From chemistry-request@server.ccl.net Tue Aug 21 10:29:27 2001 Received: from dedalus.lcc.ufmg.br ([150.164.65.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7LETOM06024 for ; Tue, 21 Aug 2001 10:29:25 -0400 Received: from localhost (noronha@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id LAA33877 for ; Tue, 21 Aug 2001 11:29:08 -0300 Date: Tue, 21 Aug 2001 11:29:07 -0300 (BSC) From: antonio luiz oliveira de noronha To: chemistry@ccl.net Subject: Program to build organometalic compounds Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCL friends Is there any FREE program to build organometalic compounds?? It doesn't matter if the OS is win32 or Linux ( Linux is preferred ). I would aprecciate any help Regards From chemistry-request@server.ccl.net Mon Aug 20 20:33:43 2001 Received: from janus.hosting4u.net ([209.15.2.37]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7L0XhM29667 for ; Mon, 20 Aug 2001 20:33:43 -0400 Received: (qmail 15510 invoked from network); 21 Aug 2001 00:33:43 -0000 Received: from zeus.hosting4u.net (HELO proinformatix.com) (209.15.2.56) by mail-gate.hosting4u.net with SMTP; 21 Aug 2001 00:33:43 -0000 Received: from yersina ([202.138.17.3]) by proinformatix.com ; Mon, 20 Aug 2001 19:33:40 -0500 Reply-To: From: "Sergio Manzetti" To: "Chemistry Discussion G" Subject: Fluor atoms in AUTODOCK Date: Tue, 21 Aug 2001 10:32:25 -0700 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 V5.00.2919.6700 Importance: Normal Hello everyone, I am trying to dock a ligand with three fluor atoms onto a receptor. The PDBQ file must contain the right abbreviation for the atom, according to the relevant references from Scripps, but the F for fluor (obtained from autodock website) is not recognized by the autodock3 script. Has anybody an idea of what kind of abbreviation I must use? Best Regards Sergio ____________________________________________________________________________ ___________________________ Sergio Manzetti Research Scholar Centre of Molecular Biotechnology/ Supercomputer Facility Queensland University of Technology 2 George St. BRISBANE 4000 QLD AUSTRALIA email: s.manzetti@student.qut.edu.au Tlf: +61 7 3864 1434 www: http://www.life.sci.qut.edu.au/html/research/cmgenetics.html www2: http://www.its.qut.edu.au/hpc/ From chemistry-request@server.ccl.net Tue Aug 21 10:26:12 2001 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7LEQCM05723 for ; Tue, 21 Aug 2001 10:26:12 -0400 Received: from sun1.lrz-muenchen.de by mailrelay1.lrz-muenchen.de with ESMTP for chemistry@ccl.net; Tue, 21 Aug 2001 16:26:04 +0200 Received: from localhost (ui22204@localhost) by sun1.lrz-muenchen.de (8.8.8+Sun/8.8.8) with ESMTP id QAA03390 for ; Tue, 21 Aug 2001 16:26:03 +0200 (MET DST) X-Authentication-Warning: sun1.lrz-muenchen.de: ui22204 owned process doing -bs Date: Tue, 21 Aug 2001 16:26:03 +0200 (MET DST) From: Eugene Leitl X-X-Sender: To: Subject: Re: SSE & compilers (fwd) Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII -- Eugen* Leitl leitl ______________________________________________________________ ICBMTO : N48 10'07'' E011 33'53'' http://www.lrz.de/~ui22204 57F9CFD3: ED90 0433 EB74 E4A9 537F CFF5 86E7 629B 57F9 CFD3 ---------- Forwarded message ---------- Date: Tue, 21 Aug 2001 16:11:59 +0200 (CEST) From: David van der Spoel To: Dan Kirkpatrick Cc: beowulf@beowulf.org Subject: Re: SSE & compilers On Tue, 21 Aug 2001, Dan Kirkpatrick wrote: >1. What do you know about SSE ? Apparently the p III and P 4 have extra >hardware for fp work which is ignored by current compilers but can buy big >factors in speed... >we can code in assembler for it pretty easily if the PIII prcocessors have >it. Comments? We have rewritten the inner loops of our molecular dynamics code GROMACS (http://www.gromacs.org) using SSE (and 3DNow!). This roughly doubles the performance on Pentium 3's. You do need a 2.4 kernel for SSE, 3DNow will work with recent 2.2 kernels as well. Note that it is single precision only on P3's. P4's can also do double precision SSE, but only with twofold unrolling (SIMD) compared to 4-fold in single precision. This effectively halves the performance. >2. Apparently there are several optimizing compilers out there (like >portland) which do better than gcc. Any suggestions? Information on costs? YMMV but Portland did not help more than 5% on our MD code (the C/Fortran version that is). Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf From chemistry-request@server.ccl.net Tue Aug 21 11:38:46 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7LFciM08787 for ; Tue, 21 Aug 2001 11:38:45 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 15ZDbz-0007CR-00; Tue, 21 Aug 2001 17:38:39 +0200 Received: from vejas.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id RAA22758 for ; Tue, 21 Aug 2001 17:59:54 +0200 (GMT) Date: Wed, 22 Aug 2001 05:38:12 +0200 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <15128862525.20010822053812@vaidila.vdu.lt> To: CCL Subject: heme-His: charge ? Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Model: Heme and axial ligand His (covalent binding to iron). Fe is III. Here is the resting state of peroxidase's active center. Has that heme-His complex the +1 charge ? A.Ziemys From chemistry-request@server.ccl.net Tue Aug 21 11:39:25 2001 Received: from Lilly.com ([40.33.1.27]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7LFdOM08811; Tue, 21 Aug 2001 11:39:24 -0400 Received: from LILLY.COM ([40.59.1.39]) by CARLTN.D48.LILLY.COM (PMDF V5.2-31 #34229) with ESMTP id <01K7E5EX0ZMO001F7T@CARLTN.D48.LILLY.COM>; Tue, 21 Aug 2001 10:37:26 EST Received: from mcntusmail12.d51.lilly.com (mcntusmail12.d51.lilly.com [40.1.129.133]) by NEWMAN.D52.LILLY.COM (PMDF V5.2-31 #37480) with ESMTP id <01K7E5H8DAI8009E1O@NEWMAN.D52.LILLY.COM>; Tue, 21 Aug 2001 10:39:19 -0500 (EST) Content-return: prohibited Date: Tue, 21 Aug 2001 10:34:30 -0500 From: CHEN_QI@Lilly.com Subject: programs to build dna and rna To: chemistry@ccl.net, Computational Chemistry List Message-id: MIME-version: 1.0 X-Mailer: Lotus Notes Release 5.0.4a July 24, 2000 Content-type: multipart/alternative; boundary="=_alternative 0056009805256AAF_=" X-MIMETrack: Serialize by Router on USMAIL12/AM/LLY(Release 5.07a |May 14, 2001) at 08/21/2001 10:34:30 AM, Serialize complete at 08/21/2001 10:34:30 AM This is a multipart message in MIME format. --=_alternative 0056009805256AAF_= Content-Type: text/plain; charset="us-ascii" Hi, does anyone know the programs for building DNA and RNA models based on a known structure of similar sequence? Thanks! Qi Chen qichen@lilly.com --=_alternative 0056009805256AAF_= Content-Type: text/html; charset="us-ascii"
Hi, does anyone know the programs for building DNA and RNA models based on a known structure of similar sequence? Thanks!
Qi Chen
qichen@lilly.com --=_alternative 0056009805256AAF_=-- From chemistry-request@server.ccl.net Tue Aug 21 15:06:08 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7LJ68M14431 for ; Tue, 21 Aug 2001 15:06:08 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id PAA29500; Tue, 21 Aug 2001 15:06:07 -0400 (EDT) Date: Tue, 21 Aug 2001 15:06:07 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: It is time for CCL fund raiser... My hand is trembling {:-)} Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, This is just a thank you note to all of you for supporting CCL list with your input, output, contributions, donations, and purchases. We are "in business" for more than 10 years thanks to your support and participation. There are not that many lists which are academically based and keep going for so long. It feels good... {:-)}. Please make sure that you view the page: http://www.ccl.net/cgi-bin/donors (BTW, if I missed someone, bug me immediately -- I am a very poor accountant). and share my thanks to those who make the CCL running not only through their contributions to CCL discussions, but also through their donations or purchases. This summer we were in operation without major breakdowns, though we are constantly under attack. I was peeking mostly every day from my laptop in Poland, but I could not do much due to the latency. Students were keeping the operation running. We got lots of viruses, since many of our subscribers are using MS Windows, and when they have the chemistry@ccl.net in their address books, we get the viral presents from them. Our filters were quite vigilant about the viruses, but human still needs to see each and every message, since filters work under the principle: "Better safe than sorry". We also saved you from a lot of mail about new "EXCITING" sites, new "DEALS", greatest "FREE OFFERS", and other junk mail. Thanks to you though, we had a stream of very good messages and summaries, which make CCL worth subscribing to. But now, I need to ask you again for your help. I have a group of devoted students who do the chores and development for CCL, and I would greatly appreciate your assistance. Keeping this resource running requires a lot of manual work and maintenance. Computers break, wires fall, lights go off, hackers break in, viruses spread, and disks go bad... You know the feeling... For students who work for CCL, this is a great opportunity to do something useful, learn, and get some pocket money (Yes, I wish I could pay them more, but... -- they volunteer a lot, but still, the income is what makes them come to work for CCL rather than for McDonalds). So your donations or purchases HELP A LOT!!! You can either donate us some money, or buy CD Set with CCL archives from us (you will be normally billed, we accept all forms of payments). So please look at our page: http://search.ccl.net/chemistry/aboutccl/supporting/ and consider helping CCL so I can have student assistants next quarter. If you cannot help financially, try to ask your boss, if he/she can. If your boss is not willing, try to contribute software to our archives, try to answer questions on CCL, or maybe ask thoughtful questions yourself to keep this resource lively and useful to computational chemists. Thank you for your past and present contributions and support and the feeling that CCL is useful and popular. Jan Labanowski Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Tue Aug 21 15:13:44 2001 Received: from hermes.bmc.uu.se ([130.238.39.159]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7LJDhM14547 for ; Tue, 21 Aug 2001 15:13:43 -0400 Received: from XRAY.bmc.uu.se ([130.238.37.10]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with ESMTP id se for ; Tue, 21 Aug 2001 21:15:08 +0200 Received: from zorn.bmc.uu.se (IDENT:spoel@zorn.bmc.uu.se [130.238.37.95]) by XRAY.bmc.uu.se (8.9.3/8.8.7) with ESMTP id VAA19667 for ; Tue, 21 Aug 2001 21:15:21 +0200 Date: Tue, 21 Aug 2001 19:15:51 +0200 (CEST) From: David van der Spoel X-Sender: spoel@zorn.bmc.uu.se To: chemistry@ccl.net Subject: GROMACS 3.0: fastest MD Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCL-ers, I am pleased to announce GROMACS 3.0, which is without any doubt the fastest molecular dynamics code on workstation types machines, since we have handcoded the innerloops for Pentium 3 (using SSE) and AMD Athlon (using 3DNow!). GROMACS is a feature laiden simulation and analysis package which is free to download from http://www.gromacs.org under the GNU public license (GPL). We would like to encourage anyone to test the package on their favorite system. We would also like to invite anyone to collaborate with us to make the package even more complete, for instance by adding support code for popular force fields. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Tue Aug 21 15:36:50 2001 Received: from cranc02.cra.canon.com ([146.184.1.62]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7LJanM15009 for ; Tue, 21 Aug 2001 15:36:49 -0400 Received: by cranc02.cra.canon.com with Internet Mail Service (5.5.2653.19) id ; Tue, 21 Aug 2001 12:41:13 -0700 Message-ID: <3FD2BCBD9153D41192B100C04F1FD832067F06@cranc02.cra.canon.com> From: "Thoms, Travis" To: "Computational Chemistry List (E-mail)" Subject: DeFT compilation and usage Date: Tue, 21 Aug 2001 12:41:12 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Greetings: I have recently compiled DeFT for use on my OS/2 box (yes, yes. snicker, snicker), but I am having trouble using it because I dont understand how the deft_script operates. First, does one run the script to activate the program (ie. C:] script) or do you run the program to call the script (C:] DeFT script)? I cannot try out one or the other at this point because the script has many unix command line calls which I must somehow decipher for OS/2. Secondly, DeFT doesn't seem to still be maintained. Is it no longer usable, or of any value? Are there better free DFT software packages that can be used? Thanks, Travis Thoms Research Associate Canon R&D Center Americas. inc. Telephone: 1-408-468-2864 Facsimile:1-408-468-2810 tthoms@cra.canon.com From chemistry-request@server.ccl.net Tue Aug 21 15:47:57 2001 Received: from mailhub.appstate.edu ([152.10.1.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7LJltM15272 for ; Tue, 21 Aug 2001 15:47:56 -0400 Received: from ws1.appstate.edu (SYSTEM@ws1.appstate.edu [152.10.1.40]) by mailhub.appstate.edu (8.11.0/8.10.1) with ESMTP id f7LJdol27085 for ; Tue, 21 Aug 2001 15:39:50 -0400 Received: from CONVERSION-DAEMON.appstate.edu by appstate.edu (PMDF V6.0-025 #41615) id <01K7EG9BSW3K9JPT2D@appstate.edu> for CHEMISTRY@ccl.net; Tue, 21 Aug 2001 15:47:54 -0400 (EDT) Received: from kohn.appstate.edu ("port 4337"@cohn.chem.appstate.edu [152.10.114.100]) by appstate.edu (PMDF V6.0-025 #41615) with ESMTP id <01K7EG9AHENM9JQI47@appstate.edu> for CHEMISTRY@ccl.net; Tue, 21 Aug 2001 15:47:29 -0400 (EDT) Date: Tue, 21 Aug 2001 15:47:20 -0400 From: Steve Williams Subject: somewhat off topic query X-Sender: willsd@imap.appstate.edu To: CHEMISTRY@ccl.net Message-id: <5.1.0.14.0.20010821145447.00a7c0b8@imap.appstate.edu> MIME-version: 1.0 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Content-type: text/plain; charset=us-ascii; format=flowed I apologize for the off topic question here, but I thought that the ccl community has a lot of expertise and maybe someone out there knows something about this: I have a friend who wants to know about the existence of software to simulate laser spectroscopy experiments: But, aren't there software companies or colleges somewhere who have created, for example, a virtual laser lab that allows students to do two-color pump-probe experiments? In its most eleborate form, I visualize a program that provides the students with an optical toolbar containing prisms, beam splitters, PMT's, pyroelectric detectors, oscilloscopes, amps, etc. Thanks in advance for any information you might have on this topic. Due to the off topic nature of this question, please send any replies directly to me (willsd@appstate.edu) rather than using any more valuable ccl bandwith.