From chemistry-request@ccl.net Tue Aug 5 11:16:35 2003 Received: from bureau6.utcc.utoronto.ca (bureau6.utcc.utoronto.ca [128.100.132.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h75FGZNG023184 for ; Tue, 5 Aug 2003 11:16:35 -0400 Received: from mditdell.mdit.utoronto.ca ([128.100.251.12] HELO MditDell ident: IDENT-NOT-QUERIED [port 1136]) by bureau6.utcc.utoronto.ca with SMTP id <464332-29570>; Tue, 5 Aug 2003 11:16:31 -0400 From: "William Wei" To: "CCLers" Cc: "Samy Meroueh" Subject: Date: Tue, 5 Aug 2003 11:17:31 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 Importance: Normal Dear CCLers, While I use DOCK5, I can not pass the dock test. I always met a "Sefmentation fault" error. Could anybody give me some idea that what can cause this problem? Thank you very much! William ------------------------- William Wei Faculty of Pharmacy 19 Russell Street Toronto, ON. M5S 2S2 Tel: 1-416-946-8469 Fax: 1-416-978-8511 Email: william~at~phm.utoronto.ca william.wei~at~utoronto.ca From chemistry-request@ccl.net Tue Aug 5 04:20:16 2003 Received: from yangtze.hku.hk (yangtze.hku.hk [147.8.148.244]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h758KENG013052 for ; Tue, 5 Aug 2003 04:20:15 -0400 Received: from localhost (xzheng@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id h758bFk25975 for ; Tue, 5 Aug 2003 16:37:15 +0800 Date: Tue, 5 Aug 2003 16:37:14 +0800 (HKT) From: Zheng Xiao To: CCL Subject: N2+ cation 2PIU state by G98? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I am puzzled by some of the data in G1 database. For example, how to make a G98 input file to calculate the energy of N2+ cation to retrieve the ionization potential of nitrogen by G1 method? Since there are two electronic states for N2+ cation of the same multiplicity (2PIU and 2SGG), I wonder how to specify each of them by G98 input. Thanks in advance. Sincerely yours, ZX -- C---------------------------------------C C Zheng Xiao C C Ph.D. Candidate C C Department of Chemistry C C University of Hong Kong C C---------------------------------------C From chemistry-request@ccl.net Tue Aug 5 13:31:13 2003 Received: from lulu.it.northwestern.edu (lulu.it.northwestern.edu [129.105.16.54]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h75HVDNG025856 for ; Tue, 5 Aug 2003 13:31:13 -0400 Received: (from mailnull@localhost) by lulu.it.northwestern.edu (8.12.9/8.12.9) id h75HVIJm017052 for ; Tue, 5 Aug 2003 12:31:18 -0500 (CDT) Received: from HUI.northwestern.edu (cheme-50.chem-eng.northwestern.edu [129.105.205.50]) by lulu.it.northwestern.edu via smap (V2.0) id xma016873; Tue, 5 Aug 03 12:31:10 -0500 Message-Id: <5.2.0.9.2.20030805121621.01fc2830/at/lulu.it.northwestern.edu> X-Sender: cli099/at/lulu.it.northwestern.edu X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Tue, 05 Aug 2003 12:31:11 -0500 To: chemistry/at/ccl.net From: Chunhui Subject: searching molecules automatically Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCLers, I apologize if this question is off topic here. I have a batch of molecules, say thousands, in the format of .mol. I wonder if somebody can give me some suggestions about how to search these molecules automatically through databases, such as CAS Registry, or any other type of compound database. I want to see if these molecules exist or not. not necessarily for free. thanks a lot! Chunhui From chemistry-request@ccl.net Tue Aug 5 12:52:22 2003 Received: from ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h75GqLNG025135 for ; Tue, 5 Aug 2003 12:52:21 -0400 Received: from mumbai.ks.uiuc.edu (mumbai.ks.uiuc.edu [130.126.120.104]) by ks.uiuc.edu (8.12.9/8.11.2) with ESMTP id h75GqRCr019610 for ; Tue, 5 Aug 2003 11:52:27 -0500 (CDT) Received: from localhost (emad@localhost) by mumbai.ks.uiuc.edu (8.11.6/8.9.3) with ESMTP id h75GqR003093 for ; Tue, 5 Aug 2003 11:52:27 -0500 X-Authentication-Warning: mumbai.ks.uiuc.edu: emad owned process doing -bs Date: Tue, 5 Aug 2003 11:52:27 -0500 (CDT) From: Emad Tajkhorshid To: computational Chemistry List Subject: Heme charges Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, We just optimized the geometry of a porphyrin ring using DFT and calculated ESP charges for the molecule. The iron carries a significant amoount of positive charge according to population analyses done on the system (it is formally 2+), but the ESP charge for it is negative! The iron atom is completely burried inside the molecule, and that may be one reason of getting this strange result. Has anybody else had similar problems? Any comments, references, or suggestions are appreciated. Thanx a lot. Emad ------------------ Emad Tajkhorshid, Ph.D. http://www.ks.uiuc.edu/~emad Assistant Director of Research NIH Resource for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute, 405 N. Mathews, Urbana, IL 61801, USA Tel:(217)244-4361 Fax:(217)244-6078 Email: emad/at/ks.uiuc.edu From jkl@ccl.net Tue Aug 5 18:10:00 2003 -0400 Return-Path: Received: from postfix3-1.free.fr (postfix3-1.free.fr [213.228.0.44]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h75M9xA24825 for ; Tue, 5 Aug 2003 18:09:59 -0400 (EDT) From: Konrad Hinsen Organization: CNRS To: Emad Tajkhorshid , computational Chemistry List Subject: CCL: Re: Heme charges Date: Tue, 5 Aug 2003 23:01:56 +0200 References: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Message-Id: <200308052301.56801.hinsen*at*cnrs-orleans.fr> On Tuesday 05 August 2003 18:52, Emad Tajkhorshid wrote: > We just optimized the geometry of a porphyrin ring using DFT and > calculated ESP charges for the molecule. The iron carries a significant > amoount of positive charge according to population analyses done on the > system (it is formally 2+), but the ESP charge for it is negative! The > iron atom is completely burried inside the molecule, and that may be on= e > reason of getting this strange result. Has anybody else had similar > problems? Any comments, references, or suggestions are > appreciated. The result of an ESP calculation depends a lot on how the evaluation poin= ts on=20 the surface are chosen. If you have chosen them in such a way that they d= on't=20 probe the ion at all, then the result you get for the ion is merely a num= ber,=20 a number that improves the fit of the electrostatic potential at the=20 evaluation points, with no particular physical interpretation. Depending = on=20 your application, that may well be what you want. Other options: 1) Try to choose other evaluation points (but don't put any of them too n= ear=20 to an atom). This may be difficult for heme. 2) Fix the ion charge in whatever way you consider reasonable, and do the= ESP=20 fit only for the remaining partial charges. --=20 -------------------------------------------------------------------------= ------ Konrad Hinsen | E-Mail: hinsen*at*cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais -------------------------------------------------------------------------= ------ From chemistry-request@ccl.net Tue Aug 5 17:02:16 2003 Received: from gibson.acpub.duke.edu (gibson.acpub.duke.edu [152.3.233.8]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h75L2GNG029754 for ; Tue, 5 Aug 2003 17:02:16 -0400 Received: from yefremov.acpub.duke.edu (yefremov.acpub.duke.edu [152.3.232.42]) by gibson.acpub.duke.edu (8.12.9/8.12.9/Duke-5.0.0) with ESMTP id h75L2Gta022113 for ; Tue, 5 Aug 2003 17:02:16 -0400 From: jz7!at!duke.edu Received: (from nobody@localhost) by yefremov.acpub.duke.edu (8.9.3/8.9.3) id RAA28330 for chemistry!at!ccl.net; Tue, 5 Aug 2003 17:02:17 -0400 (EDT) To: chemistry!at!ccl.net Subject: how to estimate the dielectric constant Date: Tue, 05 Aug 2003 17:02:17 -0400 Message-ID: <1060117337.3f301b59aafc3!at!yefremov.acpub.duke.edu> X-Mailer: Duke Web Mail v1.1.4 20-February-2002 MIME-Version: 1.0 Content-Type: text/plain Content-Transfer-Encoding: 8bit X-Originating-IP: 152.3.169.5 X-PMX-Version: 4.0.2.71298 Hi there, Would someone please suggest what calculation method can estimate the dielectric constant for a specific compound? The literature don't have dielectric constant for it. Thanks a lot!