From owner-chemistry@ccl.net Thu May 3 06:26:00 2007 From: "Biju A R biju.ar]-[gmail.com" To: CCL Subject: CCL: calculation of lattice energy Message-Id: <-34178-070503061938-28077-3hQ1sqbLGWEkS64JajNzDQ[A]server.ccl.net> X-Original-From: "Biju A R" Date: Thu, 3 May 2007 06:19:34 -0400 Sent to CCL by: "Biju A R" [biju.ar(a)gmail.com] Dear Users, I am using Accelrys suit cerius2 for calculating experimental lattice energy of a manganese acetylacetone complex by giving experimental structure(.cif file). But here one acetylacetone molecule has disorder. Full acetyl acetone molecule is split into two fragments with occupation 0.5. Because of this while calculating lattice energy van der waals energy is coming large positive value and hence the final lattice enegry. Is there any method to find experimental lattice energy(without minimization) of a disordered molecule.Any help is greatly appreciated. Biju From owner-chemistry@ccl.net Thu May 3 11:51:00 2007 From: "Alexander Chris Hoepker ach42!=!cornell.edu" To: CCL Subject: CCL:G: looking for free GUI for Mac Message-Id: <-34179-070503082524-31926-GdSaKIKxV14bemziIfyCTA[a]server.ccl.net> X-Original-From: "Alexander Chris Hoepker" Date: Thu, 3 May 2007 08:25:21 -0400 Sent to CCL by: "Alexander Chris Hoepker" [ach42.(0).cornell.edu] Hi, I'm looking for a free graphical interface for Mac that reads output files from Gaussian and allows one to easily modify the structure. I would be willing to spend some money but certainly not close to a mille dollars. Thanks for your help. Alex From owner-chemistry@ccl.net Thu May 3 14:03:01 2007 From: "Fco. Javier Modrego modrego:-:unizar.es" To: CCL Subject: CCL:G: looking for free GUI for Mac Message-Id: <-34180-070503135631-3174-duMIk8V+4xYqEwBYy4cXyA===server.ccl.net> X-Original-From: "Fco. Javier Modrego" Content-Type: text/plain; charset="us-ascii" ; format="flowed" Date: Thu, 3 May 2007 18:56:28 +0200 Mime-Version: 1.0 Sent to CCL by: "Fco. Javier Modrego" [modrego]-[unizar.es] Hi, There are several options. You can try either Molden or Gabedit both are free and run nicely on OS X (you must install X11). You can have a look also to wxDragon. Greetings, F.J. Modrego >Sent to CCL by: "Alexander Chris Hoepker" [ach42.|.cornell.edu] >Hi, > >I'm looking for a free graphical interface for Mac that reads output >files from Gaussian and allows one >to easily modify the structure. I would be willing to spend some >money but certainly not close to a >mille dollars. >Thanks for your help. > >Alex From owner-chemistry@ccl.net Thu May 3 14:37:00 2007 From: "Barry Hardy barry.hardy:tiscalinet.ch" To: CCL Subject: CCL: eCheminfo Autumn meeting, Bursary Awards, CFP Message-Id: <-34181-070503141514-9308-JlIneMCaW8AOmX7tfEcuhw%a%server.ccl.net> X-Original-From: "Barry Hardy" Date: Thu, 3 May 2007 14:15:10 -0400 Sent to CCL by: "Barry Hardy" [barry.hardy/a\tiscalinet.ch] I enclose below our bursary award announcement and Call for Contributed Talks & Posters to eCheminfo's Autumn Community of Practice meeting at Bryn Mawr College. Through my own fault of being occupied with teaching and proposal writing work the past few weeks, notices on the bursary opportunities and CFP have not been sent out :(, so I am extending the submission deadline until May 18. I hope you can join us for the kind of smaller learning-centered meeting that we host on the beautiful and intimate college campus atmosphere at Bryn Mawr and to join the excellent cross-sector and international group of presenters, workshop leaders and participants who will be there to participate in a rewarding knowledge sharing and networking experience. best regards Barry Hardy Call for Contributed Talks & Posters to eCheminfo Program We invite contributed papers from members of academic, government research and commercial organizations on areas of new research and innovation involving drug discovery research informatics. The work presented should involve innovative new method development or application to drug discovery problems and involving methods from computational chemistry, computational biology, cheminformatics or bioinformatics. Studies including experimental work in medicinal chemistry, screening, experimental toxicology, pre-clinical evaluation, lead optimisation and translational medicine are welcome. Abstracts (300-500 words) should be submitted to echeminfo -[at]- douglasconnect.com by 18 May 2007, and be accompanied by a short biography of the presenting author (300-500 words). Abstracts approved by the scientific organizing committee will be selected for scheduling on the conference program and in meeting poster sessions. Authors will be notified of acceptance by 31 May. Bursary Awards for eCheminfo Program Bursary Awards will be used to support the attendance of a selection of academic young investigators at the meeting and workshops. Applicants can be working in any area of research related to drug discovery at the postdoctoral, graduate student and senior undergraduate levels. To apply for the bursary please send an email with a) your abstract and biography (300-500 words each), b) your CV of 1-2 pages, c) a short description of your interests and career motivations related to drug discovery (300-500 words) to echeminfo -[at]- douglasconnect.com by 18 May 2007. The recipients of the bursary awards will be selected based on an evaluation of the quality and innovation of the described research and the potential positive impact of attendance at the meeting on their research and career progress. Recipients will be notified of acceptance by 31 May. We gratefully acknowledge the support of our Sponsors including Schering-Plough, Merck, Johnson & Johnson, Tripos, and SimBioSys. Meeting Program Latest Advances in Drug Discovery & Development 15-18 October 2007 Community of Practice Meeting, Autumn 2007 a joint InnovationWell and eCheminfo InterAction Meeting Bryn Mawr College, Philadelphia http://www.echeminfo.com/COMTY_conferences (Last year's agenda is given at http://www.echeminfo.com/comty_conferenceprogram) The conference program will cover Structure-based Drug Design, chaired by Jose Duca (Schering- Plough), Fragment-based Drug Discovery, chaired by Maria Kontoyianni (Crystax Pharmaceuticals), Structural Biology, chaired by Max Cummings (Johnson & Johnson PR&D) and Predictive ADME/Toxicology, chaired by Tony Hopfinger (University of New Mexico College of Pharmacy). A variety of workshops will be held throughout the meeting. The approach will be hands-on using an IT classroom and a set of workshops led by application scientists using leading drug discovery software packages. The following two forums will be held at the meeting: actice Early registration and reduced rates runs through end of June. 50% academic discounts are available. eCheminfo Program The program will consist of two primary components, seminar sessions and workshops, accompanied by a significant amount of discussion and networking activity. A focus of this meeting is to present and discuss research involving methods and practical approaches which the attendees will be able to take back to their labs and apply to their projects. Last year's sessions were well attended and evaluated with a mix of industry case-studies and applications, discussion of methods and results and incorporation of the medicinal/synthetic chemistry element with great emphasis on scientific discussions. The seminar program will have four main conference sessions: Structure-based Drug Design, chaired by Jose Duca (Schering-Plough) Fragment-based Drug Discovery, chaired by Maria Kontoyianni (Crystax Pharmaceuticals) Structural Biology, chaired by Max Cummings (Johnson & Johnson PR&D) Predictive ADME/Toxicology, chaired by Tony Hopfinger (University of New Mexico College of Pharmacy) Confirmed Invited Speakers for eCheminfo Program (Preliminary List): Stephen Burley (SGX Pharmaceuticals), Georgia McGaughey (Merck), Charles Lesburg (Schering-Plough), Rick Beger (FDA), Marc Nicklaus (NIH), Woody Sherman (Schrodinger), Daniel Cheney (Bristol Myers Squibb), Paul Labute (Chemical Computing Group), Ajay Jain (UCSF), Alan Cheng (Amgen), Tony Hopfinger (University of New Mexico), Anthony Klon (Pharmacopeia Drug Discovery), Artem Cherkasov (University of British Columbia), Dennis Pelletier (Pfizer), Chaohong Sun (Abbott), Xavier Barril (University of Barcelona), Jose Duca (Schering-Plough), Terry Stouch (Lexicon Pharmaceuticals), Natasja Brooijmans (Wyeth), Gerard Kleywegt (University of Uppsala), Vladimir Poirikov (Russian Academy of Sciences), Christoph Helma (in silico toxicology), Ann Richard (EPA), Judy Madden (Liverpool John Moores University), Julian Tirado-Rives (Yale), Heather Carlson (University of Michigan), Joseph Tomaszewski (NCI), Joseph Contrera (FDA), Christopher Austin (NIH), Jerome Hert (UCSF) Workshops A variety of workshops will be held throughout the meeting. The approach will be hands-on using an IT classroom and a set of workshops led by application scientists using leading drug discovery software packages. Each workshop will be accompanied by practitioner-led discussions of the methods worked on by the group. Topics to be covered: Virtual Screening & Docking; Structure-based Drug Design; Ligand Optimisation & Library Design; Structure Search, Similarity and Property Estimation; Data Mining, Analysis & Visualisation; Integration of Cheminformatics & Bioinformatics Tools & Data; Latest advances in ADME & Predictive Toxicology; Pharmacokinetics & Pharmacodynamics and Physiological-based Simulation. Forums The following two forums will be held during the meeting: A. Mon Oct 15th - Virtual Screening & Docking - Comparative Methodology & Best Practice B. Thursday, Friday Oct 18th,19th - Forum & Workshop on International Cooperation in ADME/Tox (More Information on eCheminfo website.) InnovationWell program http://innovationwell.net/ In our initial community of practice meetings including our InnovationWell meeting last October at Bryn Mawr, Philadelphia we have discussed recent and coming developments of relevance to drug, life science and healthcare product development, drug and patient safety and translational medicine. This year's InnovationWell program at Bryn Mawr will have themes running throughout the meeting covering areas of innovation (systems biology, toxicology, metabolomics, biomarkers, diagnostics, emerging biotech & nanotech, knowledge management) and which will have a second topic division by session in terms of therapeutic area (diabetes, oncology, cardiology, anti-inflammatory, anti-viral). Each session will include discussion leadership from a therapeutic specialty providing a clinical perspective on the deployment and integration of emerging areas of life science, diagnostics and knowledge management technologies so as to progress Critical Path goals in clinical development and safety. Barry Hardy Community of Practice Manager Douglas Connect Switzerland Tel: +41 61 851 0170 From owner-chemistry@ccl.net Thu May 3 15:12:01 2007 From: "Hoa Nguyen hoagiaonguyen*yahoo.com" To: CCL Subject: CCL:G: looking for free GUI for Mac Message-Id: <-34182-070503141059-7406-1UOF7US3qInhXFe6IbApcg-.-server.ccl.net> X-Original-From: Hoa Nguyen Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-804554412-1178212252=:53365" Date: Thu, 3 May 2007 10:10:52 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Hoa Nguyen [hoagiaonguyen%a%yahoo.com] --0-804554412-1178212252=:53365 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Alex, You should try out the CSEO. http://www.cseo.net/ Hoa Nguyen Graduate Student Department of Chemistry University of Utah "Alexander Chris Hoepker ach42!=!cornell.edu" wrote: Sent to CCL by: "Alexander Chris Hoepker" [ach42.,.cornell.edu] Hi, I'm looking for a free graphical interface for Mac that reads output files from Gaussian and allows one to easily modify the structure. I would be willing to spend some money but certainly not close to a mille dollars. Thanks for your help. Alexhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Ahhh...imagining that irresistible "new car" smell? Check outnew cars at Yahoo! Autos. --0-804554412-1178212252=:53365 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Alex,

You should try out the CSEO.
http://www.cseo.net/

Hoa Nguyen
Graduate Student
Department of Chemistry
University of Utah

"Alexander Chris Hoepker ach42!=!cornell.edu" <owner-chemistry,ccl.net> wrote:

Sent to CCL by: "Alexander Chris Hoepker" [ach42.,.cornell.edu]
Hi,

I'm looking for a free graphical interface for Mac that reads output files from Gaussian and allows one
to easily modify the structure. I would be willing to spend some money but certainly not close to a
mille dollars.
Thanks for your help.

Alex






Ahhh...imagining that irresistible "new car" smell?
Check out new cars at Yahoo! Autos. --0-804554412-1178212252=:53365-- From owner-chemistry@ccl.net Thu May 3 20:19:00 2007 From: "Scott Brozell srb.:.osc.edu" To: CCL Subject: CCL: COLUMBUS Port to GFORTRAN Message-Id: <-34183-070503183330-3703-g9sKEnK9uqFRADQRa4d2bg%%server.ccl.net> X-Original-From: Scott Brozell Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Thu, 3 May 2007 17:40:35 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Scott Brozell [srb|*|osc.edu] Hi, On Tue, 1 May 2007, Thomas E Sorensen tes*uwm.edu wrote: > Has anyone ported COLUMBUS to GFORTRAN? I was hoping to get updated "install.automatic" scripts before I try the port myself. > Yes, but the porting that I know of is only in the unreleased beta version of COLUMBUS 6.0, which employs a new installation mechanism. My guess is that for the latest released version there exists a port or that it would not be difficult to produce a patch. There may be caveats. I have subscribed you to the COLUMBUS mailing list and invite those interested in COLUMBUS http://www.univie.ac.at/columbus/ to subscribe also: http://email.osc.edu/mailman/listinfo/columbus Scott From owner-chemistry@ccl.net Thu May 3 22:31:01 2007 From: "Joseph E. Maxwell jemaxwell~~jaymax.com" To: CCL Subject: CCL: Homology Modeling and Threading Message-Id: <-34184-070503173757-29571-nKxIQREAREsdVyL+B1SLJw[-]server.ccl.net> X-Original-From: "Joseph E. Maxwell" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 03 May 2007 14:40:39 -0700 MIME-Version: 1.0 Sent to CCL by: "Joseph E. Maxwell" [jemaxwell]*[jaymax.com] Hello Group, Can someone recommend a reliable software that is reasonably priced, Free/Shareware or Open Source for Homology Modeling and/or Threading? Thanks