From chemistry-request@ccl.net Wed Jul 6 08:04:43 2005 Received: from smtp.prodigy.net.mx (nlpproxy06.prodigy.net.mx [148.235.52.26]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j66C4fAO028098 for ; Wed, 6 Jul 2005 08:04:42 -0400 Disposition-notification-to: dglossman.-at-.prodigy.net.mx Received: from smtp.prodigy.net.mx (nlpproxy06 [148.235.52.26]) by smtp.prodigy.net.mx (iPlanet Messaging Server 5.2 HotFix 2.05 (built Mar 3 2005)) with ESMTP id <0IJ70002M4LZCZ.-at-.smtp.prodigy.net.mx>; Wed, 06 Jul 2005 02:54:00 -0500 (CDT) Received: from NANO (dsl-200-78-92-156.prodigy.net.mx [200.78.92.156]) by smtp.prodigy.net.mx(iPlanet Messaging Server 5.2 HotFix 2.05 (built Mar 3 2005))with ESMTP id <0IJ700CW44LVGI.-at-.smtp.prodigy.net.mx>; Wed, 06 Jul 2005 02:53:59 -0500 (CDT) Date: Wed, 06 Jul 2005 01:52:19 -0600 From: "Dr. Daniel Glossman-Mitnik" Subject: CCL: software for the prediction of solubility To: chemistry.-at-.ccl.net Message-id: MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Mailer: Microsoft Outlook, Build 10.0.2627 Content-type: multipart/alternative; boundary="----=_NextPart_000_000A_01C581CD.57D8C530" Importance: Normal X-Priority: 3 (Normal) X-MSMail-priority: Normal X-imss-version: 2.028 X-imss-result: Passed X-imss-scores: Clean:57.73517 C:2 M:3 S:5 R:5 X-imss-settings: Baseline:4 C:4 M:4 S:4 R:4 (8.0000 8.0000) X-Spam-Status: No, score=3.7 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,DNS_FROM_RFC_WHOIS,HTML_90_100,HTML_FONT_BIG, HTML_MESSAGE,RCVD_IN_NJABL_PROXY autolearn=no version=3.0.4 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_000A_01C581CD.57D8C530 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 =20 Dear netters: =20 I would like to receive advice on software that can be used to predict the solubility of a substance in different solvents (not necessarily water) or a mix of solvents. My task is: I have a sustance X and I want to find the best solvent (or a mix) to disolve it. =20 Thanks in advance, =20 Daniel =20 *********************************************************************** Dr. Daniel Glossman-Mitnik Grupo NANOCOSMO - CIMAV Nanotecnolog=EDa Computacional, Simulaci=F3n y Modelado Molecular Miguel de Cervantes 120 - Comp. Ind. Chihuahua Chihuahua, Chih. 31109 - MEXICO Tel.: (52) 614 4391151 FAX: (52) 614 4391130 Part.: (52) 614 4987113 Cel.: (52) 614 1635322 E-mail: daniel.glossman.-at-.cimav.edu.mx dglossman.-at-.prodigy.net.mx *********************************************************************** =20 ------=_NextPart_000_000A_01C581CD.57D8C530 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear netters:

I would like to receive advice on software that can be used to predict the solubility

of a substance in different solvents (not necessarily water) or a mix of = solvents.

My task is: I have a sustance X and I want to find the best solvent (or a = mix) to

disolve it.

Thanks in advance,

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Daniel

********************************************************************= ***

Dr. Daniel Glossman-Mitnik

&n= bsp; Gru= po NANOCOSMO - CIMAV

Nanotecnolog=EDa Computacional, Simulaci=F3n y Modelado = Molecular=

Miguel de Cervantes 120 = - Comp. Ind. Chihuahua

&n= bsp; Chihuahua, Chih. 31109 - MEXICO

Tel.: (52) 614 4391151 FAX: (52) 614 4391130

&nbs= p; Part.: (52) 614 4987113 Cel.: (52) 614 = 1635322

&nbs= p; E-mail: daniel.glossman.-at-.cimav.edu.mx

&nbs= p; dglossman.-at-.prodigy.net.mx

********************************************************************= ***

------=_NextPart_000_000A_01C581CD.57D8C530-- From chemistry-request@ccl.net Wed Jul 6 09:39:32 2005 Received: from colibri.its.uu.se (colibri.its.UU.SE [130.238.4.154]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j66DdTWY002335 for ; Wed, 6 Jul 2005 09:39:30 -0400 Received: by colibri.its.uu.se (Postfix, from userid 211) id 6950F191; Wed, 6 Jul 2005 14:35:50 +0200 (DFT) Received: from colibri.its.uu.se(127.0.0.1) by colibri.its.uu.se via virus-scan id s14357; Wed, 6 Jul 05 14:35:44 +0200 Received: from [130.238.236.136] (kemi136.kemi.uu.se [130.238.236.136]) (using TLSv1 with cipher RC4-SHA (128/128 bits)) (No client certificate requested) by colibri.its.uu.se (Postfix) with ESMTP id DD737191 for ; Wed, 6 Jul 2005 14:35:44 +0200 (DFT) Mime-Version: 1.0 (Apple Message framework v622) In-Reply-To: <1120566100.16312.39.camel@Pauli> References: <1120566100.16312.39.camel@Pauli> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <980cc13da6ed2a5eb6f1acc72140c693|at|kemi.uu.se> Content-Transfer-Encoding: 7bit From: Torben Rasmussen Subject: Re: CCL: computer (hardware?) problem From: Ulrike Salzner Date: Wed, 6 Jul 2005 14:32:37 +0200 To: chemistry|at|ccl.net X-Mailer: Apple Mail (2.622) X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Hi Ulrike, This is perhaps a long shot, but have you tried to replace the SATA HD with an ATA HD? We experienced some strange instabilities with some of our nodes with SATA HDs, which was fixed by replacing the HDs with older ATA drives! It is fairly cheap and easy to test at least! Regards, Torben. On Jul 5, 2005, at 14:21, owner-chemistry|at|ccl.net wrote: > Dear all, > I have a very strange problem with a computer. It is a P4 2.8 GHz, 1GB > of RAM, 120 GB SATA HD, purchased in February 2004. For about 11 month > the machine was doing fine. Then jobs all of a sudden started to exit > randomly. At first I had Windows on it and used G98. Since I wanted to > upgrade anyways, I installed Fedora Core 3 and G03. The problem, > remained. Small jobs finish, bigger ones exit or remain in the queue, > collecting time and doing nothing. Since there is warranty and I > suspect > it is a hardware problem, I contacted the company. They took the > computer kept it for 2 months!!! for testing but claim there is nothing > wrong. They exchanged the memory anyways. The problem persists. > > I reinstalled the system, the problem remains. Right now there is a > job > stuck in link 103 for 3 1/2 hours. The CPU usage (top command) changes > between 0 and 99% but there seems to be no more progress. Is there any > trick to test what the machine is actually doing and to check what > causes the jobs to get kicked out? The same jobs run just fine on all > my > other computers, which are installed and configured in exactly the same > way. > > One thing I noticed is a message upon booting: "overclocking failure, > press F2 to load default values". I did this. Could this be a hint the > BIOS is configured wrong? Could the problem have to do with the power > management? I am at a loss. > > Any hints would be greatly appreciated. > Thanks, > Ulrike > -- > Ulrike Salzner > Associate Professor > Department of Chemistry > Bilkent University > 06800 Bilkent, Ankara > Turkey > > > > -= 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 is mail bouncing from ccl.net domain due to spam filters, > please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > From chemistry-request@ccl.net Wed Jul 6 03:04:39 2005 Received: from email1.uk.evotecoai.com (email1.evotecoai.com [195.172.92.249]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j6674YV3006731 for ; Wed, 6 Jul 2005 03:04:35 -0400 Received: from uk-abi-sma02.uk.evotecoai.com (Not Verified[10.1.48.40]) by email1.uk.evotecoai.com with NetIQ MailMarshal (v6,0,3,8) id ; Wed, 06 Jul 2005 08:07:56 +0100 X-MimeOLE: Produced By Microsoft Exchange V6.5.7226.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Subject: RE: Help with MOE Date: Wed, 6 Jul 2005 08:04:32 +0100 Message-ID: <24A00467861F604F8453636A0DAB58E11C57FD:at:uk-abi-sma02.uk.evotecoai.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Help with MOE Thread-Index: AcV9no2J10Bz5viuTkCnlYoF53+UFgBGJVoFANBtYCA= From: "Robinson, James" To: X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j6674dV3006741 Its is possible to use a wash function, this deprotonates acids and protonates amines. James -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request:at:ccl.net] On Behalf Of Axel Mathieu Sent: 02 July 2005 04:36 To: chemistry:at:ccl.net Subject: CCL:Help with MOE Hello Sandeep, I've you're looking for the same function as in InsightII to adjust hydrogens according to pH, I did not find one. However, this should not be too difficult to script and maybe CCG already has one. You can look at their site (SVL exchange) or directly contact support. APM ________________________________ From: Computational Chemistry List on behalf of SANDEEP KUMAR Sent: Thu 6/30/2005 11:29 AM To: chemistry:at:ccl.net Subject: CCL:Help with MOE Hello: I was wondering if there is a simple way to set the pH for a protein-ligand complex in MOE (Molecular Operations Environment from CCG) for the purpose of molecular electrostatics and simulations calculations. Any input shall be greatly appreciated. Yours sincerely, Sandeep Kumar ------------------------------------------------------------------- Dr. Sandeep Kumar, Associate Research Scientist, Johns Hopkins University Department of Biology, 106 Mudd Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA. Phone: 410-516-8433, Email: kumarsan:at:jhu.edu. URL: http://myprofile.cos.com/Kumarsan. or https://jshare.johnshopkins.edu/skumar23/public_html/ -= 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 Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST:at:ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs use the Web based form from CCL Home Page From chemistry-request@ccl.net Wed Jul 6 14:17:55 2005 Received: from mrbusi2.netcologne.de (mrbusi2.netcologne.de [194.8.194.214]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j66IHoWp023215 for ; Wed, 6 Jul 2005 14:17:51 -0400 Received: from cosmologic.de (xdsl-213-196-200-142.netcologne.de [213.196.200.142]) by mrbusi2.netcologne.de (Postfix) with ESMTP id 4586024004A for ; Wed, 6 Jul 2005 20:17:49 +0200 (CEST) Message-ID: <42CC204E.7010503~at~cosmologic.de> Date: Wed, 06 Jul 2005 20:17:50 +0200 From: Andreas Klamt User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6b) Gecko/20031205 Thunderbird/0.4 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry~at~ccl.net Subject: Re: CCL: software for the prediction of solubility To: chemistry~at~ccl.net References: In-Reply-To: Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=1.5 required=5.0 tests=ADDRESS_IN_SUBJECT, FORGED_RCVD_HELO autolearn=no version=3.0.4 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear Daniel, I dare to say, that our COSMOtherm software, which is a combination of the quantum chemical dielectric solvation model COSMO and a very efficient statistical thermodynamics of interacting surfaces is the most general and efficient software for this task. We and aour customers have done a lot of solvent screening projects of the kind you described. We can treat almost any solvent, including mixtures and ionic liquids, and even can include temperature dependence, if required. For more details see all the publications listed on www.cosmologic.de/publications.html I hope you will like it Andreas Dr. Daniel Glossman-Mitnik wrote: > > > > > Dear netters: > > > > I would like to receive advice on software that can be used to predict > the solubility > > of a substance in different solvents (not necessarily water) or a mix > of solvents. > > My task is: I have a sustance X and I want to find the best solvent > (or a mix) to > > disolve it. > > > > Thanks in advance, > > > > Daniel > > > > *********************************************************************** > > Dr. Daniel Glossman-Mitnik > > Grupo NANOCOSMO - CIMAV > > Nanotecnologma Computacional, Simulacisn y Modelado Molecular > > Miguel de Cervantes 120 - Comp. Ind. Chihuahua > > Chihuahua, Chih. 31109 - MEXICO > > Tel.: (52) 614 4391151 FAX: (52) 614 4391130 > > Part.: (52) 614 4987113 Cel.: (52) 614 1635322 > > E-mail: daniel.glossman~at~cimav.edu.mx > > > dglossman~at~prodigy.net.mx > > > *********************************************************************** > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt~at~cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From chemistry-request@ccl.net Wed Jul 6 14:25:05 2005 Received: from web32705.mail.mud.yahoo.com (web32705.mail.mud.yahoo.com [68.142.207.249]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j66IP0Np023763 for ; Wed, 6 Jul 2005 14:25:00 -0400 Received: (qmail 50461 invoked by uid 60001); 6 Jul 2005 17:24:59 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:In-Reply-To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=N22H92BDW6DlENsd7hUuSeB79ocRYrOuqTTPFkx9ujpTOtXnaJVyCEEd4+QtVB34rUpK0mCnIX7Wdy32Eq+kvCSvATs+xXWSdj0Zp4kDiEps9NmzsxTWxZW5CBFMC/gVdvLSrzf/9kHphFbvS5FQtptqDCVpZUn3fCo1KuLz4QA= ; Message-ID: <20050706172459.50459.qmail~at~web32705.mail.mud.yahoo.com> Received: from [61.1.212.96] by web32705.mail.mud.yahoo.com via HTTP; Wed, 06 Jul 2005 10:24:59 PDT Date: Wed, 6 Jul 2005 10:24:59 -0700 (PDT) From: gurusamy gurusamy Subject: MD simulation tutorial To: chemistry~at~ccl.net In-Reply-To: <980cc13da6ed2a5eb6f1acc72140c693~at~kemi.uu.se> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1345753218-1120670699=:50326" Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=1.5 required=5.0 tests=DEAR_SOMETHING, DNS_FROM_RFC_ABUSE,FROM_HAS_MIXED_NUMS,HTML_30_40,HTML_MESSAGE autolearn=no version=3.0.4 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net --0-1345753218-1120670699=:50326 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit DEAR SIR I am in need of a tutorial for running MDsimulationof a peptide in lipid bilayer thanks. Torben Rasmussen wrote: > Ulrike Salzner > Associate Professor > Department of Chemistry > Bilkent University > 06800 Bilkent, Ankara > Turkey > > > > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > > 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 is mail bouncing from ccl.net domain due to spam filters, > please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > -= 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 is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ Mr. P. Gurusamy, Lecturer in Chemistry (S.G), Department of Chemistry, Sri. Ramasay Naidu Memorial College, Sattur-626203, Virudhunagar District, Tamilnadu, India. --------------------------------- Sell on Yahoo! Auctions - No fees. Bid on great items. --0-1345753218-1120670699=:50326 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

DEAR SIR

I am in need of a tutorial for running MDsimulationof a peptide in lipid bilayer

thanks.

Torben Rasmussen <Torben.Rasmussen~at~kemi.uu.se> wrote:

> Ulrike Salzner
> Associate Professor
> Department of Chemistry
> Bilkent University
> 06800 Bilkent, Ankara
> Turkey
>
>
>
> To send e-mail to subscribers of CCL put the string CCL: on your
> Subject: line
>
> 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 is mail bouncing from ccl.net domain due to spam filters,
> please
> use the Web based form from CCL Home Page
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
> +-+
>
>
>
>
>

-= 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 is mail bouncing from ccl.net domain due to spam filters, please
use the Web based form from CCL Home Page
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

Mr. P. Gurusamy,
Lecturer in Chemistry (S.G),
Department of Chemistry,
Sri. Ramasay Naidu Memorial College,
Sattur-626203,
Virudhunagar District,
Tamilnadu,
India.

Sell on Yahoo! Auctions - No fees. Bid on great items. --0-1345753218-1120670699=:50326-- From chemistry-request@ccl.net Wed Jul 6 14:28:51 2005 Received: from smtp-gw2.fusemail.net (smtp-gw2.fusemail.net [65.61.162.171]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j66ISoPu024068 for ; Wed, 6 Jul 2005 14:28:50 -0400 Received: from fusemail.com by smtp-gw2.fusemail.net with esmtp (FuseMail extSMTP) id 1DqEc6-0003Y0-E2 for chemistry|at|ccl.net; Wed, 06 Jul 2005 14:27:14 -0400 Received: from fusemail.com by fuse1.fusemail.net with asmtp (TLSv1:AES256-SHA:256) (FuseMail extSMTP) id 1DqEdU-000466-Vw for chemistry|at|ccl.net; Wed, 06 Jul 2005 13:28:41 -0500 Message-ID: <42CC22D9.2090909|at|pobox.com> Date: Wed, 06 Jul 2005 14:28:41 -0400 From: "Andrew D. Fant" User-Agent: Mozilla Thunderbird 1.0.2 (X11/20050627) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry|at|ccl.net Subject: Concord/Corina replacements for Linux X-Enigmail-Version: 0.90.2.0 X-Enigmail-Supports: pgp-inline, pgp-mime Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Good afternoon all, and thanks to everyone who responded to my previous questions about openbabel and descriptor code. I have one other question about software that has come up. Can anyone recommend a program that can generate 3D structures of any quality of all from 2D representations? I know that Concord and Corina can do this, but I am doing this for my own education/edification and would rather not blow the rent money on this project. I'm hoping to take some data I have pulled from various publications on my laptop on a train trip and putter with it en route, so a web-based tool is less than ideal. If anyone has any suggestions, I would be most appreciative. Thanks, Andy From chemistry-request@ccl.net Wed Jul 6 15:28:14 2005 Received: from monty.richmond.edu (monty.richmond.edu [141.166.24.29]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j66JS9QX028136 for ; Wed, 6 Jul 2005 15:28:09 -0400 Received: from rayon.richmond.edu (rayon.richmond.edu [141.166.30.10]) by monty.richmond.edu (8.11.6/8.11.6) with ESMTP id j66IoRf29999 for ; Wed, 6 Jul 2005 14:50:27 -0400 Received: from pollux.richmond.edu (pollux.richmond.edu [141.166.8.36]) by rayon.richmond.edu (8.12.11/8.12.11) with ESMTP id j66IoPwo001270 for ; Wed, 6 Jul 2005 14:50:25 -0400 Received: from castor.richmond.edu ([141.166.8.35]) by pollux.richmond.edu with Microsoft SMTPSVC(5.0.2195.6713); Wed, 6 Jul 2005 14:50:25 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.0.6603.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C5825B.924B9BF9" Subject: Gaussian03 and Red Hat Enterprise 3 x86_64 Date: Wed, 6 Jul 2005 14:50:25 -0400 Message-ID: <12E81F39195C00468C4DE42509951D3804C0164B_at_castor.richmond.edu> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Gaussian03 and Red Hat Enterprise 3 x86_64 Thread-Index: AcWCW5HBwogKGWWrRCuFpXpvDa2XHg== From: "Parish, Carol" To: X-OriginalArrivalTime: 06 Jul 2005 18:50:25.0829 (UTC) FILETIME=[92502D50:01C5825B] X-Spam-Detail: -2.63 ALL_TRUSTED,HTML_90_100,HTML_MESSAGE X-Scanned-By: MIMEDefang 2.49 on 141.166.30.10 X-Spam-Status: No, score=0.2 required=5.0 tests=HTML_90_100,HTML_MESSAGE autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net This is a multi-part message in MIME format. ------_=_NextPart_001_01C5825B.924B9BF9 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi, =20 Has anyone successfully installed and run the AMD64 Gaussian03 binary under RHEL 3 (64-bit version)? =20 =20 Thanks, Carol =20 ------_=_NextPart_001_01C5825B.924B9BF9 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi,

Has anyone successfully installed and run the AMD64 Gaussian03 = binary under RHEL 3 (64-bit version)?

Thanks, Carol

------_=_NextPart_001_01C5825B.924B9BF9-- From chemistry-request@ccl.net Wed Jul 6 16:14:26 2005 Received: from poster.sci.kun.nl (poster.sci.kun.nl [131.174.124.7]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j66KEK3f031920 for ; Wed, 6 Jul 2005 16:14:21 -0400 Received: from multi.science.ru.nl [131.174.16.159] (helo=multi.science.ru.nl) by poster.sci.kun.nl (8.12.10/5.0) with ESMTP id j66JZev7028252 for ; Wed, 6 Jul 2005 21:35:40 +0200 (MEST) Received: from solo.sci.kun.nl [131.174.16.134] (helo=sci.kun.nl) by multi.science.ru.nl (8.12.10/5.0) with ESMTP id j66JZXEx005004; Wed, 6 Jul 2005 21:35:33 +0200 (MEST) From: Egon Willighagen Reply-To: e.willighagen:at:science.ru.nl To: chemistry:at:ccl.net Subject: Re: CCL: Concord/Corina replacements for Linux X-Enigmail-Version: 0.90.2.0 Date: Wed, 6 Jul 2005 21:35:36 +0200 User-Agent: KMail/1.8.1 References: <42CC22D9.2090909:at:pobox.com> In-Reply-To: <42CC22D9.2090909:at:pobox.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200507062135.36850.e.willighagen:at:science.ru.nl> X-Spam-Score: -1.665 () BAYES_00 X-Scanned-By: MIMEDefang 2.48 on 131.174.16.159 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net On Wednesday 6 July 2005 20:28, Andrew D. Fant wrote: > Good afternoon all, and thanks to everyone who responded to my previous > questions about openbabel and descriptor code. I have one other > question about software that has come up. The Chemistry Development Kit (http://cdk.sf.net/) can do this and is free to download. The involved Java class is ModelBuilder3D [1]. A live demo is available from: http://www.chemistry-development-kit.org/ Just enter a SMILES or upload a molecular file, and a 3D model will be displayed using Jmol [2]. Egon 1. http://cdk.sf.net/apicvs/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.html 2. http://www.jmol.org/ -- e.willighagen:at:science.ru.nl PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 From chemistry-request@ccl.net Wed Jul 6 15:28:24 2005 Received: from fenyo.mail.t-online.hu (fenyo.mail.t-online.hu [195.228.240.95]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j66JSIsW028176 for ; Wed, 6 Jul 2005 15:28:19 -0400 Received: from chemaxon.com (a84-0-129-119.adsl-pool.axelero.hu [84.0.129.119]) by fenyo.mail.t-online.hu (8.13.4/8.12.11) with ESMTP id j66JSFsX054722 for ; Wed, 6 Jul 2005 21:28:17 +0200 (CEST) Message-ID: <42CC30CF.3090704:at:chemaxon.com> Date: Wed, 06 Jul 2005 21:28:15 +0200 From: Miklos Vargyas User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6) Gecko/20040113 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry:at:ccl.net Subject: Re: CCL: Concord/Corina replacements for Linux X-Enigmail-Version: 0.90.2.0 References: <42CC22D9.2090909:at:pobox.com> In-Reply-To: <42CC22D9.2090909:at:pobox.com> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-VBMilter: scanned X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Hi Andy, try Marvin! It is available on the internet, just follow the link below: http://www.chemaxon.hu/marvin/sketch/demo-applet.html Draw a structure in the sketch window, then select Edit->Clean->3D. Then you can either pop up a 3D viewer (View->Open 3D viewer) or save the 3D structure in a suitable file (e.g. mol). In case you need to convert many structures the MolConverter tool comes handy as it can batch process your molecules. You may wish to visit the molconverter page at http://www.chemaxon.hu/marvin/doc/user/molconvert.html. Regards, Miklos Andrew D. Fant wrote: >Good afternoon all, and thanks to everyone who responded to my previous >questions about openbabel and descriptor code. I have one other >question about software that has come up. Can anyone recommend a >program that can generate 3D structures of any quality of all from 2D >representations? I know that Concord and Corina can do this, but I am >doing this for my own education/edification and would rather not blow >the rent money on this project. I'm hoping to take some data I have >pulled from various publications on my laptop on a train trip and putter >with it en route, so a web-based tool is less than ideal. If anyone has >any suggestions, I would be most appreciative. > >Thanks, > Andy > > >-= 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 is mail bouncing from ccl.net domain due to spam filters, please >use the Web based form from CCL Home Page >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > From chemistry-request@ccl.net Wed Jul 6 15:43:16 2005 Received: from ipex1.johnshopkins.edu (ipex1.johnshopkins.edu [162.129.8.141]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j66JhCZZ029256 for ; Wed, 6 Jul 2005 15:43:12 -0400 Received: from jhem1.jhmi.edu (HELO jhumail.jhu.edu) (162.129.8.22) by ipex1.johnshopkins.edu with ESMTP; 06 Jul 2005 15:43:11 -0400 X-BrightmailFiltered: true X-Brightmail-Tracker: AAAAAA== X-IronPort-AV: i="3.93,265,1115006400"; d="scan'208"; a="74792147:sNHT29879420" Received: from [128.220.21.114] by jhumail.jhu.edu (mshttpd); Wed, 06 Jul 2005 15:43:11 -0400 From: SANDEEP KUMAR To: fant$at$pobox.com Cc: chemistry$at$ccl.net Reply-To: kumarsan$at$jhu.edu Message-ID: <94832e07b3c1.42cbfc0f$at$jhumail.jhu.edu> Date: Wed, 06 Jul 2005 15:43:11 -0400 X-Mailer: Sun Java(tm) System Messenger Express 6.1 HotFix 0.11 (built Jan 28 2005) MIME-Version: 1.0 Content-Language: en Subject: Re: CCL: Concord/Corina replacements for Linux X-Enigmail-Version: 0.90.2.0 X-Accept-Language: en Priority: normal Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.6 required=5.0 tests=FORGED_RCVD_HELO, FROM_ENDS_IN_NUMS autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Hi Andrew: If you don't wish to use CORINA at all (not even the 1 month free trial version), then you might like to try this. Lets say you have *.cdx (chemdraw) files for 2D representation of your molecules. Take one of these at a time and open it in Chem3d. In chem3d, use edit --> select all to select all the atoms. Then, Tools ---> Cleanup Structure and then MM2 --> minimize energy. If your molecules are small enough, this process shall be fast. However, it takes a lot of time with MM2 if the molecules are big. Once you have minimized structure, then save as MDL molfile (*.mol). The molfile will save the coordinates in 3D. I hope this helps. Sincerely, Sandeep Kumar ------------------------------------------------------------------- Dr. Sandeep Kumar, Associate Research Scientist, Johns Hopkins University Department of Biology, 106 Mudd Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA. Phone: 410-516-8433, Email: kumarsan$at$jhu.edu. URL: http://myprofile.cos.com/Kumarsan. or https://jshare.johnshopkins.edu/skumar23/public_html/ ----- Original Message ----- From: "Andrew D. Fant" Date: Wednesday, July 6, 2005 2:28 pm Subject: CCL: Concord/Corina replacements for Linux X-Enigmail-Version: 0.90.2.0 > Good afternoon all, and thanks to everyone who responded to my > previousquestions about openbabel and descriptor code. I have one > otherquestion about software that has come up. Can anyone > recommend a > program that can generate 3D structures of any quality of all from 2D > representations? I know that Concord and Corina can do this, but I am > doing this for my own education/edification and would rather not blow > the rent money on this project. I'm hoping to take some data I have > pulled from various publications on my laptop on a train trip and > putterwith it en route, so a web-based tool is less than ideal. If > anyone has > any suggestions, I would be most appreciative. > > Thanks, > Andy > > > -= 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 is mail bouncing from ccl.net domain due to spam filters, > pleaseuse the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > > From chemistry-request@ccl.net Wed Jul 6 16:39:19 2005 Received: from mx5.net.nih.gov (mailfwd.nih.gov [165.112.130.36]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j66KdHoX001770 for ; Wed, 6 Jul 2005 16:39:17 -0400 Received: from mx5.net.nih.gov (localhost [127.0.0.1]) by mx5.net.nih.gov (8.12.10/8.11.6) with ESMTP id j66JmUnk008689 for ; Wed, 6 Jul 2005 15:48:30 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by mx5.net.nih.gov (8.12.10/8.11.6) with ESMTP id j66JmUk6008686 for ; Wed, 6 Jul 2005 15:48:30 -0400 Date: Wed, 6 Jul 2005 15:42:30 -0400 From: Rick Venable To: chemistry:at:ccl.net Subject: Re: CCL: MD simulation tutorial To: chemistry:at:ccl.net In-Reply-To: <20050706172459.50459.qmail:at:web32705.mail.mud.yahoo.com> Message-ID: References: <20050706172459.50459.qmail:at:web32705.mail.mud.yahoo.com> ReplyTo: Rick_Venable:at:nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, score=1.4 required=5.0 tests=ADDRESS_IN_SUBJECT autolearn=no version=3.0.4 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Most people in that position are actually in need of a tutorial on running lipid bilayer simulations. The methods are somewhat distinct > from simple aqueous solvation. Any such tutorial would be highly simulation package dependent; there is also not complete agreement in the field concerning all of the technical nuances. On Wed, 6 Jul 2005, gurusamy gurusamy wrote: > I am in need of a tutorial for running MDsimulationof > a peptide in lipid bilayer thanks. > > Mr. P. Gurusamy, > Lecturer in Chemistry (S.G), > Department of Chemistry, > Sri. Ramasay Naidu Memorial College, > Sattur-626203, > Virudhunagar District, > Tamilnadu, > India. ------------------------------------- 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:at:nih.gov ALT email: rvenable:at:speakeasy.org ------------------------------------- nekcihC toboR From chemistry-request@ccl.net Wed Jul 6 17:03:28 2005 Received: from uni-bonn.de (mail.uni-bonn.de [131.220.15.112]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j66L3OW9003765 for ; Wed, 6 Jul 2005 17:03:24 -0400 Received: from [82.83.227.97] (account mweigt HELO [192.168.100.2]) by uni-bonn.de (CommuniGate Pro SMTP 4.2.10) with ESMTP id 18974063 for chemistry %x% ccl.net; Wed, 06 Jul 2005 22:03:23 +0200 Message-ID: <42CC3910.3000005 %x% uni-bonn.de> Date: Wed, 06 Jul 2005 22:03:28 +0200 From: Mathias Weigt User-Agent: Mozilla Thunderbird 1.0.2 (X11/20050527) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry %x% ccl.net Subject: Re: CCL: Concord/Corina replacements for Linux X-Enigmail-Version: 0.90.2.0 References: <42CC22D9.2090909 %x% pobox.com> In-Reply-To: <42CC22D9.2090909 %x% pobox.com> X-Enigmail-Version: 0.90.2.0 X-Enigmail-Supports: pgp-inline, pgp-mime Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Andrew D. Fant wrote: >Good afternoon all, and thanks to everyone who responded to my previous >questions about openbabel and descriptor code. I have one other >question about software that has come up. Can anyone recommend a >program that can generate 3D structures of any quality of all from 2D >representations? I know that Concord and Corina can do this, but I am >doing this for my own education/edification and would rather not blow >the rent money on this project. I'm hoping to take some data I have >pulled from various publications on my laptop on a train trip and putter >with it en route, so a web-based tool is less than ideal. If anyone has >any suggestions, I would be most appreciative. > > Marvin from CHEMAXON can do this i think... Mathias Weigt From chemistry-request@ccl.net Wed Jul 6 21:16:28 2005 Received: from smtp.goldrush.com (smtp.goldrush.com [206.171.171.11]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j671GQAo020294 for ; Wed, 6 Jul 2005 21:16:27 -0400 Received: from [127.0.0.1] (x2-04b-28.goldrush.com [64.162.11.28]) by smtp.goldrush.com (8.12.8/8.12.8) with ESMTP id j671GHCn011270 for ; Wed, 6 Jul 2005 18:16:24 -0700 Message-ID: <42CC8258.2010506$at$goldrush.com> Date: Wed, 06 Jul 2005 18:16:08 -0700 From: Steve Bowlus User-Agent: Mozilla Thunderbird 1.0.2 (Windows/20050317) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry$at$ccl.net Subject: Re: CCL: Concord/Corina replacements for Linux References: <42CC22D9.2090909$at$pobox.com> In-Reply-To: <42CC22D9.2090909$at$pobox.com> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-MailScanner: Found to be clean X-MailScanner-SpamCheck: X-MailScanner-From: chezbowlus$at$goldrush.com X-Spam-Status: No, score=0.1 required=5.0 tests=DNS_FROM_AHBL_RHSBL autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net I have used the 3D conversion/optimization in ChemSketch (ACD Labs) for this purpose. sb Andrew D. Fant wrote: >Good afternoon all, and thanks to everyone who responded to my previous >questions about openbabel and descriptor code. I have one other >question about software that has come up. Can anyone recommend a >program that can generate 3D structures of any quality of all from 2D >representations? I know that Concord and Corina can do this, but I am >doing this for my own education/edification and would rather not blow >the rent money on this project. I'm hoping to take some data I have >pulled from various publications on my laptop on a train trip and putter >with it en route, so a web-based tool is less than ideal. If anyone has >any suggestions, I would be most appreciative. > >Thanks, > Andy > > >-= 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 is mail bouncing from ccl.net domain due to spam filters, please >use the Web based form from CCL Home Page >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > > > > > From chemistry-request@ccl.net Wed Jul 6 18:47:58 2005 Received: from heinlein.acpub.duke.edu (heinlein.acpub.duke.edu [152.3.233.9]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j66Mlu7J011007 for ; Wed, 6 Jul 2005 18:47:56 -0400 Received: from godzilla.acpub.duke.edu (godzilla.acpub.duke.edu [152.3.233.25]) by heinlein.acpub.duke.edu (8.12.11/8.12.10/Duke-5.0.0) with ESMTP id j66Mlrwq025645 for ; Wed, 6 Jul 2005 18:47:54 -0400 Received: (from jz7@localhost) by godzilla.acpub.duke.edu (8.12.10/8.12.9/Submit) id j66MloiP024710; Wed, 6 Jul 2005 18:47:50 -0400 (EDT) Date: Wed, 6 Jul 2005 18:47:50 -0400 (EDT) From: jz7$at$duke.edu Sender: jz7$at$duke.edu To: chemistry$at$ccl.net Subject: about MM3 force field Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-PMX-Version: 4.7.1.128075, Antispam-Engine: 2.0.3.2, Antispam-Data: 2005.7.6.30 X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net Dear all, I am running calculation (MD) on 1,8-diphenyl-naphthalene and similiar but longer structure using MM3 force field. Because it's a big conjugated system, I assigned all the carbon atoms to be pi-atom. However, the rings are tended to be in a plane for longer diphenyl-naphthalene molecules (1,8-diphenyl-naphthalene is ok). From the X-ray/NMD experiment, the phenyl rings should be almost perpendicular to the naphthalene. Would anyone please tell me whether my treatment is wrong or what else force field is better for this kind of molecule (for MD simulation)? Thanks a lot! From chemistry-request@ccl.net Wed Jul 6 17:33:49 2005 Received: from web33803.mail.mud.yahoo.com (web33803.mail.mud.yahoo.com [66.163.178.50]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j66LXkwi006133 for ; Wed, 6 Jul 2005 17:33:47 -0400 Received: (qmail 20247 invoked by uid 60001); 6 Jul 2005 20:33:44 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=jAJ5CLYdV6uNsBY96Afo3mPOWmCvwfh/w8CNaLaASN6/aN8mumSnn4IgDk5o+1z8GQyA2kHhczAJGUfSXtvYyJ5i7HsiusWWZsW/utYw1633sk1tdxqmXvou4C95hJ1J4f+0tmxXt0WJpBQThZcgrPy0LxvCvgZr27c9Gpwp0v0= ; Message-ID: <20050706203344.20245.qmail$at$web33803.mail.mud.yahoo.com> Received: from [24.49.179.202] by web33803.mail.mud.yahoo.com via HTTP; Wed, 06 Jul 2005 13:33:44 PDT Date: Wed, 6 Jul 2005 13:33:44 -0700 (PDT) From: michelle claro Subject: 3D to chemical name To: chemistry$at$ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1946771480-1120682024=:19053" Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=1.4 required=5.0 tests=DNS_FROM_RFC_ABUSE, FROM_ENDS_IN_NUMS,HTML_20_30,HTML_MESSAGE autolearn=no version=3.0.4 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net --0-1946771480-1120682024=:19053 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello, I have about 50 pdb structures (no protein in the pdb just the ligand) but I need the chemical names in order to purchase them. What is the easiest way to get a chemical name from a pdb? Thanks in advance. M. Claro __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --0-1946771480-1120682024=:19053 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

Hello,

I have about 50 pdb structures (no protein in the pdb just the ligand) but I need the chemical names in order to purchase them. What is the easiest way to get a chemical name from a pdb? Thanks in advance.

M. Claro

__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com --0-1946771480-1120682024=:19053-- From chemistry-request@ccl.net Wed Jul 6 19:23:37 2005 Received: from rproxy.gmail.com (rproxy.gmail.com [64.233.170.204]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j66NNZIB012991 for ; Wed, 6 Jul 2005 19:23:35 -0400 Received: by rproxy.gmail.com with SMTP id a41so56537rng for ; Wed, 06 Jul 2005 16:23:34 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:in-reply-to:mime-version:content-type:references; b=E+zWQzOVetYd4CZ64UgRowYa9abuyxq9HapEZS6/HGJ0cB5voYVYa1M9MpmPBF+CH+4+aGT90cIbZtpi74lL3TO3FEQRt4TORWPLy4nZSDg/zofQx0qOsT5Lzqhn45/MHh63tQ/RKh784A/y3mTDjVcCrc0mjVWt2q3kg7xexr4= Received: by 10.38.149.61 with SMTP id w61mr219973rnd; Wed, 06 Jul 2005 15:29:09 -0700 (PDT) Received: by 10.38.90.4 with HTTP; Wed, 6 Jul 2005 15:29:09 -0700 (PDT) Message-ID: Date: Wed, 6 Jul 2005 19:29:09 -0300 From: Luciano Costa Reply-To: Luciano Costa To: chemistry$at$ccl.net Subject: Re: CCL: Gaussian03 and Red Hat Enterprise 3 x86_64 In-Reply-To: <12E81F39195C00468C4DE42509951D3804C0164B$at$castor.richmond.edu> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_Part_3982_1978155.1120688949272" References: <12E81F39195C00468C4DE42509951D3804C0164B$at$castor.richmond.edu> X-Spam-Status: No, score=0.1 required=5.0 tests=HTML_60_70,HTML_MESSAGE, RCVD_BY_IP autolearn=failed version=3.0.4 X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net ------=_Part_3982_1978155.1120688949272 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Carol, I think that you should send a email to 'gaussian development session',=20 because here we used a script that they send us. This script is used for active this gaussian version to AMD64. On 7/6/05, Parish, Carol wrote: >=20 > Hi, >=20 > Has anyone successfully installed and run the AMD64 Gaussian03 binary=20 > under RHEL 3 (64-bit version)?=20 >=20 > Thanks, Carol >=20 > ------=_Part_3982_1978155.1120688949272 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

Hi Carol,

I think that you should send a email to 'gaussian development session', bec= ause here we used a script that they send us.

This script is used for active this gaussian version to AMD64.

On 7/6/05, Parish, Carol <cparish@ri= chmond.edu> wrote:

Hi,

Has anyone successfully installed and run the AMD64 Gaussian03 binary under RHEL 3 (64-bit version)?

Thanks, Carol

------=_Part_3982_1978155.1120688949272--