From chemistry-request@ccl.net Tue Sep 30 02:38:57 2003 Received: from nankai.edu.cn (sun.nankai.edu.cn [202.113.16.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8U6cFmK032241 for ; Tue, 30 Sep 2003 02:38:19 -0400 Received: (eyou send program); Tue, 30 Sep 2003 14:38:52 +0800 Received: from unknown (HELO 192.168.0.103) (unknown@128.195.87.184) by 202.113.16.21 with SMTP; Tue, 30 Sep 2003 14:38:52 +0800 Date: Mon, 29 Sep 2003 23:37:36 -0700 From: John Lee X-Mailer: The Bat! (v1.62r) Reply-To: John Lee X-Priority: 3 (Normal) Message-ID: <5975540.20030929233736..at..joyie.com> To: "chemistry..at..ccl.net" , dengolovanov Subject: Re[2]: CCL:symmitric keyword and water cluster [?? Probable Spam] In-Reply-To: <44539363673.20030929182858..at..pisem.net> References: <737846248.20030928233024..at..joyie.com> <44539363673.20030929182858..at..pisem.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.9 required=7.0 tests=EMAIL_ATTRIBUTION,FROM_ENDS_IN_NUMS,IN_REP_TO, MAILTO_TO_SPAM_ADDR,REFERENCES,REPLY_WITH_QUOTES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi , I tried loose and IOP(2/16,17,18), but the results are not symmetry. I also using opt=zmatrix. I did one simulation with 3 water molecules without symmetric z-matrix input(as follow). However the results is pretty symmetric. Could it be the problem with the symmetric input? I checked it before to run the job. It is a symmetric structure shown in gv. # opt(calcall,maxcycle=360) freq rb3lyp/3-21g* #p gfinput iop(6/7=3) iop(6/42=6) iop(6/33=2) #scf(tight,maxcycle=300) test pop=mk wat3 0 1 H O 1 1.000000 H 2 0.999978 1 120.000728 H 2 3.525815 1 58.808882 3 -179.449096 O 2 3.127199 1 74.684490 3 -179.449096 H 5 1.000402 2 4.220905 1 172.926737 H 2 2.099893 1 155.119757 5 2.758432 O 2 3.036371 1 163.084350 5 2.758432 H 8 0.999460 2 92.633292 1 176.877814 Monday, September 29, 2003, 7:28:58 AM, you wrote: d> Hello John, d> Monday, September 29, 2003, 10:30:24 AM, you wrote: JL>> Hi CCL-ers JL>> I tried to optimize water cluster with 3 waters or even more JL>> (4,5..). In order to keep the symmetric structure, I used the JL>> symmetric input z-matrix as follow. But the result is not JL>> symmetric. The input keyword is like: JL>> # opt=(calcfc,gdiis,maxcycle=350) freq=noraman rb3lyp/6-311++g(d,p) JL>> #scf(maxcycle=350) JL>> Maybe I should use symmetric keyword, but I don't know how to use it. JL>> Does anyone could help me about this. How to get the optimized JL>> structure of water cluster. And how to use symmetric keyword. JL>> 0 1 JL>> O JL>> O 1 B1 JL>> O 2 B1 1 60.0 JL>> H 1 B2 3 A1 2 D1 JL>> H 1 B3 4 A2 3 D2 JL>> H 2 B2 1 A1 3 D1 JL>> H 2 B3 6 A2 1 D2 JL>> H 3 B2 2 A1 1 D1 JL>> H 3 B3 8 A2 2 D3 JL>> Variables: JL>> B1 2.53540324 JL>> B2 1.05113591 JL>> B2 1.05113591 JL>> B3 0.99000000 JL>> A1 16.89494000 JL>> A2 106.96310000 JL>> D1 173.74583000 JL>> D2 108.87723000 JL>> D3 -D2 d> Try summetry=loose if it doesn't help try IOP(2/16=3, 2/17=1, 2/18=1) -- Best regards, John mailto:g03..at..joyie.com From chemistry-request@ccl.net Tue Sep 30 05:50:04 2003 Received: from smtp2.ruc.dk (smtp2.ruc.dk [130.225.220.70]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8U9nWmK008944 for ; Tue, 30 Sep 2003 05:49:33 -0400 Received: by smtp2.ruc.dk (Postfix, from userid 504) id A0DA312A0C45; Tue, 30 Sep 2003 11:49:35 +0200 (CEST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtp2.ruc.dk (Postfix) with ESMTP id 6960112A0C41; Tue, 30 Sep 2003 11:49:34 +0200 (CEST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 30 Sep 03 11:49:30 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 30 Sep 03 11:49:30 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: jz7^at^duke.edu Date: Tue, 30 Sep 2003 11:49:22 +0200 Subject: Re: CCL:question about CIS excited states calculation Reply-To: spanget^at^ruc.dk Cc: chemistry^at^ccl.net Message-ID: <3F796DC6.19197.5C96DAA@localhost> Priority: normal In-reply-to: <008201c38691$89b890a0$eaed0398@CONCORDIA> X-mailer: Pegasus Mail for Windows (v4.01) X-Spam-Status: No, hits=2.5 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,RCVD_IN_OSIRUSOFT_COM, X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: ** X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Jeny: > I had expected that if I include more orbitals, I should get closer > result to the "true value". And when the number of orbitals is greater > than some certain number, the result should not change much. But the > calculation results showed great fluctuation when I include more and > more orbitals. So what is the problem? The convergence of the CI expansion is very slow! And CIS is only a very limited CI expansion procedure; it does not include doubly and multiply excited configurations that describe electronic correlation effects. In semiempirical procedures this deficiency of CIS is usually compensated for by an artificial screening of the electron repulsion terms. Hence, procedures like CNDO/S and INDO/S that are parametrized for CIS calculations should not be extended to include doubly or higher excited configurations without reconsideration of the electron repulsion parameters. Jens >--< Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget^at^ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~spanget =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Tue Sep 30 03:19:50 2003 Received: from cirse.saclay.cea.fr (cirse.saclay.cea.fr [132.166.192.127]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8U7JHmK001685 for ; Tue, 30 Sep 2003 03:19:18 -0400 Received: from argiope.saclay.cea.fr (argiope.saclay.cea.fr [132.166.192.108]) by cirse.saclay.cea.fr (8.12.10/8.12.9/CEAnet-Internet.2.0) with ESMTP id h8U7JCvk023290 for ; Tue, 30 Sep 2003 09:19:12 +0200 (MEST) Received: from nenuphar.saclay.cea.fr (unverified) by argiope.saclay.cea.fr (Content Technologies SMTPRS 4.3.10) with ESMTP id for ; Tue, 30 Sep 2003 09:18:06 +0200 Received: from penelope.saclay.cea.fr (penelope.saclay.cea.fr [132.166.189.102]) by nenuphar.saclay.cea.fr (8.12.10/8.12.9/CEAnet-Internet.2.0) with ESMTP id h8U7JBcb017301 for ; Tue, 30 Sep 2003 09:19:12 +0200 (MEST) Received: by penelope.saclay.cea.fr with Internet Mail Service (5.5.2653.19) id ; Tue, 30 Sep 2003 09:24:52 +0200 Message-ID: <3808A7D2DCEAD6118B63009027287265014921)at(azurite.saclay.cea.fr> From: VITORGE Pierre 094605 To: "'chemistry)at(ccl.net'" Subject: CCL: 2 Gb physical Memory for G98W with Windows2000 Date: Tue, 30 Sep 2003 09:19:11 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Is it actually possible to use more than 1 Gb physical memory with Gaussian 98 for Windows? I have just increased the Memory of my computer from 1 to 2 Gb. The computer see the 2Mb memory, however, when I typically used card %chk=1500Mb my Gaussian test job did not run, while it was OK with typically card %chk=750Mb I do not know where the problem comme from: Hardware? Microsoft 2000? Gaussain 98W? The reference of the new memories is exactly the same as that of the old one, both bought from Dell company in March and September 2003 respectively. Pierre Vitorge CEA DEN Saclay DPC/SECR/LSRM & UMR 8587 (CEA-Universite d'Evry-CNRS) Bat.391 Pe.40a 91191 Gif sur Yvette cedex France tel.(+33) 169-08-32-65, secr.: (+33)169-08-32-50, fax:(+33)169-08-32-42 http://perso.club-internet.fr/vitorgen/pierre From chemistry-request@ccl.net Tue Sep 30 08:35:07 2003 Received: from sunchem.chem.uga.edu (sunchem.chem.uga.edu [128.192.5.2]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h8UCYamK013823 for ; Tue, 30 Sep 2003 08:34:36 -0400 Received: (qmail 14520 invoked by uid 728); 30 Sep 2003 12:32:23 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 30 Sep 2003 12:32:23 -0000 Date: Tue, 30 Sep 2003 08:32:23 -0400 (EDT) From: Zhi-Xiang Wang To: chemistry..at..ccl.net Subject: QM/MM in Nwchem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi all I plan to use Nwchem program to do QM/MM optimization and QM/MM dynamics. I would appreciate any suggestion and comments about its performance Thanks Zhixiang From chemistry-request@ccl.net Tue Sep 30 03:09:55 2003 Received: from yangtze.hku.hk (yangtze.hku.hk [147.8.148.244]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8U79MmK001432 for ; Tue, 30 Sep 2003 03:09:23 -0400 Received: from localhost (alarry@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id h8U7Rjn18230 for ; Tue, 30 Sep 2003 15:27:45 +0800 Date: Tue, 30 Sep 2003 15:27:45 +0800 (HKT) From: Wong Lai Ho To: CHEMISTRY..at..ccl.net Subject: Make use of crystal structure Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear cclers, Is there any (free) software that can convert a crystal to my desirable structure by symmetry? Since the structure I downloaded in Protein Data Bank contains only 1/4 pieces of the system. Thank you in advance Best Regards Larry Wong The Department of Chemistry The University of Hong Kong From chemistry-request@ccl.net Tue Sep 30 12:03:31 2003 Received: from web21208.mail.yahoo.com (web21208.mail.yahoo.com [216.136.175.166]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h8UG2wmK022455 for ; Tue, 30 Sep 2003 12:02:58 -0400 Message-ID: <20030930160257.31329.qmail_at_web21208.mail.yahoo.com> Received: from [129.109.73.75] by web21208.mail.yahoo.com via HTTP; Tue, 30 Sep 2003 09:02:56 PDT Date: Tue, 30 Sep 2003 09:02:56 -0700 (PDT) From: IEJMD Subject: Internet Electronic Conference of Molecular Design 2003 To: chemistry_at_ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Call for papers Internet Electronic Conference of Molecular Design 2003 IECMD 2003, November 23 - December 6 An Electronic conference for presenting and discussing recent developments in Molecular Design will be held during November 23 - December 6, 2003, on the World-Wide Web. IECMD 2003 covers all areas of molecular design and uses the Internet for exchanging chemical information. IECMD 2003 accepts electronic papers in the following categories: Posters Research notes Communications Full papers Reviews Paper Submission Papers should be submitted as Word files to iejmd_at_yahoo.com. All papers will be peer reviewed. Accepted papers will be published as PDF files on the IECMD 2003 Web site, http://www.biochempress.com. There will be no registration for visitors of IECMD 2003, and all PDF papers will be free for download. After the Conference, all accepted papers will be published in IEJMD - the Internet Electronic Journal of Molecular Design. Important Dates October 1, 2003 - Titles and authors due November 1, 2003 - Papers due, for peer review November 15, 2003 - Final Papers due November 23, 2003 - Conference begins December 6, 2003 - Conference ends For detailed Instructions for Authors, see http://www.biochempress.com Instruction for authors and a Word template for preparing the paper are available for download. IECMD 2003 will cover all aspects of computer-assisted molecular design applications in chemistry, biochemistry, biology, chemical and pharmaceutical industry, including: Computer-aided organic synthesis Chemical structure and reactivity investigated with molecular mechanics, quantum chemistry, and molecular dynamics methods Definition, calculation and evaluation of novel structural descriptors Chemical database searching, clustering, similarity and diversity measure Prediction of physico-chemical properties with Quantitative Structure-Property Relationships (QSPR) Quantitative Structure-Activity Relationships (QSAR) models for biological activity, toxicity, mutagenicity, and carcinogenicity Prediction of chromatographic retention parameters and design of stationary phases for chromatography Modeling of bioorganic compounds, such as proteins, enzymes, and nucleic acids New algorithms for modeling chemical and biochemical phenomena, such as global optimization methods, simulated annealing, neural networks, genetic algorithms, ant colony algorithm Design of special materials, catalysts, high energy compounds, polymers, molecular machines ********************************* Dr. Ovidiu Ivanciuc Sealy Center for Structural Biology, Department of Human Biological Chemistry & Genetics, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-1157 USA __________________________________ Do you Yahoo!? The New Yahoo! Shopping - with improved product search http://shopping.yahoo.com From chemistry-request@ccl.net Tue Sep 30 12:36:56 2003 Received: from webmail.ksu.edu (webmail.ksu.edu [129.130.39.18]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8UGaPmK024107 for ; Tue, 30 Sep 2003 12:36:25 -0400 X-WebMail-UserID: seabra Date: Tue, 30 Sep 2003 11:35:24 -0500 Sender: seabra From: seabra To: CHEMISTRY:at:ccl.net X-EXP32-SerialNo: 00002882 Subject: CCL: laptops in computational chemistry? Message-ID: <3F97829D:at:webmail.ksu.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.62 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello, Has anyone here had any experience trying to run calculations on a laptop? How well do the mobile versions of processors work? Any comment is appreciated. Gustavo Seabra. ---------------------------------------------------------------------- Gustavo de Miranda Seabra seabra:at:ksu.edu Graduate Student Chemistry Department Kansas State University ---------------------------------------------------------------------- From chemistry-request@ccl.net Tue Sep 30 11:16:05 2003 Received: from mercure.neokimia.com (mercure.med.usherbrooke.ca [132.210.158.207]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8UFFYmK020300 for ; Tue, 30 Sep 2003 11:15:34 -0400 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: Make use of crystal structure X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Date: Tue, 30 Sep 2003 11:13:35 -0400 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Make use of crystal structure Thread-Index: AcOHVVRiukwCWrrsSAehfCopOZ/koAAC8Ulg From: "Axel Mathieu" To: "Wong Lai Ho" , "CCL" X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h8UFG5mK020314 Larry, This site has come to be very handy for me ... http://pqs.ebi.ac.uk/ Just enter your pdb code in the appropriate box (or search using keywords) and you'll get the downloadable coordinates as in the crystal structure ... APM -----Original Message----- From: Wong Lai Ho [mailto:alarry:at:yangtze.hku.hk] Sent: 30 septembre, 2003 03:28 To: CHEMISTRY:at:ccl.net Subject: CCL:Make use of crystal structure Dear cclers, Is there any (free) software that can convert a crystal to my desirable structure by symmetry? Since the structure I downloaded in Protein Data Bank contains only 1/4 pieces of the system. Thank you in advance Best Regards Larry Wong The Department of Chemistry The University of Hong Kong -= 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, jkl:at:ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Tue Sep 30 11:41:08 2003 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8UFeYmK021465 for ; Tue, 30 Sep 2003 11:40:34 -0400 To: chminf-l/at/listserv.indiana.edu, chemistry/at/server.ccl.net, qsar_society/at/accelrys.com Subject: Call for Papers - Pharmacophores/3D Searching MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1CF1 March 04, 2003 Message-ID: From: Osman F Guner Date: Tue, 30 Sep 2003 08:40:31 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 09/30/2003 08:40:35, Serialize complete at 09/30/2003 08:40:35 Content-Type: multipart/alternative; boundary="=_alternative 0055D4FB88256DB1_=" X-Spam-Status: No, hits=1.5 required=7.0 tests=HTML_10_20,HTML_MESSAGE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multipart message in MIME format. --=_alternative 0055D4FB88256DB1_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable ADVANCES IN PHARMACOPHORES AND 3D SEARCHING Venue: ACS Spring 2004 National Meeting Place: Anaheim Convention Center, Anaheim, CA Dates: March 28 - April 1, 2004 Organized by ACS Chemical Information Division (CINF) Co-Sponsored by ACS Division of Medicinal Chemistry (MEDI), and ACS Division of Computers in Chemistry (COMP) Pharmacophores / 3D Searching is one of the most successful methods in=20 Computer-Aided Drug Design. In this symposium, we will review the recent=20 developments in this field. The topics that will be covered are: - Advances in 3D Searching technology + 3D indexing; data mining; querying; 3D knowledge management - Advances in Pharmacophores + Creative use of pharmacophores; receptor-based pharmacophores;=20 predictive pharmacophore models - Use of Pharmacophores for: + ADME/Tox predictions; Novel lead identification; Structure-based=20 design; in flavors and fragrance industries; agrochemicals - 3D Database building + structure generation; addressing conformational flexibility; storage=20 of receptor-ligand complexes If you are interested in any one of the above topics, we encourage you to=20 submit a paper through the OASYS (http://oasys.acs.org/oasys.htm). The=20 deadline for submitting abstracts for this symposium is December 1st,=20 2003. The following provides some guidelines on submitting your abstract through = OASYS. SUBMIT A TEST ABSTRACT IF YOU HAVE NEVER USED OASYS. 1. If you would like to try submitting an abstract with an image, prepare=20 a GIF or JPEG image with a graphics package. Once in OASYS, you'll see=20 instructions for creating graphics and improving the=20 quality of your graphics (you won't need these tips to create your test=20 graphic). 2. Enter the author submittal site at http://oasys.acs.org/oasys.htm. 3. Click the link to the CINF division, and select the appropriate=20 symposium 4. Follow the prompts to submit an abstract. 5. When you come to the Submit Abstract Text page, answer "yes" to "does=20 your abstract contain an image?". 6. Follow the prompts to submit the abstract text and image. If you have=20 entered it successfully, you will see the Submit to Program Officials=20 page. 7. Complete the submission by clicking the next Submit button. You will=20 receive an email showing you an example of the confirming email authors=20 receive. 8. To retrieve your abstract, you can click the View/Modify/Withdraw=20 Abstract or Preprint on the OASYS home page and enter your abstract ID and = password. Note that authors who submit an email address will receive this confirming = email. Other authors will get no notice of receipt. Scheduling notices will be sent by ACS after the final program has been=20 submitted. Presenting authors will receive an email message telling them=20 when and where their presentations are scheduled. Osman F. G=FCner, Ph.D. Executive Director Cheminformatics and Rational Drug Design Accelrys Inc., 858-799-5341 osman/at/accelrys.com, http://www.accelrys.com --=_alternative 0055D4FB88256DB1_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
ADVANCES IN PHARMACOPHORES AND 3D SE= ARCHING

Venue: ACS Spring 2004 National Meeting
Place: Anaheim Convention Center, Anaheim, CA
Dates: March 28 - April 1, 2004

Organized by ACS Chemical Information Division (CINF)
Co-Sponsored by ACS Division of Medi= cinal Chemistry (MEDI), and
ACS Division of Computers in Chemist= ry (COMP)

Pharmacophores / 3D Searching is one of the most successful methods in Computer-Aided Drug Design.  In this symposium, we will review the recent developments in this field.  = ;The topics that will be covered are:
- Advances in 3D Searching technolog= y
   + 3D indexing; data min= ing; querying; 3D knowledge management
- Advances in Pharmacophores
   + Creative use of pharm= acophores; receptor-based pharmacophores; predictive pharmacophore models
- Use of Pharmacophores for:
   + ADME/Tox predictions; Novel lead identification; Structure-based design; in flavors and fragrance industries; agrochemicals
- 3D Database building
   + structure generation; addressing conformational flexibility; storage of receptor-ligand complexes=

If you are interested in any one of the above topics, we encourage you to submit a paper through the OASYS (http://oasys.acs.org/oasys.htm).  The deadline for submitting abstracts for this symposium is December 1st, 2003.

The following provides some guidelin= es on submitting your abstract through OASYS.

SUBMIT A TEST ABSTRACT IF YOU HAVE NEVER USED OASYS.=
1. If you would like to try submitting an abstract with an image, prepare a GIF or JPEG image with a graphics package. Once in OASYS, you'll see instructions for creating graphics and improving the
quality of your graphics (you won't need these tips to create your test graphic).
2. Enter the author submittal site at http://oasys.acs.org/oasys.htm.
3. Click the link to the CINF division, and select the appropriate symposiu= m
4. Follow the prompts to submit an abstract.
5. When you come to the Submit Abstract Text page, answer "yes" to "does your abstract contain an image?".
6. Follow the prompts to submit the abstract text and image. If you have entered it successfully, you will see the Submit to Program Officials page.=
7. Complete the submission by clicking the next Submit button. You will receive an email showing you an example of the confirming email authors receive.
8. To retrieve your abstract, you can click the View/Modify/Withdraw Abstra= ct or Preprint on the OASYS home page and enter your abstract ID and password.=

Note that authors who submit an email address will receive this confirming email. Other authors will get no notice of receipt.

Scheduling notices will be sent by ACS after the final program has been submitted. Presenting authors will receive an email message telling them when and where their presentations are scheduled.

Osman F. G=FCner, Ph.D.
Executive Director
Cheminformatics and Rational Drug Design
Accelrys Inc.,  858-799-5341
osman/at/accelrys.com, http://www.accelrys.com --=_alternative 0055D4FB88256DB1_=-- From jkl@ccl.net Tue Sep 30 14:41:57 2003 -0400 Return-Path: Message-ID: <001a01c38781$cb3a6a80$e97d2dd2@fuyao> From: "fuyao" To: Subject: problem with PCM in g98 Date: Wed, 1 Oct 2003 02:36:41 +0800 Dear CCLers, I performed "scrf(PCM,read,solvent=1)" calculation on some large molecules evaluate their solvation energy. I have noticed the size of molecule may be too large.So I try to reduce the number of the TESSERAE, ie.even the situation is setting as "tsnum=10".But it still failed in Gaussian output file as follow: Cycle 1 Pass 1 IDiag 1: **** POLARISABLE CONTINUUM MODEL - UNIVERSITY OF PISA ***** PEDRA: too many spheres; increase Omega Error termination via Lnk1e in /usr/local/g98/l502.exe. Job cpu time: 0 days 5 hours 29 minutes 32.9 seconds. File lengths (MBytes): RWF= 733 Int= 0 D2E= 0 Chk= 23 Scr= 1 Do you have any suggestion on this problem? Could IEFPCM in G03 work well in this problem? Thank you in advance! ******************************************* Yao Fu Department of Chemistry University of Science & Technology of China Hefei, Anhui 230026P. R. China Tel:86-551-3640051(House) 86-551-3606640(Office) Mobile:86-13855190155 Fax:86-551-3606689 E-mail: fuyao)at(mail.ustc.edu.cn or pandafuyao)at(hotmail.com ******************************************* From jkl@ccl.net Tue Sep 30 14:55:13 2003 -0400 Return-Path: Date: Tue, 30 Sep 2003 14:53:21 -0400 (EDT) From: Steve Heller To: chemistry.-at-.ccl.net Subject: Student Travel Grants for AMDET-1 conference Message-ID: ADMET 1 - February 11-13, 2004 in San Diego CA Conference url: www.schergao.com/admet ADMET I will be an international meeting bringing together leaders in the computational and experimental areas of ADMET. The meeting will consist of invited lectures, poster talks, as well as scientific and vendor workshop presentations. The lectures will focus on theory and application of both computational and experimental ADMET approaches. In addition, lecturers will be asked to mention explicitly how they handle structural diversity and noisy data characteristic of ADMET problems. The Conference organizer, Scherago International, is sponsoring ADMET student travel grant awards of $250 each. This year there will be four (4) travel grants. The deadline for applying for these ADMET travel grants is the same as the poster submission deadline: December 3, 2003. Students who receive travel grant awards will also receive their registration fee paid for by Scherago International. Undergraduate and Graduate students who wish their posters to be considered for the ADMET Student Travel Grant awards must first submit their abstract online via the web submission form and then send an e-mail to Professor Tony Hopfinger, University of Illinois at Chicago, USA (hopfingr.-at-.uic.edu) with the following information: 1. Name 2. Title of Poster paper submitted 3. E-mail address 4. Phone number The four (4) students will received the travel grants (and complimentary registration)be notified by the end of December 2003. From chemistry-request@ccl.net Tue Sep 30 14:31:30 2003 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8UIUsmK028209 for ; Tue, 30 Sep 2003 14:30:54 -0400 To: chminf-l=at=listserv.indiana.edu, chemistry=at=server.ccl.net, qsar_society=at=accelrys.com Subject: Call for Papers - ACS Cheminformatics Division MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1CF1 March 04, 2003 Message-ID: From: Osman F Guner Date: Tue, 30 Sep 2003 11:30:51 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 09/30/2003 11:30:55, Serialize complete at 09/30/2003 11:30:55 Content-Type: multipart/alternative; boundary="=_alternative 00656D0588256DB1_=" X-Spam-Status: No, hits=5.1 required=7.0 tests=HTML_00_10,HTML_FONT_BIG,HTML_MESSAGE, RCVD_IN_OSIRUSOFT_COM,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: ***** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multipart message in MIME format. --=_alternative 00656D0588256DB1_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Hello all: We invite you to participate with the Chemical Information Division (CINF) = Program at the upcoming ACS National Meeting at Anaheim. The deadline=20 for submitting abstracts is December 1st 2003. Instructions on submitting = abstracts through the OASYS is given at the end of this message. The eleven symposia organized by CINF are listed below in alphabetical=20 order, together with the symposium organizers' contact details. If you=20 have any questions, feel free to contact the session organizer directly. Anaheim, March 28-April 1, 2004 Division of Chemical Information Program Chair: O. F. G=FCner, Accelrys Inc, 9685 Scranton Road, San Diego, = CA 92121-3752, 858-799-5341, fax 858-799-5100, e-mail: osman=at=accelrys.com=20 1- Advances in pharmacophores and 3D searching (Cosponsored with comp and=20 medi). O. F. G=FCner 2- Chemical information needs for industrial and engineering chemistry=20 (Cosponsored with iec). T. Wright, MDL Information Systems, Inc, 14600=20 Catalina Street, San Leandro, CA 94577, 510-357-2222, fax 510-614-3652,=20 e-mail: terryw=at=mdli.com 3- CINF serves SCHB: Patent information for small chemical businesses=20 (Cosponsored with chal and schb). A. Engel, Paterra, Inc, 526 N Spring=20 Mill Road, Villanova, PA 19085-1928, 610-527-4500, fax 610-527-2041,=20 e-mail: aengel=at=paterra.com 4- Electronic Lab Notebooks R. Lysakowski Jr., Executive Director,=20 Collaborative Electronic Notebook Systems Association, 800 West Cummings=20 Park, Suite 5400, Woburn, MA 01801, 781-935-9600, fax 781-935-3113,=20 e-mail: rich=at=censa.org 5- Environmental Chemistry: Where to find your information (Cosponsored=20 with envr and toxi). E. Kajosalo, Libraries, Massachusetts Institute of=20 Technology, 77 Masschusetts Avenue, Room 14S-134, Cambridge, MA 02155,=20 617-253-9795, fax 617-253-6365, e-mail: kajosalo=at=mit.edu 6- General papers O. F. G=FCner 7- How do the changes in 21-CFR part 11 affect you? (Cosponsored with=20 anyl, chas, laba and medi). D. A. Evans, MDL Information Systems, 14600=20 Catalina Street, San Leandro, CA 94577, 510-357-2222 x1145, fax=20 510-614-3651, e-mail: davide=at=mdli.com 8- Informatics challenges in Nanotechnology (Cosponsored with comp and=20 inor). S. C. McGrother, Accelrys Inc, 9685 Scranton Rd, San Diego, CA=20 92121, 858-799-5355, fax 858-799-5100, e-mail: smcgrother=at=accelrys.com 9- Poster session O. F. G=FCner 10- Research collaboratories, virtual laboratories, and Grid computing=20 (Cosponsored with comp). G. Grethe, Consultant, 352 Channing Way, Alameda, = CA 94502-7409, 510-333-7526, fax 510-865-5152, e-mail:=20 ggrethe=at=comcast.net; W. A. Warr, Wendy Warr & Associates, 6 Berwick Court, = Holmes Chapel, Cheshire, CW4 7HZ, United Kingdom, 011 44 1477 533837, fax=20 +44-1477-533837, e-mail: wendy=at=warr.com 11- The bigger picture: linking bioinformatics to cheminformatics=20 (Cosponsored with biot, medi and comp). M. A. Miller, LION bioscience,=20 Inc, 955 Ridge Hill Lane, Suite 30, Midvale, UT 84047, 801 569 1390, fax=20 801 365 3949, e-mail: mitchell.miller=at=lionbioscience.com The following provides some guidelines on submitting your abstract through = OASYS. SUBMIT A TEST ABSTRACT IF YOU HAVE NEVER USED OASYS. 1. If you would like to try submitting an abstract with an image, prepare=20 a GIF or JPEG image with a graphics package. Once in OASYS, you'll see=20 instructions for creating graphics and improving the quality of your=20 graphics (you won't need these tips to create your test graphic). 2. Enter the author submittal site at http://oasys.acs.org/oasys.htm. 3. Click the link to the CINF division, and select the appropriate=20 symposium 4. Follow the prompts to submit an abstract. 5. When you come to the Submit Abstract Text page, answer "yes" to "does=20 your abstract contain an image?". 6. Follow the prompts to submit the abstract text and image. If you have=20 entered it successfully, you will see the Submit to Program Officials=20 page. 7. Complete the submission by clicking the next Submit button. You will=20 receive an email showing you an example of the confirming email authors=20 receive. 8. To retrieve your abstract, you can click the View/Modify/Withdraw=20 Abstract or Preprint on the OASYS home page and enter your abstract ID and = password. Note that authors who submit an email address will receive this confirming = email. Other authors will get no notice of receipt. Scheduling notices will be sent by ACS after the final program has been=20 submitted. Presenting authors will receive an email message telling them=20 when and where their presentations are scheduled. Osman F. G=FCner, Ph.D. Executive Director Cheminformatics and Rational Drug Design Accelrys Inc., 858-799-5341 osman=at=accelrys.com, http://www.accelrys.com --=_alternative 00656D0588256DB1_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Hello all:

We invite you to participate with the Chemical Information Division (CINF) Program at the upcoming ACS National Meeting at Anaheim.   The deadline for submitting abstracts is December 1st 2003.  Instructions on submitting abstracts through the OASYS is given at the end of this message.

The eleven symposia organized by CINF are listed below in alphabetical order, together with the symposium organiz= ers' contact details.  If you have any questions, feel free to contact the session organizer directly.



Anaheim,
March 28-April 1, 2004

Division of Chemical Information


Program Chair: O. F. G=FCner, Accelrys Inc, 9685 Scranton Road, San Diego, CA 92121-3752, 858-799-5341, fax 858-799-5100, e-mail: osman=at=accelrys.com


1- Advances in pharmacophores and 3D searching (Cosponsored with comp and medi). O. F. G=FCner

2- Chemical information needs for industrial and engin= eering chemistry (Cosponsored with iec). T. Wright, MDL Information Systems, Inc, 14600 Catalina Street, San Leandro, CA 94577, 510-357-2222, fax 510-61= 4-3652, e-mail: terryw=at=mdli.com

3- CINF serves SCHB: Patent information for small chem= ical businesses (Cosponsored with chal and schb). A. Engel, Paterra, Inc, 526 N Spring Mill Road, Villanova, PA 19085-1928, 610-527-4500, fax 610-527= -2041, e-mail: aengel=at=paterra.com

4- Electronic Lab Notebooks R. Lysakowski Jr., Exe= cutive Director, Collaborative Electronic Notebook Systems Association, 800 West Cummings Park, Suite 5400, Woburn, MA 01801, 781-935-9600, fax 781-935-3113, e-mail: rich=at=censa.org

5- Environmental Chemistry: Where to find your informa= tion (Cosponsored with envr and toxi). E. Kajosalo, Libraries, Massachusetts Institute of Technology, 77 Masschusetts Avenue, Room 14S-134, Cambridge, MA 02155, 617-253-9795, fax 617-253-6365, e-mail: kajosalo=at=mit.edu

6- General papers O. F. G=FCner

7- How do the changes in 21-CFR part 11 affect you? (Cosponsored with anyl, chas, laba and medi). D. A. Evans, MDL Information Systems, 14600 Catalina Street, San Leandro, CA 94577, 510-357-2222 x1145, fax 510-614-3651, e-mail: davide=at=mdli.com

8- Informatics challenges in Nanotechnology (Cospo= nsored with comp and inor). S. C. McGrother, Accelrys Inc, 9685 Scranton Rd, San Diego, CA 92121, 858-799-5355, fax 858-799-5100, e-mail: smcgrother@accelry= s.com

9- Poster session O. F. G=FCner

10- Research collaboratories, virtual laboratories, and Grid computing (Cosponsored with comp). G. Grethe, Consultant, 352 Channing Way, Alameda, CA 94502-7409, 510-333-7526, fax 510-865-5152, e-mail: ggrethe=at=comcast.net; W. A. Warr, Wendy Warr & Associates, 6 Berwick Court, Holmes Chapel, Cheshire, CW4 7HZ, United Kingdom, 011 44 1477 533837, fax +44-1477-533837, e-mail: wendy=at=warr.com

11- The bigger picture: linking bioinformatics to chem= informatics (Cosponsored with biot, medi and comp). M. A. Miller, LION bioscience, Inc, 955 Ridge Hill Lane, Suite 30, Midvale, UT 84047, 801 569 1390, fax 801 365 3949, e-mail: mitchell.miller=at=lionbioscience.com


The following provides some guidelines on submitting your abstract through OASYS.

SUBMIT A TEST ABSTRACT IF YOU HAVE NEVER USED OASYS.
1. If you would like to try submitting an abstract with an image, prepare a GIF or JPEG image with a graphics package. Once in OASYS, you'll see instructions for creating graphics and improving the quality of your graphi= cs (you won't need these tips to create your test graphic).
2. Enter the author submittal site at http://oasys.acs.org/oasys.htm.
3. Click the link to the CINF division, and select the appropriate symposiu= m
4. Follow the prompts to submit an abstract.
5. When you come to the Submit Abstract Text page, answer "yes" to "does your abstract contain an image?".
6. Follow the prompts to submit the abstract text and image. If you have entered it successfully, you will see the Submit to Program Officials page.=
7. Complete the submission by clicking the next Submit button. You will receive an email showing you an example of the confirming email authors receive.
8. To retrieve your abstract, you can click the View/Modify/Withdraw Abstra= ct or Preprint on the OASYS home page and enter your abstract ID and password.=

Note that authors who submit an email address will receive this confirming email. Other authors will get no notice of receipt.

Scheduling notices will be sent by ACS after the final program has been submitted. Presenting authors will receive an email message telling them when and where their presentations are scheduled.




Osman F. G=FCner, Ph.D.
Executive Director
Cheminformatics and Rational Drug Design
Accelrys Inc.,  858-799-5341
osman=at=accelrys.com, http://www.accelrys.com --=_alternative 00656D0588256DB1_=-- From chemistry-request@ccl.net Tue Sep 30 15:48:45 2003 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8UJmEmK031364 for ; Tue, 30 Sep 2003 15:48:14 -0400 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id h8UJmFxL001931 for ; Tue, 30 Sep 2003 14:48:15 -0500 (CDT) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.10.2+Sun/8.9.1) with ESMTP id h8UJmEc19109 for ; Tue, 30 Sep 2003 14:48:14 -0500 (CDT) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Tue, 30 Sep 2003 14:48:14 -0500 (CDT) From: Jim Phillips To: chemistry|at|ccl.net Subject: NAMD 2.5 (Parallel MD) Release Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-0.4 required=7.0 tests=USER_AGENT_PINE,X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL, NAMD is a molecular dynamics program, file compatible with X-PLOR, CHARMM, and AMBER, scalable to hundreds of processors, and available as source code or binaries for a variety of platforms, free of charge. Try it out! Thanks! -Jim +--------------------------------------------------------------------+ | | | NAMD 2.5 Release Announcement | | | +--------------------------------------------------------------------+ September 29, 2003 The Theoretical and Computational Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.5 has several advantages over NAMD 2.4: - Improved parallel scaling and serial performance. - Trajectory reading and interaction energy analysis. - Improved constant pressure simulation and coordinate wrapping. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. For your convenience, NAMD has been ported to and will be installed on the machines at the NSF-sponsored national supercomputing centers. If you are planning substantial simulation work of an academic nature you should apply for these resources. Benchmarks for your proposal are available at http://www.ks.uiuc.edu/Research/namd/performance.html The Theoretical and Computational Biophysics Group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to namd|at|ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! From chemistry-request@ccl.net Tue Sep 30 16:58:32 2003 Received: from c3p0.ou.edu (oumail.zero.ou.edu [129.15.0.75] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8UKw0mK001158 for ; Tue, 30 Sep 2003 16:58:00 -0400 Received: from e500-6.ou.edu (ip-129-15-0-76.zero.ou.edu [129.15.0.76]) by c3p0.ou.edu (iPlanet Messaging Server 5.2 HotFix 1.16 (built May 14 2003)) with SMTP id <0HM10000POWOZJ_at_c3p0.ou.edu> for chemistry_at_ccl.net; Tue, 30 Sep 2003 15:58:00 -0500 (CDT) Received: from unknown(129.15.0.75) by e500-6.ou.edu via csmap id 6076; Tue, 30 Sep 2003 15:59:52 -0500 (CDT) Received: from htwork (chem-bchm-202.chem.ou.edu [129.15.13.202]) by c3p0.ou.edu (iPlanet Messaging Server 5.2 HotFix 1.16 (built May 14 2003)) with SMTP id <0HM1000EXOTCZJ_at_c3p0.ou.edu> for chemistry_at_ccl.net; Tue, 30 Sep 2003 15:56:00 -0500 (CDT) Date: Tue, 30 Sep 2003 15:57:47 -0500 From: haitao Subject: How do I output forces in an MD simulation using CHARMM? To: chemistry_at_ccl.net Message-id: <000f01c38795$80fc4880$ca0d0f81_at_ou.edu> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-Mailer: Microsoft Outlook Express 5.50.4133.2400 Content-type: multipart/alternative; boundary="Boundary_(ID_8dMHWcCbQItX1qwvbQBBrA)" X-Priority: 3 X-MSMail-priority: Normal X-Spam-Status: No, hits=0.2 required=7.0 tests=HTML_60_70,HTML_MESSAGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. --Boundary_(ID_8dMHWcCbQItX1qwvbQBBrA) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT Thanks to any help! --Boundary_(ID_8dMHWcCbQItX1qwvbQBBrA) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: 7BIT
Thanks to any help!
--Boundary_(ID_8dMHWcCbQItX1qwvbQBBrA)-- From jkl@ccl.net Tue Sep 30 19:37:39 2003 -0400 Return-Path: Reply-To: From: "Mark Thompson" To: , Cc: Subject: CCL: question about CIS excited states calculation Date: Tue, 30 Sep 2003 16:37:14 -0700 Message-ID: <000801c387ab$c6d43820$0200a8c0@planaria> Jeny, The answer depends on the type of Hamiltonian you are using. Since you also posted this to the ArgusLab users group, I'll limit my answer to the semi-empirical ZINDO method. Zerner and coworkers parameterized ZINDO to reproduce low-energy singlet excitations for organic systems containing pi-electrons. The size of the CI they used for small (e.g. benzene) molecules was generally ~10 occupied into ~10 virtual MOs for the CI active space. Even then, ZINDO is really only accurate to within ~700 cm-1 - 1000 cm-1 with experiment. As Jens Spanget-Larsen noted, the formula for the two-electron integrals and other parameters used to get the ZINDO ground state compensate somewhat for the limitation of singles-only excited configurations. For porphyrins, bacteriochlorophylls, etc, I've used CI expansions of the order of 20 x 20 and obtained good results. It is critical that you include all the "important" orbitals for the excited states you want to study. For example, the pi-pi* spectra for benzene: you want to make sure to include the 6 pi-orbitals. Don't split groups of symmetry related orbitals: if you do, the excited states will have the wrong energy splittings and relative intensities (for porphyrins you want to include all of Gouterman's 4-pi orbitals, at the least, or you'll never get the relative intensities of the Qy and Qx states correct). For transition metal systems, like ferrocene or metallo-porphyrins, you'll want to make sure to include all the MOs that are dominated by the metal d-orbitals (or you'll never see the d->d*, d->ligand*, and ligand->d* excitated states). I disagree with John McKelvey's recommendation to use all single-excited configurations. Simple variational degrees of freedom may depress your low-lying excited states as you make the CI expansion larger, and give the impression of higher accuracy. However, when one includes a single-excited configuration that is 130,000 cm-1 in energy, why not also include double or triple-excitations of lower energy? Are they not perhaps more imporant to the final result? Its probably best to keep with as modest a CI expansion as possible with the caveat of including all the "important" orbitals. Zerner recommended including all single excited configurations up to an energy of ~75,000 cm-1. Anything above that and double-excitations start to become important (doubles generally start to appear at ~85,000 cm-1 for small to medium sized organic systems like benzene, etc). Its important to remember that ZINDO has traditionally been a qualitative tool. It's parameterization was never rigorously refined like Jimmy Stewart's PM3. There are no well-defined error bars on the ZINDO method. However, ZINDO has proven enormously useful over the years and has been extended to include: excited states with double- and triple-excited configurations, solvent effects, transition metal system, polarizabilities, hyperpolarizabilities, etc. ZINDO has also been used successfully with the RPA treatment for excitations even though it was never parameterized for that approach. ZINDO-RPA describes the low-energy excited states of the bacteriochlorophyll-b dimer from Rps. viridis reaction center quite well and gets the correct sign for the rotational strength. When studying a new molecule, I generally do a ZINDO SCF first and look at the energies of the MOs. I make sure that any CI expansion I use will not split orbitals that are symmetry related or even those that are very close in energy. If there are any metals present, I try to identify the MOs that represent the metal's valence shell. I generally start with a 10x10 CI and ask ArgusLab to print the CI Hamiltonian matrix: which causes the energies of the pure configurations to be output to the .out file as well. This allows me to examine the energies of the pure configurations. You should make sure you are consistent. If you are studying a series of substituted benzenes of similar size, a consistent treatment of the CI expansion across the series is more imporant than fine-tuning the CI expansion for each molecule. The quickest off-the-cuff answer is to generally do all single-excitations > from the highest 10 occupied into the lowest 10 virtual MOs for molecules of the size of benzene and up to perhaps porphyrins. Large chromophore arrays (like the photosynthetic reaction center) or fullerenes would require a larger CI expansion. If you have any examples of molecules you are studying, please feel free to send them to me and I'll take a look. Mark *************************** Mark Thompson, PhD Planaria Software LLC PO Box 55207 Seattle, WA 98155 mark-.at.-arguslab.com http://www.arguslab.com *************************** -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request-.at.-ccl.net]On Behalf Of jz7-.at.-duke.edu Sent: Monday, September 29, 2003 6:57 AM To: chemistry-.at.-ccl.net Subject: CCL:question about CIS excited states calculation Dear all, I just began to use CIS to calculate excited states properties, such as state dipole moment, transition dipole moment and energy. But I am confused about how many occupied and unoccupied orbitals to choose when using CIS to calculate excited states. I had expected that if I include more orbitals, I should get closer result to the "true value". And when the number of orbitals is greater than some certain number, the result should not change much. But the calculation results showed great fluctuation when I include more and more orbitals. So what is the problem? Really thanks a lot! Best, Jeny From mark@arguslab.com Tue Sep 16 14:42:43 2003 Return-Path: Reply-To: From: "Mark Thompson" To: chemistry.-at-.ccl.net> Cc: Date: Tue, 16 Sep 2003 11:42:35 -0700 Message-ID: <000001c37c82$4be5cd10$0200a8c0@planaria> Subject: CCL: Ewald Sums and Amber 1-4 interactions. I've been examining some old MD code of mine and I believe there is a problem with how I've handled the scaled 1-4 electrostatic terms in Amber when treating the long-range electrostatics using the Ewald method. Amber scales the 1-4 electrostatic terms by a scale factor. It's unclear to me how this should be accounted for in the Ewald method. These interactions are already included in the k-space sum and usually are corrected for in the real-space exclusion correction. Its not clear to me how the scaled-1-4 term can be accounted for other than to do the real-space Ewald treatment of the 1-4 term and then multiply in the Amber scaling term. Any ideas, pointers would be appreciated. I'll summarize for the list. Cheers, Mark Thompson *************************** Mark Thompson, PhD Planaria Software LLC PO Box 55207 Seattle, WA 98155 http://www.arguslab.com *************************** From mark@arguslab.com Fri Sep 12 09:47:26 2003 Return-Path: Reply-To: From: "Mark Thompson" Message-ID: <000e01c37934$63892b20$0200a8c0@planaria> To: Cc: Subject: CCL: ArgusLab is now free for Academic users. ArgusLab 3.1 is now free for Academic users and departments. Visit http://www.arguslab.com to download the program. Enjoy, Mark Thompson *************************** Mark Thompson, PhD Planaria Software LLC PO Box 55207 Seattle, WA 98155 ArgusLab available at : http://www.arguslab.com *************************** From jkl@ccl.net Tue Sep 30 22:01:21 2003 -0400 Return-Path: Reply-To: From: "Mark Thompson" To: "Dr. Jan K Labanowski" Cc: , Subject: CCL: ArgusLab 4.0 Beta Release Available Date: Tue, 30 Sep 2003 19:00:56 -0700 Message-ID: <000001c387bf$da1b6e80$0200a8c0@planaria> ArgusLab 4.0 beta release is available. This release can be accessed from our website: http://www.arguslab.com ArgusLab 4.0 includes: Gaussian 98 & Gaussian 03 interface Enhancements to ZINDO support Enhancements to PDB support Improved GUI with Molecule Treeview and Builder Toolkit windows. Calculation results saved in Molecule Treeview. Many calculation results and properties can be visualized with a single click. Copy/paste of calculation results and properties into other Windows applications or to file. Electric fields for SCF, CI, EHT, MNDO, AM1, PM3, ZINDO. Peptide builder one-click QuickPlot for surfaces. lots more... Please try this release and send us your feedback at: http://www.arguslab.com/feedback.htm Enjoy, Mark Thompson *************************** Mark Thompson, PhD Planaria Software LLC PO Box 55207 Seattle, WA 98155 mark~at~arguslab.com http://www.arguslab.com *************************** ===================================================== From chemistry-request@ccl.net Tue Sep 30 22:43:57 2003 Received: from prserv.net (asmtp1.prserv.net [32.97.166.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h912hPmK012616 for ; Tue, 30 Sep 2003 22:43:25 -0400 Received: from attglobal.net (dhcp065-029-082-127.indy.rr.com[65.29.82.127]) by prserv.net (asmtp1) with SMTP id <2003100102432325103bhekfe> (Authid: usinet.jmmckel); Wed, 1 Oct 2003 02:43:23 +0000 Message-ID: <3F79F752.9CE24338/at/attglobal.net> Date: Tue, 30 Sep 2003 21:36:18 +0000 From: John McKelvey Reply-To: jmmckel/at/attglobal.net Organization: McKelvey Computational Chemistry X-Mailer: Mozilla 4.75 [en]C-CCK-MCD (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: mark/at/arguslab.com CC: chemistry/at/ccl.net, jz7/at/duke.edu Subject: Re: CCL: question about CIS excited states calculation References: <000801c387ab$c6d43820$0200a8c0@planaria> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-1.8 required=7.0 tests=DATE_IN_PAST_03_06,EMAIL_ATTRIBUTION,QUOTED_EMAIL_TEXT, REFERENCES,REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_XM, X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) All, I would like to disagree with Mark Thompson's reply, at least in part. First I would like to point out that I have spent 25+ years working with Zerner's INDO/S in industry and as a consultant. I helped industry help support the development of Zerner's ZINDO to a significant financial extent, and have used INDO/S for practical, industrial applications since 1977. I, along with many people, have noticed that limited singles CI using INDO/S for molecules that absorb in the visible region often are too short in wavelength by as much as 75 to 300 NM! Further, Nishimoto, the author of the Nishimoto-Mataga integrals, has made the same observation using the NM integrals [the same ones used in INDO/S] in PPP , or pi only, CI, exactly as has been found for INDO/S. I have done thousands of calculations for dyes using INDO/S, and have vitrually always found this problem for visible transitions for dyes. I have also found in the last year that ~85-90% of the error for these dyes can be eliminated using all singles CI. Qualitative, descriptive explanations can be had with 10up/10down CIS, but not quantitative results in the visible region. John McKelvey McKelvey Computational Chemistry Carmel, IN Mark Thompson wrote: > Jeny, > > The answer depends on the type of Hamiltonian you are using. Since you also > posted this to the ArgusLab users group, I'll limit my answer to the > semi-empirical ZINDO method. > > Zerner and coworkers parameterized ZINDO to reproduce low-energy singlet > excitations for organic systems containing pi-electrons. The size of the CI > they used for small (e.g. benzene) molecules was generally ~10 occupied into > ~10 virtual MOs for the CI active space. Even then, ZINDO is really only > accurate to within ~700 cm-1 - 1000 cm-1 with experiment. As Jens > Spanget-Larsen noted, the formula for the two-electron integrals and other > parameters used to get the ZINDO ground state compensate somewhat for the > limitation of singles-only excited configurations. For porphyrins, > bacteriochlorophylls, etc, I've used CI expansions of the order of 20 x 20 > and obtained good results. > > It is critical that you include all the "important" orbitals for the excited > states you want to study. For example, the pi-pi* spectra for benzene: you > want to make sure to include the 6 pi-orbitals. Don't split groups of > symmetry related orbitals: if you do, the excited states will have the wrong > energy splittings and relative intensities (for porphyrins you want to > include all of Gouterman's 4-pi orbitals, at the least, or you'll never get > the relative intensities of the Qy and Qx states correct). For transition > metal systems, like ferrocene or metallo-porphyrins, you'll want to make > sure to include all the MOs that are dominated by the metal d-orbitals (or > you'll never see the d->d*, d->ligand*, and ligand->d* excitated states). > > I disagree with John McKelvey's recommendation to use all single-excited > configurations. Simple variational degrees of freedom may depress your > low-lying excited states as you make the CI expansion larger, and give the > impression of higher accuracy. However, when one includes a single-excited > configuration that is 130,000 cm-1 in energy, why not also include double or > triple-excitations of lower energy? Are they not perhaps more imporant to > the final result? Its probably best to keep with as modest a CI expansion > as possible with the caveat of including all the "important" orbitals. > Zerner recommended including all single excited configurations up to an > energy of ~75,000 cm-1. Anything above that and double-excitations start to > become important (doubles generally start to appear at ~85,000 cm-1 for > small to medium sized organic systems like benzene, etc). > > Its important to remember that ZINDO has traditionally been a qualitative > tool. It's parameterization was never rigorously refined like Jimmy > Stewart's PM3. There are no well-defined error bars on the ZINDO method. > However, ZINDO has proven enormously useful over the years and has been > extended to include: excited states with double- and triple-excited > configurations, solvent effects, transition metal system, polarizabilities, > hyperpolarizabilities, etc. ZINDO has also been used successfully with the > RPA treatment for excitations even though it was never parameterized for > that approach. ZINDO-RPA describes the low-energy excited states of the > bacteriochlorophyll-b dimer from Rps. viridis reaction center quite well and > gets the correct sign for the rotational strength. > > When studying a new molecule, I generally do a ZINDO SCF first and look at > the energies of the MOs. I make sure that any CI expansion I use will not > split orbitals that are symmetry related or even those that are very close > in energy. If there are any metals present, I try to identify the MOs that > represent the metal's valence shell. I generally start with a 10x10 CI and > ask ArgusLab to print the CI Hamiltonian matrix: which causes the energies > of the pure configurations to be output to the .out file as well. This > allows me to examine the energies of the pure configurations. You should > make sure you are consistent. If you are studying a series of substituted > benzenes of similar size, a consistent treatment of the CI expansion across > the series is more imporant than fine-tuning the CI expansion for each > molecule. > > The quickest off-the-cuff answer is to generally do all single-excitations > from the highest 10 occupied into the lowest 10 virtual MOs for molecules of > the size of benzene and up to perhaps porphyrins. Large chromophore arrays > (like the photosynthetic reaction center) or fullerenes would require a > larger CI expansion. > > If you have any examples of molecules you are studying, please feel free to > send them to me and I'll take a look. > > Mark > > *************************** > Mark Thompson, PhD > Planaria Software LLC > PO Box 55207 > Seattle, WA 98155 > > mark/at/arguslab.com > http://www.arguslab.com > *************************** > > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request/at/ccl.net]On > Behalf Of jz7/at/duke.edu > Sent: Monday, September 29, 2003 6:57 AM > To: chemistry/at/ccl.net > Subject: CCL:question about CIS excited states calculation > > Dear all, > > I just began to use CIS to calculate excited states properties, such as > state dipole moment, transition dipole moment and energy. But I am > confused about how many occupied and unoccupied orbitals to > choose when using CIS to calculate excited states. > > I had expected that if I include more orbitals, I should get closer > result to the "true value". And when the number of orbitals is greater > than some certain number, the result should not change much. But the > calculation results showed great fluctuation when I include more and > more orbitals. So what is the problem? > > Really thanks a lot! > > Best, > Jeny