From chemistry-request@ccl.net Fri Nov 5 10:02:03 2004 Received: from webmail.mta.ca (postal.mta.ca [138.73.1.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iA5F2206032257 for ; Fri, 5 Nov 2004 10:02:02 -0500 Received: from nobody by webmail.mta.ca with local (Exim 4.20) id 1CQ5qo-0007D7-D0 for CHEMISTRY$at$ccl.net; Fri, 05 Nov 2004 11:18:06 -0400 Received: from 138.73.24.157 ( [138.73.24.157]) as user khunter$at$mailserv.mta.ca by webmail.mta.ca with HTTP; Fri, 5 Nov 2004 11:18:06 -0400 Message-ID: <1099667886.418b99ae5c83f$at$webmail.mta.ca> Date: Fri, 5 Nov 2004 11:18:06 -0400 From: khunter$at$mta.ca To: CHEMISTRY$at$ccl.net Subject: CCL: question about nitro groups in AMBER MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.157 X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net In AMBER each atom has a designated type which is defined to set of parameters in AMBER. It appears that nitro groups are not able to be characterized by the existing atom type definitions. Are NO2 groups able to be studied with AMBER? Have the parameters for NO2 been determined previously? Is it possible to define your own parameters manually and if so how? Is there a systematic method to how parameters are defined in AMBER? Any assistance would be greatly appreciated. Ken Hunter Mount Allsion University From chemistry-request@ccl.net Fri Nov 5 03:10:35 2004 Received: from mail.biovertis.com (81-223-198-148.arsenal.xdsl-line.inode.at [81.223.198.148]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iA58AYsE003197 for ; Fri, 5 Nov 2004 03:10:35 -0500 Received: from mail.biovertis.com (localhost [127.0.0.1]) by localhost (Postfix) with ESMTP id B156D68A9E; Fri, 5 Nov 2004 09:23:45 +0100 (CET) Received: by mail.biovertis.com (Postfix, from userid 65534) id 8241568AA1; Fri, 5 Nov 2004 09:23:45 +0100 (CET) Received: from mail.biovertis.com (localhost [127.0.0.1]) by mail.biovertis.com (Postfix) with ESMTP id 2DE9A68A9E; Fri, 5 Nov 2004 09:23:44 +0100 (CET) Message-ID: <1022837.1099643024162.SLOX.WebMail.wwwrun_at_mail.biovertis.com> Date: Fri, 5 Nov 2004 09:23:44 +0100 (CET) From: =?UTF-8?Q?Dirk_Cla=C3=9Fen-Houben?= To: chemistry_at_ccl.net Subject: nmrcore/nmrclust Cc: sjm_at_le.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Priority: 3 (normal) X-Mailer: SuSE Linux Openexchange Server 4 - WebMail (Build 2.3826) X-Operating-System: Linux 2.4.21-241-default i386 (JVM 1.3.1_04) Organization: biovertis - information-driven drug design AG X-Spam-Checker-Version: SpamAssassin 2.64 (2004-01-11) on mail.biovertis.com X-Spam-Level: X-Spam-Status: No, hits=0.1 required=5.0 tests=AWL autolearn=ham version=2.64 Hi everybody, has anybody succesfully used nmrcore on a linux computer (redhat enterprise 3 WS). The program seems to be written for sgi irix and I get this error message: nmrcore: Exec format error. Wrong Architecture. If anybody has a version running on linux please chare that one with me. Thanks in advance for your help and kind regards, Dirk. Dirk Classen-Houben BV Biotechnologies GmbH (Biovertis - information-driven drug design AG) Campus Vienna Biocenter 6 1030 Vienna, Austria Phone +43-1-7989303-111 Fax +43-1-7989303-400 Email dirk.classen-houben_at_biovertis.com From chemistry-request@ccl.net Fri Nov 5 11:40:49 2004 Received: from simbiosys.ca ([65.18.214.160]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iA5Gem06006546 for ; Fri, 5 Nov 2004 11:40:48 -0500 Received: from phobos.simbiosys.ca (CPE0080c6f1fcb9-CM000f9f7b41ce.cpe.net.cable.rogers.com [69.195.104.248]) (authenticated (0 bits)) by simbiosys.ca (8.12.10/8.11.0) with ESMTP id iA5GroKj021379 for ; Fri, 5 Nov 2004 11:53:51 -0500 X-Authentication-Warning: simbiosys.ca: simbiosys owned process doing -bs From: Aniko Simon Organization: SimBioSys Inc. To: CHEMISTRY/at/ccl.net Subject: CCL: SimBioSys User Group Meeting, Toronto, Nov 22-23, 2004 Date: Fri, 5 Nov 2004 11:54:06 -0500 User-Agent: KMail/1.5.3 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200411051154.06291.aniko/at/simbiosys.ca> X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net SimBioSys Inc. will be hosting our second users group meeting Nov. 23-24, 2004 at the University of Toronto's MDIT centre. This meeting will provide users with hands on training on the very latest versions of SPROUT and eHiTS. In addition there will be ample opportunity for attendees to work on their own systems with guidance from the instructor. In addition, SimBioSys is please to announce Dr. Johnathan Cechetto, of McMasters University, as our invited speaker at this event. Dr. Cechetto is the manager of McMasters HTS Lab, and was responsible for a HTS Data Mining and Docking competition organized at McMasters. Dr. Cechetto will be presenting results from this exciting competition. SPROUT is a mature, powerful de novo ligand design package that allows users a high level of control, or can be used in a more automated manner to give a wide range of results. eHiTS is the first truly exhaustive docking program which guarantees not to miss a potential hit. eHiTS is unsurpassed in accuracy and enrichment results, as recent studies have shown. In VHTS mode, eHiTS boosts ligand docking times of 1.6 sec/ligand. For more details on the program, please visit our web site: http://www.simbiosys.ca/ Registration fee is CDN $495 for academics, CDN $995 for participants from industry. Current customers or those that purchase SPROUT or eHiTS prior to Nov 23rd can attend this hands-on tutorial session free of charge. We look forward seeing you, Aniko Simon VP of Business Development From chemistry-request@ccl.net Fri Nov 5 12:02:39 2004 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iA5H2c06008607 for ; Fri, 5 Nov 2004 12:02:38 -0500 Received: from gamow.scripps.edu (gamow [137.131.252.67]) by relay1.scripps.edu (8.12.11/TSRI-5.0.2rAV) with ESMTP id iA5HFoGL023224; Fri, 5 Nov 2004 09:15:50 -0800 (PST) Received: from quine.scripps.edu (dhcp-252-217 [137.131.252.217]) by gamow.scripps.edu (SGI-8.12.5/TSRI-5.0.1) with SMTP id iA5HFYoT541572; Fri, 5 Nov 2004 09:15:35 -0800 (PST) Received: by quine.scripps.edu (sSMTP sendmail emulation); Fri, 5 Nov 2004 09:15:48 -0800 Date: Fri, 5 Nov 2004 09:15:48 -0800 From: "David A. Case" To: khunter$at$mta.ca, chemistry$at$ccl.net Subject: Re: CCL:question about nitro groups in AMBER Message-ID: <20041105171548.GF4016$at$scripps.edu> References: <1099667886.418b99ae5c83f$at$webmail.mta.ca> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <1099667886.418b99ae5c83f$at$webmail.mta.ca> User-Agent: Mutt/1.4.1i X-CanItPRO-Stream: admin redirected to 10_OptOut X-Spam-Score: undef - spam-scanning disabled X-Canit-Stats-ID: 4285567 - 5dd56bda4e5a X-Scanned-By: CanIt (www . canit . ca) X-Spam-Status: No, hits=2.4 required=7.5 tests=OPT_HEADER autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Fri, Nov 05, 2004, khunter$at$mta.ca wrote: > In AMBER each atom has a designated type which is defined to set of > parameters in AMBER. It appears that nitro groups are not able to be > characterized by the existing atom type definitions. Are NO2 groups able to > be studied with AMBER? Have the parameters for NO2 been determined > previously? Is it possible to define your own parameters manually and if so > how? Is there a systematic method to how parameters are defined in AMBER? > Amber does have a systematic way of handling pretty arbitrary organic compounds, although I don't personally know how well it performs for nitro groups. Take a look at chapter 4 of the Users' Manual, available at http://amber.scripps.edu/doc8/amber8.pdf ...good luck...dave case From chemistry-request@ccl.net Thu Nov 4 23:54:23 2004 Received: from mail.ncsa.uiuc.edu (mail.ncsa.uiuc.edu [141.142.2.28]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iA54sLsE022126 for ; Thu, 4 Nov 2004 23:54:21 -0500 X-Envelope-From: spamidig..at..ncsa.uiuc.edu Received: from vasantam.ncsa.uiuc.edu (12-221-104-133.client.insightBB.com [12.221.104.133]) by mail.ncsa.uiuc.edu (8.11.7/8.11.7) with ESMTP id iA555mH27947; Thu, 4 Nov 2004 23:05:48 -0600 Message-Id: <6.0.0.22.2.20041104230153.0218c848..at..ncsa.uiuc.edu> X-Sender: spamidig..at..ncsa.uiuc.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 6.0.0.22 Date: Thu, 04 Nov 2004 23:05:56 -0600 To: Tom Kuppens , CHEMISTRY..at..ccl.net From: Sudhakar Pamidighantam Subject: Re: CCL:Gaussian/Gamess distributed computing In-Reply-To: References: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_1485886==.ALT" X-NCSA-MailScanner-Information: Please contact the help..at..ncsa.uiuc.edu for more information X-NCSA-MailScanner: Found to be clean X-Spam-Status: No, hits=2.6 required=7.5 tests=HTML_MESSAGE,RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --=====================_1485886==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Chemviz (chemviz.ncsa.uiuc.edu) does distribute gamess runs on a distributed set of resources using condor technology. A distributed computational chemistry grid system is designed and tested in GridChem ( see www.gridchem.org) and a virtual organization is being created for this and a first version of this is expected to be released in first quarter 05. Sudhakar. At 03:57 AM 11/4/2004, Tom Kuppens wrote: >Hi there, > >I'm curious if there are people working in a distributed computing >environment with Gaussian98/03 or Gamess... > >I've created a system that allows me to automaticaly schedule and >distribute gaussian jobs (in the near future also gamess jobs) over a >heterogenous group of linux machines. So each job is distributed to a >single node. I do a lot of geometry optimizations (eg an average of 250 >gaussian jobs per molecule - B3LYP/6-31G*). Parallellisation with Linda >gives bad efficiency compared to distribution of the problems to single >nodes. Parallel Gaussian however is great when using very large basis sets >(cc-pVTZ etc) on relatively large problems. > >I am really interested if there are others who do the same, or if this >can be done by large/small GNU/commercial packages. > >Also, is there someone who knows if Gaussian is run in a "Grid" >infrastructure somewhere? > >Thanks, > >Tom Kuppens > >Research group Quantumchemistry >Department of Inorganic and Physical Chemistry WE06V >Ghent University >Krijgslaan 281 - S3, 9000 Ghent, Belgium >Tel +32(0)9 264 4444 >Fax +32(0)9 264 4983 >-- >http://allserv.UGent.be/~tkuppens/ >---- > Life would be so much easier if we only had the source code. > -- Anonymous > > > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY..at..ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST..at..ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow..at..nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ Sudhakar Pamidighantam, Ph. D. NCSA ph:333-5831 e-mail:sudhakar..at..ncsa.edu --=====================_1485886==.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Chemviz (chemviz.ncsa.uiuc.edu) does distribute gamess runs on a distributed set of resources using condor technology.
A distributed computational chemistry grid system is designed and tested in GridChem ( see www.gridchem.org= ) and a virtual organization is being created
for this and a first version of this is expected to be released in first quarter 05.

Sudhakar.

At 03:57 AM 11/4/2004, Tom Kuppens wrote:

Hi there,

I'm curious if there are people working in a distributed computing
environment with Gaussian98/03 or Gamess...

I've created a system that allows me to automaticaly schedule and
distribute gaussian jobs (in the near future also gamess jobs) over a
heterogenous group of linux machines. So each job is distributed to a
single node. I do a lot of geometry optimizations (eg an average of 250
gaussian jobs per molecule - B3LYP/6-31G*). Parallellisation with Linda
gives bad efficiency compared to distribution of the problems to single
nodes. Parallel Gaussian however is great when using very large basis sets
(cc-pVTZ etc) on relatively large problems.

I am really interested if there are others who do the same, or if this
can be done by large/small GNU/commercial packages.

Also, is there someone who knows if Gaussian is run in a "Grid"
infrastructure somewhere?

Thanks,

Tom Kuppens

Research group Quantumchemistry
Department of Inorganic and Physical Chemistry WE06V
Ghent University
Krijgslaan 281 - S3, 9000 Ghent, Belgium
Tel  +32(0)9 264 4444
Fax  +32(0)9 264 4983
--
http://allserv.UGent.be/~tkuppens/
----
 Life would be so much easier if we only had the source code.
    -- Anonymous




-=3D This is automatically added to each message by the mailing script =3D-
To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
and send your message to:  CHEMISTRY..at..ccl.net

Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST..at..ccl.net
HOME Page: http://www.ccl.net&= nbsp; | Jobs Page: http://www.ccl.net/jo= bs

If your mail is bouncing from CCL.NET domain send it to the maintainer:
Jan Labanowski,  jlabanow..at..nd.edu (read about it on CCL Home Page)
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

Sudhakar Pamidighantam, Ph. D.
NCSA
ph:333-5831 e-mail:sudhakar..at..ncsa.edu --=====================_1485886==.ALT--