From chemistry-request@ccl.net Wed May 25 10:22:26 2005 Received: from web40906.mail.yahoo.com (web40906.mail.yahoo.com [66.218.78.203]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j4PEMKFR031152 for ; Wed, 25 May 2005 10:22:20 -0400 Received: (qmail 46512 invoked by uid 60001); 25 May 2005 13:22:18 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=vZx9kmdLyWql08ae6qbFs3G2ZVHsFiV6httm+IBV/R3oax6D3tjvLx6zKO5T041FfgLJScrdtlFyCKgrGYD+z42j+bhre/c0Fuy1dc/ljuADeL4MZnT5k9igmBUGbdreAF6G+euhn2dulSrsQrD3msj587iLgkM7ug0wVX8DHH8= ; Message-ID: <20050525132218.46510.qmail*at*web40906.mail.yahoo.com> Received: from [210.235.206.35] by web40906.mail.yahoo.com via HTTP; Wed, 25 May 2005 14:22:18 BST Date: Wed, 25 May 2005 14:22:18 +0100 (BST) From: Abhijit Chatterjee Subject: QUASI ATOM To: chemistry*at*ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-923877628-1117027338=:45076" Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=2.2 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,HTML_50_60,HTML_MESSAGE,SUBJ_ALL_CAPS autolearn=no version=3.0.3 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net --0-923877628-1117027338=:45076 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi friends, I am looking for resources for Quasi atom. The definition, how it can be implmented in density functional theory domain. Your response is highly appreciated. WIth best regards Abhijit Chatterjee --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now --0-923877628-1117027338=:45076 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi friends,
 
I am looking for resources for Quasi atom.  The definition, how it can be implmented in density functional theory domain.
 
Your response is highly appreciated.
 
WIth best regards
 
Abhijit Chatterjee

Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now --0-923877628-1117027338=:45076-- From chemistry-request@ccl.net Wed May 25 05:52:23 2005 Received: from cuces2.unisi.it (cuces2.unisi.it [193.205.4.8]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4P9qLv5023235 for ; Wed, 25 May 2005 05:52:21 -0400 Received: from PMAS-DAEMON.mailsrv.unisi.it by mailsrv.unisi.it (PMDF V6.2-X17 #30893) id <01LOO8PA6MIO91VYPQ.-at-.mailsrv.unisi.it> for chemistry.-at-.ccl.net; Wed, 25 May 2005 11:10:39 +0200 (MET-DST) Received: from CONVERSION-DAEMON.mailsrv.unisi.it by mailsrv.unisi.it (PMDF V6.2-X17 #30967) id <01LOO8P1LW8G90OU7H.-at-.mailsrv.unisi.it> for chemistry.-at-.ccl.net; Wed, 25 May 2005 11:10:28 +0200 (MET-DST) Received: from student.unisi.it (morgana.smin.unisi.it [172.16.53.95]) by mailsrv.unisi.it (PMDF V6.2-X17 #30893) with ESMTPA id <01LOO8OZSCAC91VYTL.-at-.mailsrv.unisi.it> for chemistry.-at-.ccl.net; Wed, 25 May 2005 11:10:26 +0200 (MET-DST) Date: Wed, 25 May 2005 11:12:09 +0200 From: Lucilla angeli Subject: macrocycles To: CCL Message-id: <42944169.7060704.-at-.student.unisi.it> MIME-version: 1.0 Content-type: text/plain; format=flowed; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en-us, en User-Agent: Mozilla/5.0 (X11; U; IRIX64 IP30; en-US; rv:1.4) Gecko/20030711 X-PMAS-Software: PreciseMail V2.1-1 [050524] (mailsrv.unisi.it) X-PMAS-Not-Positive: -0.900 X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear CCLers I had a question about the docking of cyclic compounds, like macrocyclic lactones or macrolides. Does anyone know or have ever applied a computational protocol to dock macrocycles with many degrees of freedom into a protein? I don't know how to approach the problem.... Perhaps a conformational analysis with Maestro and then a docking with Autodock (that, however, is not able to take into account the flexibility of the ring)...... I wait hopeful for your suggestions. Thanks in advance Lucilla Angeli From chemistry-request@ccl.net Wed May 25 04:33:26 2005 Received: from mb1i1.ns.pitt.edu (mb1i1.ns.pitt.edu [136.142.11.139]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4P8XLOB020949 for ; Wed, 25 May 2005 04:33:22 -0400 Received: from [127.0.0.1] ([136.142.109.16]) by pitt.edu (PMDF V6.2-X27 #30902) with ESMTP id <01LONUTN2O5O008HNH*at*mb1i1.ns.pitt.edu> for chemistry*at*ccl.net; Wed, 25 May 2005 04:33:19 -0400 (EDT) Date: Wed, 25 May 2005 04:33:36 -0400 From: Kadir Diri Subject: vibrationally averaged geometries To: chemistry*at*ccl.net Message-id: <42943860.2060908*at*visual1.chem.pitt.edu> MIME-version: 1.0 Content-type: text/plain; format=flowed; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en-us, en, tr User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.2) Gecko/20040803 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi everyone! I was wondering if somebody can point out references giving both equilibrium and vibrationally averaged geometries for H-bonded clusters like (H2O)n, (HF)n etc... Thanks! kadir From chemistry-request@ccl.net Wed May 25 16:16:53 2005 Received: from web50304.mail.yahoo.com (web50304.mail.yahoo.com [206.190.38.58]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j4PKGmoR009130 for ; Wed, 25 May 2005 16:16:48 -0400 Received: (qmail 18138 invoked by uid 60001); 25 May 2005 19:16:47 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=zlwmcGQMuGruWM0sSqiV8GTzRPLPYfHTaMHoRturMHwsro8CZFZrpSr3Jdm/QHtRj8EDlpOM1WMbpF28ljkJ0tz7JZDR+EDYAsG+2JX5MHt8eEMY7LrUS6SrvXewQcTIJEOOmoUyaA+FjsvIk74zB3yEhDOEP9qfZxbaaNABat4= ; Message-ID: <20050525191647.18136.qmail*at*web50304.mail.yahoo.com> Received: from [164.68.15.202] by web50304.mail.yahoo.com via HTTP; Wed, 25 May 2005 12:16:47 PDT Date: Wed, 25 May 2005 12:16:47 -0700 (PDT) From: Nhat Le Minh Subject: Gaussian 03 UFF Modification for Square planar Rhodium To: CHEMISTRY*at*ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear CCL-subscribers: My name is Alex Le, a student from Lake Forest College. I am currently doing a summer research in organometallics involving modeling a square planar Rhodium as a center atom in a hydrofomylation catalyst. We are trying to modify the UFF force field in Gaussian 03 to adopt the Rh4+1 square planar and so far there has been very little progress. I realy surprise that there is so little information available on making such modification for UFF. I just wonder if there is anyone who has successfully modifed the UFF parameters in Gaussian and he or she can share the experience. At the college Gaussian 98 and 03 are runnin on SGIs and Apple G4s. I only have the source code for Gaussian 98 for code-modification and recompilation. With best regards, Alex Nhat Minh Le (Alex Le) Delta Chi - Brotherhood of a Lifetime nworld3d*at*yahoo.com www.247lfc.com | www.sr3d.net __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From chemistry-request@ccl.net Wed May 25 12:03:01 2005 Received: from marge.bucknell.edu (marge.bucknell.edu [134.82.9.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4PG2tG2001344 for ; Wed, 25 May 2005 12:02:55 -0400 Received: from marburg.bucknell.edu (marburg.bucknell.edu [134.82.9.75]) by marge.bucknell.edu (8.12.11/8.12.11) with ESMTP id j4PEMwUP016677 for ; Wed, 25 May 2005 10:22:58 -0400 (EDT) Received: from WILLIAMS.bucknell.edu (williams.bucknell.edu [134.82.59.42]) by marburg.bucknell.edu (8.13.1/8.13.1) with ESMTP id j4PEMq94021461 for ; Wed, 25 May 2005 10:22:58 -0400 (EDT) Message-Id: <6.0.0.22.2.20050525101414.01ca7538*at*mail.bucknell.edu> X-Sender: williams*at*mail.bucknell.edu X-Mailer: QUALCOMM Windows Eudora Version 6.0.0.22 Date: Wed, 25 May 2005 10:22:47 -0400 To: chemistry*at*ccl.net From: Brian Williams Subject: TDDFT calculations using Gaussian Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Proofpoint-Spam-Details: rule=opt-in_notspam policy=opt-in score=0 mlx=0 adultscore=0 adjust=0 engine=2.5.0-05052000 definitions=2.5.0-05052407 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Greetings- I am an experimentalist attempting to learn how to use Gaussian in order to calculate molecular properties. I wish to calculate vertical excited electronic states using TDDFT, starting with an optimized ground state geometry calculated using B3LYP 6-31(d). I have not been able to locate an example of how to set up the keywords to carry this out- Foresman's book mainly discusses CIS. Thanks for any help. Brian Williams, Chemistry, Bucknell University From chemistry-request@ccl.net Wed May 25 15:57:00 2005 Received: from mail.interware.hu (mail.interware.hu [195.70.32.130]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4PJut3l008645 for ; Wed, 25 May 2005 15:56:55 -0400 Received: from caracas-0513.adsl.interware.hu ([213.178.102.1] helo=cthulhu) by mail.interware.hu with smtp (Exim 4.50 #1 (Debian)) id 1Db1zo-0001nb-6B; Wed, 25 May 2005 21:56:52 +0200 Message-ID: <001401c56163$e911c680$6501a8c0@cthulhu> From: "Gunda Tamas" To: "Lucilla angeli" , References: <42944169.7060704-.at.-student.unisi.it> Subject: Re: CCL:macrocycles Date: Wed, 25 May 2005 21:56:48 +0200 MIME-Version: 1.0 Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=response Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2527 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2527 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net I cannot give you a straight answer, just a few tips - several X-ray structures of the ribosome (DNA+protein) - macrolide complexes have been resolved lately. Maybe you can find good macrolid starting conformations from these. See for example: A.S. Mankin : Ribosomal Antibiotics, Molecular Biology, vol 35, 597 (2001); J. Retsema et al: Macrolides: structures and microbial targets, Int. J. Antimicrob. Agents vol 18, S3 (2001) as well as the web site: http://www.riboworld.com/ I hope these help Prof. Tamas E. Gunda Dept. of Pharmaceutical Chemistry University of Debrecen H-4010 Debrecen, POBox 36 Hungary tgunda {at} puma.unideb.hu ----- Original Message ----- From: "Lucilla angeli" To: "CCL" Sent: Wednesday, May 25, 2005 11:12 AM Subject: CCL:macrocycles > Dear CCLers > > I had a question about the docking of cyclic compounds, like macrocyclic lactones or macrolides. > Does anyone know or have ever applied a computational protocol to dock macrocycles with many degrees of freedom into a > protein? > I don't know how to approach the problem.... > Perhaps a conformational analysis with Maestro and then a docking with Autodock (that, however, is not able to take > into account the flexibility of the ring)...... > I wait hopeful for your suggestions. > > Thanks in advance > Lucilla Angeli > > > > -= 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 May 25 16:55:53 2005 Received: from schrodinger.com (thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4PKtoAH010403 for ; Wed, 25 May 2005 16:55:51 -0400 Received: from SVETLA (svetla.schrodinger.com [192.156.98.141]) by schrodinger.com (8.13.3/8.12.8) with SMTP id j4PKEhWT024056 for ; Wed, 25 May 2005 13:14:43 -0700 (PDT) (envelope-from announce #%# schrodinger.com) From: Schrodinger Announcements To: CCL Subject: Schrodinger Online Seminars Date: Wed, 25 May 2005 16:14:24 -0400 Message-ID: <0525105161424.1@SVETLA> X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Schrodinger is pleased to announce its June series of webcast seminars covering technology development and novel research applications. Featured speakers include Schrodinger product managers and applications scientists. Results and methodology from a wide range of software will be discussed, including CombiGlide, Schrodinger's combinatorial docking program currently under development. The seminar schedule is given below. To learn more, and to see the full abstracts, please visit our web site at http://www.schrodinger.com/SeminarCenter.php?mID=8&sID=53&cID=0 Date/Time Seminar --------- ----------------------------------------------------------- 6/2/2005 Structure-Based Drug Design: 1 PM EDT An Introduction to Methodology and Practices Presented by: Hege Beard, Ph.D. Applications Scientist, Schrodinger 6/9/2005 Induced Fit Models of hERG Channel Blockage 1 PM EDT Presented by: Jason K. Perry, Ph.D. Applications Scientist, Schrodinger 6/16/2005 Schrodinger Induced Fit Docking: 1 PM EDT Methodology and Results Presented by: Woody Sherman, Ph.D. Applications Scientist, Schrodinger 6/23/2005 Pharmacophore Perception and Database Screening with Phase 1 PM EDT Presented by: Shashi Rao, Ph.D. Applications Scientist, Schrodinger 6/30/2005 Combinatorial Docking with CombiGlide: 1 PM EDT Methodology and Results Presented by: Leah Frye, Ph.D. CombiGlide Product Manager, Schrodinger The seminars will run for one hour, including time for questions and answers. The number of connections is limited, so please register early at http://www.schrodinger.com/SeminarCenter.php?mID=8&sID=53&cID=0 to ensure your participation. Sincerely, Mike Campbell Schrodinger Seminar Coordinator From chemistry-request@ccl.net Wed May 25 21:28:40 2005 Received: from suede.reed.edu (suede.reed.edu [134.10.2.45]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4Q1SXxW018870 for ; Wed, 25 May 2005 21:28:34 -0400 Received: from localhost (localhost.localdomain [127.0.0.1]) by suede.reed.edu (8.13.3/8.13.3) with ESMTP id j4Q0pLAd029449 for ; Wed, 25 May 2005 17:51:21 -0700 Received: from suede.reed.edu ([127.0.0.1]) by localhost (smtp-1.reed.edu [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 28977-08 for ; Wed, 25 May 2005 17:51:19 -0700 (PDT) Received: from imap.reed.edu (imap.reed.edu [134.10.2.10]) by suede.reed.edu (8.13.3/8.13.3) with ESMTP id j4Q0pGqt029417 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Wed, 25 May 2005 17:51:16 -0700 Received: from [134.10.8.138] (c008h138.acad.reed.edu [134.10.8.138]) (authenticated bits=0) by imap.reed.edu (8.12.10/8.12.10) with ESMTP id j4Q0pGPH031175 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Wed, 25 May 2005 17:51:16 -0700 Message-ID: <42951D50.4050501 :a: reed.edu> Date: Wed, 25 May 2005 17:50:24 -0700 From: Alan Shusterman Reply-To: alan.shusterman :a: reed.edu Organization: Reed College User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry :a: ccl.net Subject: Gaussian input/output samples needed Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new using ClamAV at smtp-1.reed.edu X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net I am trying to use some software that is "Gaussian-compatible", but I don't have access to Gaussian. Could someone send me: an input file for an HF/6-31G(d) calculation on a small, simple molecule, like HF or H2O the output file(s) from the calculation. Thanks, Alan -- Alan Shusterman Chemistry Department Reed College Portland, OR 97202-8199 503-517-7699 http://academic.reed.edu/chemistry/alan/ "Yield and overcome; Bend and be straight." Lao Tzu 22