; Tue, 26 Nov 2002 12:40:14 -0500 Received: from dalton.quimica.unlp.edu.ar (dalton.quimica.unlp.edu.ar [127.0.0.1]) by dalton.quimica.unlp.edu.ar (8.12.5/8.12.5) with ESMTP id gAQHe5uG002551 for ; Tue, 26 Nov 2002 14:40:05 -0300 Message-Id: <5.1.0.14.2.20021126143333.00a10cb0@dalton.quimica.unlp.edu.ar> X-Sender: pis_diez@dalton.quimica.unlp.edu.ar X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 26 Nov 2002 14:41:50 -0300 To: chemistry@ccl.net From: Reinaldo Pis Diez Subject: Tools for administrating a linux cluster Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-AntiVirus: checked by AntiVir MailGate (version: 2.0.1.7; AVE: 6.16.0.0; VDF: 6.16.0.21; host: dalton.quimica.unlp.edu.ar) Dear netters, I'd like to hear your opinions on the current tools you're using to administrate a (heterogeneous) linux cluster. I currently know some tools such Clubmask and OSCAR, both at sourceforge.net, but I don't know which are the preferences of the comp chem community on the subject. Thanks in advance. Regards, Reinaldo From chemistry-request@server.ccl.net Tue Nov 26 12:41:10 2002 Received: from dalton.quimica.unlp.edu.ar ([163.10.18.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQHeCi22494 for ; Tue, 26 Nov 2002 12:40:40 -0500 Received: from dalton.quimica.unlp.edu.ar (dalton.quimica.unlp.edu.ar [127.0.0.1]) by dalton.quimica.unlp.edu.ar (8.12.5/8.12.5) with ESMTP id gAQHe5uG002494 for ; Tue, 26 Nov 2002 14:40:05 -0300 Message-Id: <5.1.0.14.2.20021126142248.00a0fea0@dalton.quimica.unlp.edu.ar> X-Sender: pis_diez@dalton.quimica.unlp.edu.ar X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 26 Nov 2002 14:32:55 -0300 To: chemistry@ccl.net From: Reinaldo Pis Diez Subject: NMR calculations and isotopic effects in g98 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-AntiVirus: checked by AntiVir MailGate (version: 2.0.1.7; AVE: 6.16.0.0; VDF: 6.16.0.21; host: dalton.quimica.unlp.edu.ar) Dear netters, I wonder if it is possible to study isotopic effects in experimental nmr using the implemented methods to do nmr calculations in g98. I'm interested in particular in the effect of replacing some hydrogen atoms (no neutrons) by deuterium ones on the chemical shift of a carbon atom attached to or surrounded by those H atoms. I know the readisotopes option for the freq keyword but was unable to find similar information for nmr calculations. Thanks in advance. Regards, Reinaldo From chemistry-request@server.ccl.net Tue Nov 26 11:45:16 2002 Received: from viper.abbott.com ([130.36.44.77]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQGjGi18753 for ; Tue, 26 Nov 2002 11:45:16 -0500 Received: from abtmr1.abbott.com (abtmr1.abbott.com [10.254.245.1]) by viper.abbott.com (Switch-2.1.4/Switch-2.1.0) with ESMTP id gAQGkJN15694 for ; Tue, 26 Nov 2002 10:46:23 -0600 (CST) Received: from abtapn561.northamerica.intra.abbott.com (localhost [127.0.0.1]) by abtmr1.abbott.com (Switch-2.0.6/Switch-2.0.6) with ESMTP id gAQGj8j12815 for ; Tue, 26 Nov 2002 10:45:13 -0600 (CST) To: chemistry@ccl.net Cc: james.metz@abbott.com Subject: Natural products catalog in SDF format X-Mailer: Lotus Notes Release 5.0.5 September 22, 2000 Message-ID: From: james.metz@abbott.com Date: Tue, 26 Nov 2002 10:44:22 -0600 X-MIMETrack: Serialize by Router on ABTAPN561/ESVR/ABBOTT(Release 5.0.5 |September 22, 2000) at 11/26/2002 10:41:03 AM, Serialize complete at 11/26/2002 10:41:03 AM MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_alternative 005C053086256C7D_=" This is a multipart message in MIME format. --=_alternative 005C053086256C7D_= Content-Type: text/plain; charset="us-ascii" CCL, I am looking for catalogs of isolated, available natural products which are in SDF format. Does anyone know of sources for this information? Please note that I am not interested in catalogs of compounds which would typically be included in the Available Chemicals Directory (ACD), even if ACD is (often) behind current inventory. Thank you, Jim Metz James T. Metz, Ph.D. Research Investigator Chemist GPRD R46Y AP10-2 Abbott Laboratories 100 Abbott Park Road Abbott Park, IL 60064-6100 U.S.A. Office (847) 936 - 0441 FAX (847) 935 - 0548 james.metz@abbott.com --=_alternative 005C053086256C7D_= Content-Type: text/html; charset="us-ascii"
CCL,

        I am looking for catalogs of isolated, available natural products which are in SDF format.  Does anyone know of sources
for this information?

        Please note that I am not interested in catalogs of compounds which would typically be included in the Available
Chemicals Directory (ACD), even if ACD is (often) behind current inventory.

        Thank you,
        Jim Metz



James T. Metz, Ph.D.
Research Investigator Chemist

GPRD R46Y AP10-2
Abbott Laboratories
100 Abbott Park Road
Abbott Park, IL  60064-6100
U.S.A.

Office (847) 936 - 0441
FAX    (847) 935 - 0548

james.metz@abbott.com
 --=_alternative 005C053086256C7D_=-- From chemistry-request@server.ccl.net Tue Nov 26 12:25:17 2002 Received: from postoffice2.mail.cornell.edu ([132.236.56.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQHPHi21550 for ; Tue, 26 Nov 2002 12:25:17 -0500 Received: from pobox.com (arginine.chem.cornell.edu [128.253.86.74]) by postoffice2.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id MAA21242 for ; Tue, 26 Nov 2002 12:25:12 -0500 (EST) Message-ID: <3DE3AE70.2F6623B@pobox.com> Date: Tue, 26 Nov 2002 12:25:04 -0500 From: Eric Bennett X-Mailer: Mozilla 4.75 [en] (X11; U; OSF1 V5.1 alpha) X-Accept-Language: en MIME-Version: 1.0 To: Chemistry@ccl.net Subject: Re: CCL:Dielectric Constant of 4 References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Mikael Johansson wrote: > > Hello James and All! > > On Tue, 26 Nov 2002, James Robinson wrote: > > > When building homology models of proteins, is there a particular reason > > why force-field dielectric constants are set to 4. Does this apply just > > modelling GPCR models or to a wide range of enzymes and proteins? > > I guess the epsilon=4 convention has arisen as a reasonable guess for the > dielectric constant in a protein environment. It is probably very hard to > make reliable measurements of epsilon in a protein, but epsilon=4 should > not be ridiculously wrong. Lacking a good reason for not using epsilon=4 > makes it a good "standard". > > The topic is discussed for example in > T. Simonson, D. Perahia, Proc. Natl. Acad. Sci. USA 92 (1995) 1082-1086 The history of this may in part extend back to older "empirical" modeling studies like the following, in which epsilon=4 (distance-dependent) and epsilon=2 (constant) were found to give better agreement with a high resolution crystal structure: M. Whitlow and M. M. Teeter, J. Am. Chem. Soc. 108 (1986) 7163-7172 -- Eric Bennett ( ericb@pobox.com ; http://www.pobox.com/~ericb ) From chemistry-request@server.ccl.net Tue Nov 26 21:37:40 2002 Received: from yakko.cimav.edu.mx ([148.223.46.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAR2bdi28282 for ; Tue, 26 Nov 2002 21:37:39 -0500 Received: (from nobody@localhost) by yakko.cimav.edu.mx (8.11.6/8.11.2) id gAR3Pqu23125; Tue, 26 Nov 2002 20:25:52 -0700 X-Authentication-Warning: yakko.cimav.edu.mx: nobody set sender to daniel.glossman@cimav.edu.mx using -f Received: from 148.223.46.28 (SquirrelMail authenticated user daniel.glossman) by www3.cimav.edu.mx with HTTP; Tue, 26 Nov 2002 20:25:52 -0700 (MST) Message-ID: <32909.148.223.46.28.1038367552.squirrel@www3.cimav.edu.mx> Date: Tue, 26 Nov 2002 20:25:52 -0700 (MST) Subject: G98 + Linda Linux Cluster problem From: To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.8) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Netters: Following with my last question about G98+Linda on Linux Clusters, I have made some progress: Linda was installed and the paralell version has been built. Now I have g98l command to run jobs in paralell. When I tried g98l with a simple job, with 1 proccesor, the job ran fine. when I tried with more that 1 processor, the run stops with the following error: After Link 1: shmget failed shmget failed - invalid argument Any idea of what can be happening? Thanks in advance Dr. Daniel Glossman-Mitnik From chemistry-request@server.ccl.net Tue Nov 26 13:26:33 2002 Received: from kafka.net.nih.gov ([165.112.130.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQIQXi25775 for ; Tue, 26 Nov 2002 13:26:33 -0500 Received: from gandalf.cber.nih.gov (gandalf.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (/8.10.1) with ESMTP id gAQIQXWZ020692; Tue, 26 Nov 2002 13:26:33 -0500 (EST) Date: Tue, 26 Nov 2002 12:28:43 -0500 From: Rick Venable To: Eric Bennett cc: Chemistry@ccl.net Subject: Re: CCL:Dielectric Constant of 4 In-Reply-To: <3DE3AE70.2F6623B@pobox.com> Message-ID: ReplyTo: Rick_Venable@nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > > On Tue, 26 Nov 2002, James Robinson wrote: > > > When building homology models of proteins, is there a particular reason > > > why force-field dielectric constants are set to 4. Does this apply just > > > modelling GPCR models or to a wide range of enzymes and proteins? > Mikael Johansson wrote: > > I guess the epsilon=4 convention has arisen as a reasonable guess for the > > dielectric constant in a protein environment. It is probably very hard to > > make reliable measurements of epsilon in a protein, but epsilon=4 should > > not be ridiculously wrong. Lacking a good reason for not using epsilon=4 > > makes it a good "standard". > > > > The topic is discussed for example in > > T. Simonson, D. Perahia, Proc. Natl. Acad. Sci. USA 92 (1995) 1082-1086 A note on the distance-dependent dielectric: it's not epsilon=4 (just another fixed value), but epsilon=r, i.e. the dielectric is the distance between a pair of atoms when computing the electrostatic energy from the standard Coulomb expression. A computational advantage for this was that one could use r**2 to compute the energy for an atom pair, and avoid taking a square root. On Tue, 26 Nov 2002, Eric Bennett wrote: > The history of this may in part extend back to older "empirical" modeling > studies like the following, in which epsilon=4 (distance-dependent) and > epsilon=2 (constant) were found to give better agreement with a high > resolution crystal structure: > > M. Whitlow and M. M. Teeter, J. Am. Chem. Soc. 108 (1986) 7163-7172 =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Tue Nov 26 16:56:46 2002 Received: from mxout1.cac.washington.edu ([140.142.32.134]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQLuji09281 for ; Tue, 26 Nov 2002 16:56:45 -0500 Received: from mailscan-out1.cac.washington.edu (mailscan-out1.cac.washington.edu [140.142.32.138]) by mxout1.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.11) with SMTP id gAQLueVM004419 for ; Tue, 26 Nov 2002 13:56:40 -0800 Received: FROM smtp.washington.edu BY mailscan-out1.cac.washington.edu ; Tue Nov 26 13:56:39 2002 -0800 Received: from donald ([128.95.128.116]) by smtp.washington.edu (8.12.1+UW01.12/8.12.1+UW02.11) with SMTP id gAQLudmX032447 for ; Tue, 26 Nov 2002 13:56:39 -0800 Message-ID: <00e801c29596$1b696440$74805f80@donald> From: "Carsten Detering" To: Subject: insightII vs sybyl Date: Tue, 26 Nov 2002 22:52:25 +0100 Organization: University of Washington MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00E5_01C2959E.7D22F6D0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_00E5_01C2959E.7D22F6D0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I would like to thank all of those who replied to my question. Thanks!=20 Below is a summary, for those of you who are interested. Cheers, Carsten ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carsten Detering, Ph.D. University of Washington Seattle, WA 98195 Phone 206-543-5081 Fax 206-685-8665 email detering@u.washington.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Here is my original posting: Hi folks, for quite a while now, I am pondering about the folling: why is it that = most of the modellers use Sybyl rather than InsightII? In most = publications, people say in the methods section (or elsewhere) that they = used Sybyl. I was told once that InsightII was more powerful, once you = get to know it, but since I have never used Sybyl, I cannot really = compare. Maybe some of you could point out the advantages/disadvantages that you = encountered when using either of the two programs. Thanks in advance for any helpful comments. Cheers, Carsten=20 Replies: (anonymous): =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D I had the chance to work with the 2 softwares during my Ph.D. and my = post-doc and to my point of view both softwares are complementary: Sybyl is really powerfull for the molecular modelling of small = molecules. You can also perform CoMFA studies which is not possible with = InsightII. Most of the docking tools use sybyl file format as input and = output. Another big advantage is that Sybyl will be available on Linux = in Q1 2003 so if you don't have a lot of money you should be able to run = Sybyl on a good Linux-PC. InsightII is more powerfull for the molecular modelling of the proteins = (homology modelling). Nevertheless it seems that things are changing and = I heard that improvment will be done in Sybyl to work more easily with = proteins. Finally Accelerys provide a tool (Catalyst) which is really = interesting for the development of pharmacophores and to perform = pharmacophoric searches. To summarize if you want to work especially with small molecules I would = suggest Sybyl but if you are working only on proteins and you are not = at all interested by the molecular modelling of small molecules then I = would suggest InsightII. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D I think one should not just regard the InsightII and Sybyl as such, but = the entire suite of programs Accelrys and Tripos provide. In fact, = nowadays, we use Cerius2 more than InsightII. I have no clue why = modellers prefer Tripos over Accelrys; maybe it's a religious matter. In = fact, I doubt it is actually true. My personal experience is the = opposite: both at DuPont Pharma (at least when I left 4 years ago) and = at Pharmacia Accelrys software dominates. About 3 years ago, we (i.e., = Pharmacia Italia) decided to terminate all Tripos licences as Accelrys = (then MSI) provided almost all functionality we needed, while Tripos did = not. The only program Accelrys does not have is a CoMFA equivalent. = Also, LigandFit, Accelrys' docking program, is not that great (look for = a thorough comparison in a scientific journal near you soon), but we = have QXP for docking so that does not bother us too much. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= This can quickly become a religious issue - but in my opinion: Sybyl is better for small molecules Insight is marginally better for proteins Sybyl is technically a better programme (e.g. spreadsheet and programming language) And then there is the strategic point: Sybyl is soon due to be released in a Linux version=20 Insight will cease to exist once [or if?] Accelrys moves to the Microsoft Windows platform. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D our lab uses Insight for modelling purposes. It is indeed a powerful tool though a bit awkward to use. The two main disadvantages are as far as I know that it runs only on SGI type computers (expensive and a bit outdated if you compare to modern PCs), and on the other hand that it is expensive itself (>10000$ if I remember correctly) =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D I've used both these programs, though not really extensively. In my opinion they are both overpriced dinosaurs. Accelrys (if I'm up to date on the current owner) has been trying to get people to switch from Insight to Cerius for some years, but there seem to be a lot of holdouts. Not that I have ever used Cerius, or have any idea if it is much better. My opinion is that these programs have a following because they have a user interface which is adequate for most modelling and visualisation tasks, and more importantly, people have invested time and energy in learning how to use them. The force fields and other methods which they implement are by no means the academic state of the art, but they are convenient and relatively easy to use. And of course there is a distinct lack of competing software which is much better in the user interface department... Comparing Sybyl and Insight, I would say that Sybyl has a more intuitive interface for protein modelling, particularly for the manipulation of homology models. Insight is more "high tech", implements some more advanced force fields and atom typing, and has a more polished user interface, but simple operations like adding and deleting amino acids can be very frustrating. Sybyl is also more forgiving in its ability to import structures from the PDB. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D I am not sure that your statement is true as I really have little idea = which is used more. We use both. The people looking at DNA tend to use = Sybyl and the Protein people use InsightII. But, that is more a result = of what their mentors were accustom too. I also think you will find = that many publications use Amber, Charmm, or Macromolecule However, from a money point of view, the initial cost of the software is = greater for Insight (though this depends some on the modules your = purchase) and a license for Sybyl is much less than for Insight = (depending on the level of service, by 33-66%) and people who publish = tend to come from an academic setting. =20 Personally, I prefer to use Amber. Amber does not have a 'graphical = user interface' (ignoring xleap) but there are enough freeware or very = low cost programs available to help you with analysis (eg vmd, moilview, = curves, dials and windows, etc) that this is not a big problem. In = addition, Amber takes advantage of a multi-processor environment and it = scales reasonable well. And, if you are going to do anything out of the = ordinary, in our experience, it has been easier to accomplish with = Amber. I also think that people have to understand what they are doing = to a far greater extent with Amber, etc. which, in the long run, is a = good thing. Finally, I've found Tech service from Insight/Sybyl to be = less than helpful with all but the most rudimentary problems. The = Amber_reflector, on the other hand, has answered nearly all of my = questions, etc. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D I am not an unbiased observer, having worked on several modeling codes over time, but I've always thought that Sybyl was better for small-molecule/QSAR applications while Insight was better for large-molecule/MD/struct- based modeling. I think this is due to the histories behind each program... =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Unfortunately, I have not worked with Sybyl long enough to really = understand its advantages. On the other hand, I have used InsightII and = AMBER much during the past 2 years. I agree with Fred that Insight II is = powerful for homology modeling and that Sybyl is very good for small = moleules. The downside of Amber is of course that it uses command lines, = not an interactive GUI. Still, I obtained very good models from Amber = and InsightII (protein models that is!) and acceptable models in Sybyl = (small molecules). The problem with Sybly is that its conformational = searches for macrocyclic molecules still remains to be improved. When I = finished my studies and started my new job, my first objective was to = choose a modeling software (for small molecules) for which we would be = able to make protein models for rational design down the line. We were = looking for a cost effective software that would not require buying = expensive computers (I was setting up the Molecular Modeling department = for a new Biotech). Looking around, I came about MOE (Molecular = Operating Environment) from the Chemical Computing Group (CCG Inc.) = based in Montreal, QC. What is really interesting about MOE is that = there is only one price for the entire package (it is not modular) and = the price is VERY reasonable. Moreover, MOE runs on everything but MACS = for the moment!!!!! So not only can you run it on a PC for cheap, you = can also run it in windows if you cannot afford to hire a Linux = administrator (check out = http://www.bio-itworld.com/archive/071102/linux.html for a review about = cost effectiveness of using Linux). There will obviously be some loss in = computational power but it may be worth it >... Anyhow, MOE can perform everything from small molecule modeling to large = proteins, docking, flexible alignments, etc. The only thing they are = missing at the moment is a particular section to handle NMR data. It is = very user friendly and can be very easy on the point and click side to = get what you want (maybe just a littlle too easy sometimes!). I don't = understand why MOE doesn't make it in these CCL archives because I know = a several large pharmas that use it and love it, along with academic = researches and undergraduate programs using it to teach molecular = modeling techniques. With respect to price, performace, and flexibility = of use, I (would like to) believe MOE will start taking a large segment = of the industry. Moreoever, their supprt is extensive and rapid. Take a = look at http://www.chemcomp.com for more details. The only disadvantage = of MOE is that they haven't been around for a very long time and = sometimes lack the vision of a molecular modeler, but they are keen to = learn. MOE was developped by programmers, not molecular modelers so you = can modify the entire MOE environment with a bit of programming skills. = Moreover, I find interesting tools that were developed by CCG for model = analyses (tools that I did not have the chance to discover in other = programs if they exist). Needless to say, I'm convinced that MOE is a = serious competitor to the other more traditional programs. On the other = hand, I'll say the same thinig to you as a molecular modelre at = Pharmacia told me: "... not one program can perform everything you need = which is why you need them all ;o)" . MOE on the other hand, comes close = to completeness in my opinion ... I haven't had to get other programs = yet (I've had it for 9 months). =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D I have gotten the chance of using Sybyl as well as InsightII during my Ph.D. InsightII is definitely much more powerful than Sybyl, but its not just this issue that people use Sybyl more. I think its the issue of popularity and also fiscal matter. Sybyl came out long before InsightII did and also it is way too cheaper than InsightII. One gets used to a certain thing so much so that they dont wanna go learn something new when the same thing can be done with the one they have. Sybyl is definitely much more popular. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D I use both Sybyl and InsightII for modeling. I find InsightII better = for easy visualization and manipulation of molecules, especially proteins, = and for making nice-looking pictures. But Sybyl is also very good - as some others have said, it's easier to do things like conformational searches, etc. on small molecules. Also, I have used Sybyl/Composer for homology modeling of proteins and find it very good. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D eof ------=_NextPart_000_00E5_01C2959E.7D22F6D0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
I would like to thank all of those who replied to my question. = Thanks!=20
Below is a summary, for those of you who are interested.
 
Cheers,
Carsten
 
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Carsten Detering, = Ph.D.
University of=20 Washington
Seattle, WA 98195
Phone 206-543-5081
Fax=20 206-685-8665
email detering@u.washington.edu~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
Here is my original posting:
 
Hi folks,
 
for quite a while now, I am pondering about the folling: why is it = that=20 most of the modellers use Sybyl rather than InsightII? In most = publications,=20 people say in the methods section (or elsewhere) that they used Sybyl. I = was=20 told once that InsightII was more powerful, once you get to know it, but = since I=20 have never used Sybyl, I cannot really compare.
Maybe some of you could point out the advantages/disadvantages=20 that you encountered when using either of the = two programs.
Thanks in advance for any helpful comments.
 
Cheers, Carsten 
 
 
Replies: (anonymous):
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
 
I had=20 the chance to work with the 2 softwares during my Ph.D. and my post-doc = and to=20 my point of view both softwares are complementary:
Sybyl=20 is really powerfull for the molecular modelling of small molecules. You = can also=20 perform CoMFA studies which is not possible with InsightII. Most of the = docking=20 tools use sybyl file format as input and output. Another big advantage = is that=20 Sybyl will be available on Linux in Q1 2003 so if you don't have a lot = of money=20 you should be able to run Sybyl on a good Linux-PC.
InsightII = is more=20 powerfull for the molecular modelling of the proteins (homology = modelling).=20 Nevertheless it seems that things are changing and I heard that = improvment will=20 be done in Sybyl to work more easily with proteins. Finally Accelerys = provide a=20 tool (Catalyst) which is really interesting for the development of=20 pharmacophores and to perform pharmacophoric=20 searches.
To=20 summarize if you want to work especially with small molecules I would = suggest=20 Sybyl but if you are working only on proteins and you  are not at = all=20 interested by the molecular modelling of small molecules then I would = suggest=20 InsightII.
 
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
 
I=20 think one should not just regard the InsightII and Sybyl as such, but = the entire=20 suite of programs Accelrys and Tripos provide. In fact, nowadays, we use = Cerius2=20 more than InsightII. I have no clue why modellers prefer Tripos = over=20 Accelrys; maybe it's a religious matter. In fact, I doubt it is actually = true.=20 My personal experience is the opposite: both at DuPont Pharma (at least = when I=20 left 4 years ago) and at Pharmacia Accelrys software dominates.=20 About 3 years ago, we (i.e., Pharmacia = Italia) decided=20 to terminate all Tripos licences as Accelrys (then MSI) provided = almost all=20 functionality we needed, while Tripos did not. The only program Accelrys = does=20 not have is a CoMFA equivalent. Also, LigandFit, Accelrys' docking = program, is=20 not that great (look for a thorough comparison in a scientific journal = near you=20 soon), but we have QXP for docking so that does not bother us too=20 much.
 
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D
 
This can quickly become a religious issue - = but in my=20 opinion:
 Sybyl is better for small molecules
 Insight = is=20 marginally better for proteins
 Sybyl is technically a better=20 programme
(e.g. spreadsheet and programming language)

And then = there=20 is the strategic point:
 Sybyl is soon due to be released in a = Linux=20 version
 Insight will cease to exist once [or if?] = Accelrys
moves to=20 the Microsoft Windows platform.
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
 
our lab uses Insight for modelling purposes. = It is=20 indeed a
powerful tool though a bit awkward to use.

The two = main=20 disadvantages are as far as I know that it
runs only on SGI type = computers=20 (expensive and a bit
outdated if you compare to modern PCs), and on = the=20 other
hand that it is expensive itself (>10000$ if I=20 remember
correctly)
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
 
I've used both these programs, though not = really=20 extensively. In my
opinion they are both overpriced dinosaurs. = Accelrys (if=20 I'm up to date
on the current owner) has been trying to get people to = switch=20 from
Insight to Cerius for some years, but there seem to be a lot=20 of
holdouts. Not that I have ever used Cerius, or have any idea if it = is
much better.

My opinion is that these programs have a = following=20 because they
have a user interface which is adequate for most = modelling=20 and
visualisation tasks, and more importantly, people have invested=20 time
and energy in learning how to use them. The force fields and=20 other
methods which they implement are by no means the academic state = of
the art, but they are convenient and relatively easy to use. And=20 of
course there is a distinct lack of competing software which is=20 much
better in the user interface department...

Comparing = Sybyl and=20 Insight, I would say that Sybyl has a more intuitive
interface for = protein=20 modelling, particularly for the manipulation of
homology models. = Insight is=20 more "high tech", implements some more
advanced force fields and atom = typing,=20 and has a more polished user
interface, but simple operations like = adding and=20 deleting amino acids
can be very frustrating. Sybyl is also more = forgiving in=20 its ability
to import structures from the = PDB.
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
 
I am not sure that your statement is true as = I really=20 have little idea which is used more.  We use both.  The people = looking=20 at DNA tend to use Sybyl and the Protein people use InsightII.  = But, that=20 is more a result of what their mentors were accustom too.  I also = think you=20 will find that many publications use Amber, Charmm, or=20 Macromolecule

However, from a money point of view, the initial = cost of=20 the software is greater for Insight (though this depends some on the = modules=20 your purchase) and a license for Sybyl is much less than for Insight = (depending=20 on the level of service, by 33-66%) and people who publish tend to come = > from an=20 academic setting. 

Personally, I prefer to use Amber.  = Amber=20 does not have a 'graphical user interface' (ignoring xleap) but there = are enough=20 freeware or very low cost programs available to help you with analysis = (eg vmd,=20 moilview, curves, dials and windows, etc) that this is not a big = problem. =20 In addition, Amber takes advantage of a multi-processor environment and = it=20 scales reasonable well.  And, if you are going to do anything out = of the=20 ordinary, in our experience, it has been easier to accomplish with = Amber. =20 I also think that people have to understand what they are doing to a far = greater=20 extent with Amber, etc. which, in the long run, is a good thing.  = Finally,=20 I've found Tech service from Insight/Sybyl to be less than helpful with = all but=20 the most rudimentary problems.  The Amber_reflector, on the other = hand, has=20 answered nearly all of my questions, etc.
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
 
I am not an unbiased observer, having worked = on=20 several
modeling codes over time, but I've always thought = that
Sybyl was=20 better for small-molecule/QSAR applications
while Insight was better = for=20 large-molecule/MD/struct-
based modeling.  I think this is due = to the=20 histories
behind each program...
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
 
Unfortunately, I have not worked with Sybyl = long enough=20 to really understand its advantages. On the other hand, I have used = InsightII=20 and AMBER much during the past 2 years. I agree with Fred that = Insight II=20 is powerful for homology modeling and that Sybyl is very good for small=20 moleules. The downside of Amber is of course that it uses command lines, = not an=20 interactive GUI. Still, I obtained very good models from Amber=20 and InsightII (protein models that is!) and acceptable models in = Sybyl=20 (small molecules). The problem with Sybly is that its conformational = searches=20 for macrocyclic molecules still remains to be improved. When I finished = my=20 studies and started my new job, my first objective was to choose a = modeling=20 software (for small molecules) for which we would be able to make = protein models=20 for rational design down the line. We were looking for a cost effective = software=20 that would not require buying expensive computers (I was setting up the=20 Molecular Modeling department for a new Biotech). Looking around, I came = about=20 MOE (Molecular Operating Environment) from the Chemical Computing Group = (CCG=20 Inc.) based in Montreal, QC. What is really interesting about MOE is = that there=20 is only one price for the entire package (it is not modular) and the = price is=20 VERY reasonable. Moreover, MOE runs on everything but MACS for the = moment!!!!!=20 So not only can you run it on a PC for cheap, you can also run it in = windows if=20 you cannot afford to hire a Linux administrator (check out http://www.= bio-itworld.com/archive/071102/linux.html for=20 a review about cost effectiveness of using Linux). There will obviously = be some=20 loss in computational power but it may be worth it=20 >...
 
Anyhow, MOE can perform everything from small = molecule=20 modeling to large proteins, docking, flexible alignments, etc. The only = thing=20 they are missing at the moment is a particular section to handle NMR = data. It is=20 very user friendly and can be very easy on the point and click side to = get what=20 you want (maybe just a littlle too easy sometimes!). I don't = understand why=20 MOE doesn't make it in these CCL archives because I know a several large = pharmas=20 that use it and love it, along with academic researches and = undergraduate=20 programs using it to teach molecular modeling techniques. With respect = to price,=20 performace, and flexibility of use, I (would like to) believe MOE will = start=20 taking a large segment of the industry. Moreoever, their supprt is = extensive and=20 rapid. Take a look at http://www.chemcomp.com for = more=20 details. The only disadvantage of MOE is that they haven't been around = for a=20 very long time and sometimes lack the vision of a molecular modeler, but = they=20 are keen to learn. MOE was developped by programmers, not molecular = modelers so=20 you can modify the entire MOE environment with a bit of programming=20 skills. Moreover, I find interesting tools that were developed by = CCG for=20 model analyses (tools that I did not have the chance to discover in = other=20 programs if they exist). Needless to say, I'm convinced that MOE is a = serious=20 competitor to the other more traditional programs. On the other hand, = I'll say=20 the same thinig to you as a molecular modelre at Pharmacia told me: "... = not one=20 program can perform everything you need which is why you need them all = ;o)" .=20 MOE on the other hand, comes close to completeness in my opinion ... I = haven't=20 had to get other programs yet (I've had it for 9 = months).
 
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
 
I have gotten the chance of using = Sybyl as=20 well as
InsightII during my Ph.D. InsightII is definitely = much
more=20 powerful than Sybyl, but its not just this issue
that people use = Sybyl more.=20 I think its the issue of
popularity and also fiscal matter. Sybyl = came out=20 long
before InsightII did and also it is way too cheaper
than = InsightII.=20 One gets used to a certain thing so
much so that they dont wanna go = learn=20 something new
when the same thing can be done with the one=20 they
have.
Sybyl is definitely much more popular.
 
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
=
 
I use both Sybyl and InsightII for = modeling.  I find InsightII better for
easy visualization and=20 manipulation of molecules, especially proteins, and
for making = nice-looking=20 pictures. But Sybyl is also very good  - as some
others have = said, it's=20 easier to do things like conformational searches,
etc. on small = molecules.=20 Also, I have used Sybyl/Composer for homology
modeling of proteins = and find=20 it very good.
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
eof
------=_NextPart_000_00E5_01C2959E.7D22F6D0-- From chemistry-request@server.ccl.net Tue Nov 26 22:01:22 2002 Received: from hotmail.com ([64.4.21.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAR31Mi30050 for ; Tue, 26 Nov 2002 22:01:22 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 26 Nov 2002 19:01:22 -0800 Received: from 137.189.4.4 by lw14fd.law14.hotmail.msn.com with HTTP; Wed, 27 Nov 2002 03:01:22 GMT X-Originating-IP: [137.189.4.4] From: "Wing Lok Abe Kurtz Chiu" To: daniel.glossman@cimav.edu.mx Cc: chemistry@ccl.net Subject: Re: CCL:G98 + Linda Linux Cluster problem Date: Wed, 27 Nov 2002 11:01:22 +0800 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 27 Nov 2002 03:01:22.0091 (UTC) FILETIME=[43F14FB0:01C295C1] Hi, You should state too much memory than the system can be provided. You can only set the maximum memory around the physical memory of a machine in your cluster minus 70 Mb. Besides, you should use the "unlimit memoryuse" command to release the memory limit. I also recommend you to include the line "$g98root/g98/bsd/clearipc" in your script to release memory segment. This is my two percent idea. Cheers, Kurtz Dr. Wing Lok Abe Kurtz Chiu Department of Chemistry The Chinese University of Hong Kong Hong Kong SAR, China >From: >To: >Subject: CCL:G98 + Linda Linux Cluster problem >Date: Tue, 26 Nov 2002 20:25:52 -0700 (MST) > > >Dear Netters: > >Following with my last question about G98+Linda on Linux Clusters, >I have made some progress: Linda was installed and the paralell >version has been built. Now I have g98l command to run jobs in >paralell. When I tried g98l with a simple job, with 1 proccesor, >the job ran fine. when I tried with more that 1 processor, the >run stops with the following error: > >After Link 1: > >shmget failed >shmget failed - invalid argument > > >Any idea of what can be happening? > >Thanks in advance > > Dr. Daniel Glossman-Mitnik > > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: >jkl@ccl.net _________________________________________________________________ The new MSN 8: advanced junk mail protection and 2 months FREE* http://join.msn.com/?page=features/junkmail From chemistry-request@server.ccl.net Tue Nov 26 13:40:38 2002 Received: from postoffice2.mail.cornell.edu ([132.236.56.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAQIebi26861 for ; Tue, 26 Nov 2002 13:40:38 -0500 Received: from pobox.com (arginine.chem.cornell.edu [128.253.86.74]) by postoffice2.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id NAA09166 for ; Tue, 26 Nov 2002 13:40:36 -0500 (EST) Message-ID: <3DE3C01D.CF5AD285@pobox.com> Date: Tue, 26 Nov 2002 13:40:29 -0500 From: Eric Bennett X-Mailer: Mozilla 4.75 [en] (X11; U; OSF1 V5.1 alpha) X-Accept-Language: en MIME-Version: 1.0 To: Chemistry@ccl.net Subject: Re: CCL:Dielectric Constant of 4 References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Rick Venable wrote: > A note on the distance-dependent dielectric: it's not epsilon=4 (just > another fixed value), but epsilon=r, i.e. the dielectric is the distance > between a pair of atoms when computing the electrostatic energy from the > standard Coulomb expression. A computational advantage for this was > that one could use r**2 to compute the energy for an atom pair, and > avoid taking a square root. You can still use a scale factor with a distance-dependent dielectric. So my original email had a typo, but the correction is that E=4r (rather than E=r or E=4). Of course you could do E=r or E=2r etc. but the paper I was citing favored E=4r (distance dependent with scale factor) or E=2 (constant). In any event, the take home message about the historical origins of how E is chosen are the same. -- Eric Bennett ( ericb@pobox.com ; http://www.pobox.com/~ericb )