From chemistry-request@server.ccl.net Tue Jan 14 01:36:13 2003 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0E6aD421039 for ; Tue, 14 Jan 2003 01:36:13 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h0E6a9j00058; Tue, 14 Jan 2003 01:36:09 -0500 (EST) Date: Tue, 14 Jan 2003 01:36:07 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net, mel@asdn.net cc: Jan Labanowski Subject: Invitation to volume: "Software for materials & process design" Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL and ASDN Members We are putting together a special issue of Computational Materials Science (CMS) journal by Elsevier. This volume will focus on SOFTWARE DEVELOPMENT FOR PROCESS AND MATERIALS DESIGN. We now have over 20 contributions, but can still accommodate a few more high quality papers. This is a rare opportunity for software developers to present an overview of methodology, outline important aspects of implementation, and describe the domain of applications most suitable for their code. The CMS is a very popular journal in materials science community, and this volume may become a valuable source of information and a notable reference. The deadline for paper submission is extended until the end of February 2003. Please contact us at: software@asdn.net if you are considering participating in this special collection. Your prompt answer will help us to plan the organization of this volume. Please provide us with a tentative title and abstract of your paper. The papers should be about 15 pages of double spaced 12pt text. More information (preferred topics, formatting guidelines, upload instructions, deadlines, etc.), are available from the Web page: http://asdn.net/moscow/software-author-info.shtml Please do not hesitate to contact us if you need more information. Editors: Jim Greer Anatoli Korkin Jan Labanowski National Microelectronics Motorola Ohio Supercomputer Research Centre Digital DNA Labs Center Jim.Greer@nmrc.ie Anatoli.Korkin@motorola.com jkl@ccl.net ----------------- Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | E-mail: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/~jkl Columbus, OH 43212-1163 | http://www.ccl.net/ http://asdn.net/ From chemistry-request@server.ccl.net Mon Jan 13 22:58:47 2003 Received: from ALPHA6.CC.MONASH.EDU.AU ([130.194.1.25]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0E3wk418734 for ; Mon, 13 Jan 2003 22:58:46 -0500 Received: from splat.its.monash.edu.au ([130.194.1.73]) by vaxc.cc.monash.edu.au (PMDF V6.1 #39306) with ESMTP id <01KR89AW27DG94H952@vaxc.cc.monash.edu.au> for chemistry@ccl.net; Tue, 14 Jan 2003 14:54:20 +1100 Received: from splat.its.monash.edu.au (localhost [127.0.0.1]) by localhost (Postfix) with ESMTP id 98A9B130025 for ; Tue, 14 Jan 2003 14:54:18 +1100 (EST) Received: from spme.monash.edu.au (mat-wdc5.spme.monash.edu.au [130.194.138.198]) by splat.its.monash.edu.au (Postfix) with ESMTP id 2DF7513001E for ; Tue, 14 Jan 2003 14:54:15 +1100 (EST) Date: Tue, 14 Jan 2003 14:53:48 +1100 From: Wayne Cook Subject: CCL: File conversion for Zenographics Mirage X-Sender: "Wayne Cook" To: chemistry@ccl.net Message-id: <3E237BBC.3CD3E546@spme.monash.edu.au> Organization: Monash University MIME-version: 1.0 X-Mailer: Mozilla 4.79 [en]C-CCK-MCD monwin/025 (Win98; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: en Dear Folks I have a number of graphic files (*.ima and *.spe) created with an old version of Zenographics Mirage (version about 1990). Since this software does not run on modern Microsoft-based PCs does anyone have a program which can convert the files to a readable format? Thanks Wayne -- A/Prof W. D. Cook School of Physics and Materials Engineering Wellington Road Monash University Clayton Victoria Australia Postal address: A/Prof W. D. Cook School of Physics and Materials Engineering PO Box 69M Monash University 3800 Victoria Australia Phone (+61) (03) 99054926 (office)/4911 (General office) Fax (+61) + (03) 99054940 WEB http://www.spme.monash.edu.au/staff/cook.html From chemistry-request@server.ccl.net Tue Jan 14 04:24:55 2003 Received: from mail.szote.u-szeged.hu ([160.114.96.63]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0E9Ot403766 for ; Tue, 14 Jan 2003 04:24:55 -0500 Received: from ovrisc.mdche.u-szeged.hu (IDENT:qmailr@ovrisc.mdche.u-szeged.hu [160.114.101.224]) by mail.szote.u-szeged.hu (8.9.3/8.8.7) with SMTP id KAA13245 for ; Tue, 14 Jan 2003 10:24:11 +0100 Received: (qmail 26478 invoked by uid 525); 14 Jan 2003 09:24:11 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 14 Jan 2003 09:24:11 -0000 Date: Tue, 14 Jan 2003 10:24:11 +0100 (CET) From: "Dr. Csaba Hetenyi" To: Lucilla Angeli cc: chemistry@ccl.net Subject: Re: CCL:Water molecules In-Reply-To: <3E22EC5C.B47DC6B2@student.unisi.it> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Concerning the water-problem: please also read our recent paper of peptide AutoDocking: Hetenyi and van der Spoel (2002), Protein Sci. 11(7) 1729-1737. In my view, the problem of the location of water molecules on the surface of proteins is especially critical if the ligand is a peptide. Best wishes, Csaba From chemistry-request@server.ccl.net Tue Jan 14 10:10:25 2003 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0EFAO410789 for ; Tue, 14 Jan 2003 10:10:24 -0500 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #13) id 18YShr-0003zO-00; Tue, 14 Jan 2003 16:10:23 +0100 Message-ID: <3E24285A.3010608@mpi-bpc.mpg.de> Date: Tue, 14 Jan 2003 16:10:18 +0100 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en, ro MIME-Version: 1.0 To: amber , CCL Subject: MEAD on SuSE 8.1 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear Friends, Has anyone ever try to compile MEAD on SuSE Linux 8.1??? It seems that there some problems with the compiler. Sir Bashford helped me with some patches and I managed to compile only a number of applications (potential amd sav-driver are still missing.....I mean the executables and the ".o" files). The rest of apps seem fine. If somebody has ever compile succesfully MEAD on SuSE 8.1 could you tell me what is happening? I sent this to Sir Bashford also, he was very kind in studying the problem. Thanks a lot in advance, best, vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@server.ccl.net Tue Jan 14 11:26:30 2003 Received: from darius.ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0EGQT412754 for ; Tue, 14 Jan 2003 11:26:30 -0500 Received: from echo.ribotargets.com (echo [194.129.39.91]) by darius.ribotargets.com (SGI-8.9.3/8.9.3) with ESMTP id QAA16939; Tue, 14 Jan 2003 16:34:22 GMT Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 18YTpI-0003C2-00; Tue, 14 Jan 2003 16:22:08 +0000 Date: Tue, 14 Jan 2003 16:22:08 +0000 (GMT) From: Szilveszter Juhos To: Vlad Cojocaru cc: amber , CCL Subject: Re: CCL:MEAD on SuSE 8.1 In-Reply-To: <3E24285A.3010608@mpi-bpc.mpg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 14 Jan 2003, Vlad Cojocaru wrote: > Has anyone ever try to compile MEAD on SuSE Linux 8.1??? It seems > that there some problems with the compiler. though i never tried to compile it, give a try to $ make CC=egcs that will fall back to egcs. Szilva From chemistry-request@server.ccl.net Tue Jan 14 12:13:24 2003 Received: from brown.csi.cam.ac.uk ([131.111.8.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0EHDN414157 for ; Tue, 14 Jan 2003 12:13:23 -0500 Received: from prayer by brown.csi.cam.ac.uk with local (Exim 4.10) id 18YUct-0002LO-00 for chemistry@ccl.net; Tue, 14 Jan 2003 17:13:23 +0000 From: "Dr S.W. Watt" To: "ccl.net list" Subject: Compass Date: 14 Jan 2003 17:13:23 +0000 X-Mailer: Prayer v1.0.5 X-Originating-IP: [131.111.112.123] Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Message-Id: Hello all, Does anybody know how the Compass force field handles water molecules? For example, does it type the O and H atoms according to a specific model of water (i.e. SPC/E or TIPS4)?. Regards. Stephen Watt. From chemistry-request@server.ccl.net Tue Jan 14 10:24:52 2003 Received: from dqo.qo.ub.es ([161.116.74.251]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0EFOp411189 for ; Tue, 14 Jan 2003 10:24:52 -0500 Received: from qo.ub.es (unknown [161.116.74.156]) by dqo.qo.ub.es (Postfix) with ESMTP id E797115F6BC for ; Tue, 14 Jan 2003 12:05:46 -0500 (EST) Message-ID: <3E242BB2.2080602@qo.ub.es> Date: Tue, 14 Jan 2003 16:24:34 +0100 From: Oriol Pineda User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Autodock: "too many grid points" Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear all, When starting an autodock job I receive the error message "too many grid points". Does anyone know which is the maximum allowed number of grid points orhow to avoid this message? Thanks! From chemistry-request@server.ccl.net Tue Jan 14 08:44:12 2003 Received: from orion.lunarpages.com ([64.235.234.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0EDiB409026 for ; Tue, 14 Jan 2003 08:44:12 -0500 Received: from adslp43-nv-p120.adsl.netvision.net.il ([212.143.43.120] helo=TESTING) by orion.lunarpages.com with esmtp (Exim 3.36 #1) id 18YRMZ-0000gy-00 for chemistry@ccl.net; Tue, 14 Jan 2003 05:44:19 -0800 From: "Elie Cohen" To: Subject: Announcement: www.drugdesign.org has been launched Date: Tue, 14 Jan 2003 15:43:57 +0200 Message-ID: <000001c2bbd3$0260b120$8907000a@TESTING> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C2BBE3.C5E98120" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.4024 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-AntiAbuse: This header was added to track abuse, please include it with any abuse report X-AntiAbuse: Primary Hostname - orion.lunarpages.com X-AntiAbuse: Original Domain - ccl.net X-AntiAbuse: Originator/Caller UID/GID - [0 0] / [0 0] X-AntiAbuse: Sender Address Domain - drugdesign.org This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C2BBE3.C5E98120 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear Colleague, We are pleased to announce the launch of "www.drugdesign.org ", a new site on Drug Design Resources that can be reached at http://www.drugdesign.org . 'Drug Design Resources' is a non-profit website, created in December 2002 with the mission of promoting Drug Design and Molecular Modeling. We kindly initiated our first goal and started to classify and organize relevant links in the field of drug design and molecular modeling. We wish that this site will prove to be a useful resource to you and serve the scientific community. Comments, suggestions and bugs are welcome to info@drugdesign.org The Drug Design Resource Team ------=_NextPart_000_0001_01C2BBE3.C5E98120 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear Colleague,

 

We are pleased to announce the launch of “www.drugdesign.org”, a new = site on Drug Design Resources that can be reached at http://www.drugdesign.org.=

'Drug Design Resources' is a non-profit website, = created in December 2002 with the mission of promoting Drug Design and Molecular = Modeling.

We kindly initiated our first goal and started to = classify and organize relevant links in the field of drug design and molecular = modeling.

 

We wish that this site will prove to be a useful = resource to you and serve the scientific community.

 

Comments, suggestions and bugs are welcome to info@drugdesign.org=

 

The Drug Design Resource Team

 

------=_NextPart_000_0001_01C2BBE3.C5E98120-- From chemistry-request@server.ccl.net Tue Jan 14 11:58:29 2003 Received: from smtp.uh.cu ([216.72.24.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0EGwG413768 for ; Tue, 14 Jan 2003 11:58:21 -0500 Received: from fq.uh.cu (canaria.qct.fq.oc.uh.cu [192.168.3.4]) by smtp.uh.cu (Postfix) with ESMTP id 807A734277 for ; Tue, 14 Jan 2003 12:57:48 -0500 (CST) Received: from Yigni (espectro.qct.fq.oc.uh.cu [192.168.3.44]) by fq.uh.cu (8.9.0/8.8.7) with SMTP id LAA23748 for ; Tue, 14 Jan 2003 11:47:34 -0500 Message-Id: <200301141647.LAA23748@fq.uh.cu> From: "=?ISO-8859-1?Q?Reynier_Suardiaz_del_R=EDo?=" Organization: =?ISO-8859-1?Q?Qu=EDmica_-_F=EDsica?= To: chemistry@ccl.net Date: Sun, 14 Jan 2001 11:42:09 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Gaussian error output Priority: normal References: <3E22EC5C.B47DC6B2@student.unisi.it> In-reply-to: X-mailer: Pegasus Mail for Windows (v3.01d) Hello I have been using G94 to optimize some long structures with DFT, i received the following error message: Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned on. 486 basis functions 767 primitive gaussians 67 alpha electrons 67 beta electrons nuclear repulsion energy 1367.0349722544 Hartrees. One-electron integrals computed using PRISM. DenBas #5 allocation failure: iend,mxcore= 865761 467175 Error termination via Lnk1e in //g94/l302.exe. Job cpu time: 0 days 0 hours 0 minutes 0.3 seconds. File lengths (MBytes): RWF= 10 Int= 0 D2E= 0 Chk= 1 Scr= 1 What does this message mean? i accept any suggestion... _____________________________________________ Reynier Suardiaz del Rio Department of Physical Chemistry Chemistry Faculty University of Havana email: reynier@fq.uh.cu, reynier_s@yahoo.com _____________________________________________ From chemistry-request@server.ccl.net Tue Jan 14 18:46:27 2003 Received: from ntsmtp01.usc.edu ([128.125.179.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0ENkR423738 for ; Tue, 14 Jan 2003 18:46:27 -0500 Received: by NTSMTP01 with Internet Mail Service (5.5.2653.19) id ; Tue, 14 Jan 2003 15:46:27 -0800 Message-ID: <73564B8DE398D61180500008C75D7E494388C1@NTMAIL03> From: "Pandey, Jaya" To: "'chemistry@ccl.net'" Subject: Docking Date: Tue, 14 Jan 2003 15:46:25 -0800 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain Dear All, I used Bigger software for docking my ligand to a homologous structure as the structure currently is not know of my receptor. Can someone guide me as how to calculate the binding energy in order to understand the docking of my ligand. Although I can view my ligand docked to the target but I think it needs to be confirmed by some calculations, please help! Jaya From jkl@ccl.net Tue Jan 14 18:32:31 2003 -0500 Return-Path: Received: from tcp-daemon.mtaout05.icomcast.net by mtaout05.icomcast.net (iPlanet Messaging Server 5.2 HotFix 1.07 (built Nov 25 2002)) id <0H8P00121ONSYT@mtaout05.icomcast.net> (original mail from jj@eyesopen.com) ; Tue, 14 Jan 2003 11:04:41 -0500 (EST) Received: from eyesopen.com (bgp01382599bgs.montbl01.nm.comcast.net [68.35.146.26]) by mtaout05.icomcast.net (iPlanet Messaging Server 5.2 HotFix 1.07 (built Nov 25 2002)) with ESMTP id <0H8P001DVONRV7@mtaout05.icomcast.net> for chemistry@ccl.net; Tue, 14 Jan 2003 11:04:40 -0500 (EST) Organization: OpenEye Date: Tue, 14 Jan 2003 09:07:24 -0700 From: Jeremy J Yang Subject: Superimpose program In-reply-to: <3E1B0B99.3DF839A0@mercury.hec.utah.edu> To: Atchara Wijitkosoom Cc: chemistry@ccl.net Message-id: <3E2435BC.2070602@eyesopen.com> Hi - One more answer, please forgive the delay. Not being sure of your intended meaning of superimpose in this context... OpenEye Scientific Software product ROCS is a shape comparison program which can compare shapes aysymmetrically -- as substructure -- through its underlying Shape Toolkit. In development with partner Mesa Analytics and Computing is a Tversky similarity measure and clustering package based on shape fingerprints, also in development. If perhaps you're interested in graph based maximal common substructure searching, the new OpenEye product the OEChem programming toolkit has MCS built in. -Jeremy Atchara Wijitkosoom wrote: > To whom it may concern, > > Does anybody know about the superimpose program that can deal with the > structures that have different length? > > Thank you very much in advance. > > Yours, > Atchara -- Jeremy J. Yang ph: 505.473.7385 Director of Technical Support fx: 505.473.0833 Openeye Scientific Software Inc. www.eyesopen.com ************************************************************************* * Attend OpenEye CUP IV meeting in Santa Fe, 2/23-24/03 * Info and registration at http://www.eyesopen.com/events/cup_IV/ *************************************************************************