From owner-chemistry@ccl.net Tue Mar 27 01:41:00 2007 From: "David Gallagher gallagher.da]*[gmail.com" To: CCL Subject: CCL: mopac 2007 Message-Id: <-33910-070326160717-31394-Qi57K9xbAC+fi1kKRkRLfw!=!server.ccl.net> X-Original-From: "David Gallagher" Content-Type: multipart/alternative; boundary="----=_Part_108624_19985518.1174935687465" Date: Mon, 26 Mar 2007 12:01:27 -0700 MIME-Version: 1.0 Sent to CCL by: "David Gallagher" [gallagher.da : gmail.com] ------=_Part_108624_19985518.1174935687465 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline There are several free GUIs listed on the MOPAC2007 website at http://www.openmopac.net/resellers.html including those below, though I cannot offer a particular recommendation as I have not used most of them, and of course, it would depend on your specific needs: *WebMO, LLC* URL: http://www.webmo.net/index.html *Molden* is a pre/post processing program of molecular and electronic structure that runs on Windows and Linux/UNIX. http://www.cmbi.ru.nl/molden/molden.html *MOP2007* is a new MOPAC2007 GUI for Windows. Comments on this program would be appreciated! http://www.chemsoft.ch/qc/mpc.html *MolWorks* is a molecular builder and pre/post interface to MOPAC and other programs. It runs on Windows, Linux, and Mac. http://www.molworks.com/en/ *Jmol* is a very popular versatile JAVA-based program that allows structures to be examined in detail. http://jmol.sourceforge.net/ *Chime* from MDL, lets scientists view chemical structures from within popular Web browsers. http://www.mdl.com/products/framework/chime/ *Winmostar* is a Japanese and English language pre/post processing program of molecular and electronic structure that runs on Windows. http://winmostar.com/ Regards David Gallagher CAChe Research On 3/26/07, neeraj misra misraneeraj#,#gmail.com wrote: > > > Sent to CCL by: "neeraj misra" [misraneeraj%a%gmail.com] > CAN ANYONE SUGGEST ME AN EASY GUI FOR MOPAC 2007 AND WHICH IS FREE TOO.> > > > ------=_Part_108624_19985518.1174935687465 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline

There are several free GUIs listed on the MOPAC2007 website at http://www.openmopac.net/resellers.html including those below, though I cannot offer a particular recommendation as I have not used most of them, and of course, it would depend on your specific needs:

WebMO, LLC
URL: http://www.webmo.net/index.html

Molden is a pre/post processing program of molecular and electronic structure that runs on Windows and Linux/UNIX.
http://www.cmbi.ru.nl/molden/molden.html

MOP2007 is a new MOPAC2007 GUI for Windows. Comments on this program would be appreciated!
http://www.chemsoft.ch/qc/mpc.html

MolWorks is a molecular builder and pre/post interface to MOPAC and other programs. It runs on Windows, Linux, and Mac.
http://www.molworks.com/en/

Jmol is a very popular versatile JAVA-based program that allows structures to be examined in detail.
http://jmol.sourceforge.net/

Chime from MDL, lets scientists view chemical structures from within popular Web browsers.
http://www.mdl.com/products/framework/chime/

Winmostar is a Japanese and English language pre/post processing program of molecular and electronic structure that runs on Windows.
http://winmostar.com/

Regards

David Gallagher

CAChe Research

On 3/26/07, neeraj misra misraneeraj#,#gmail.com <owner-chemistry _ ccl.net> wrote:

Sent to CCL by: "neeraj  misra" [misraneeraj%a%gmail.com]
CAN ANYONE SUGGEST ME AN EASY GUI FOR MOPAC 2007 AND WHICH IS FREE TOO.

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------=_Part_108624_19985518.1174935687465-- From owner-chemistry@ccl.net Tue Mar 27 07:57:01 2007 From: "Barry Hardy barry.hardy-x-tiscalinet.ch" To: CCL Subject: CCL: Drug Discovery & Development - eCheminfo Autumn meeting, program, CFP, bursary awards Message-Id: <-33911-070327075006-1113-SqceDpA6nTTwhM7LBdSvtg[a]server.ccl.net> X-Original-From: Barry Hardy Content-Type: multipart/alternative; boundary="=====================_128872546==.ALT" Date: Tue, 27 Mar 2007 12:49:20 +0200 Mime-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy%%tiscalinet.ch] --=====================_128872546==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed I enclose below our first announcement on the program for our eCheminfo Autumn Community of Practice meeting on Drug Discovery & Development which will be held at Bryn Mawr the week of October 15. Included are descriptions of programs, workshops and forums, a CFP and information on Bursary Awards. 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: * Virtual Screening & Docking - Comparative Methodology & Best Practice * Forum & Workshop on International Cooperation in ADME/Tox Early registration runs through end of June. best regards Barry Hardy Community of Practice Manager Douglas Connect Switzerland Tel: +41 61 851 0170 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) 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), 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 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. 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 30 April 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 30 April 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. Barry Hardy Community of Practice Manager Douglas Connect Switzerland Tel: +41 61 851 0170 --=====================_128872546==.ALT Content-Type: text/html; charset="us-ascii"
I enclose below our first announcement on the program for our eCheminfo Autumn Community of Practice meeting on Drug Discovery & Development which will be held at Bryn Mawr the week of October 15. Included are descriptions of programs, workshops and forums, a CFP and information on Bursary Awards.

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:
* Virtual Screening & Docking - Comparative Methodology & Best Practice
* Forum & Workshop on International Cooperation in ADME/Tox

Early registration runs through end of June.

best regards
Barry Hardy
Community of Practice Manager
Douglas Connect
Switzerland
Tel: +41 61 851 0170

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)

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), 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

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.

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 30 April 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 30 April 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.

Barry Hardy
Community of Practice Manager
Douglas Connect
Switzerland
Tel: +41 61 851 0170

--=====================_128872546==.ALT-- From owner-chemistry@ccl.net Tue Mar 27 09:07:02 2007 From: "M. Felix majuma_._krypton.ch.pwr.wroc.pl" To: CCL Subject: CCL: NADPH cofactor in Tinker Message-Id: <-33912-070327031512-10076-3IkuDb20RQll/kUIW+zODA,,server.ccl.net> X-Original-From: "M. Felix" Date: Tue, 27 Mar 2007 03:15:09 -0400 Sent to CCL by: "M. Felix" [majuma(-)krypton.ch.pwr.wroc.pl] Dear CCL users, recently I decided to model NADPH in Tinker 4.2 using Amber94 force field. Unfortunately, this FF does not suppport parameters for NADPH. They are available on http://pharmacy.man.ac.uk/amber/ as an add-on to the original Amber package. Does anyone know how to convert these PREP and FRCMOD files to the format suitable for Tinker? I discovered that Open Babel has the ability to read PREP files, but I cannot convert them to any other format. For example: babel -iprep nadph.prp -oxyz foo.xyz gives: 0 molecules converted Any help will be appreciated. M. Felix From owner-chemistry@ccl.net Tue Mar 27 14:19:01 2007 From: "Geoffrey Hutchison geoffh..pitt.edu" To: CCL Subject: CCL: NADPH cofactor in Tinker Message-Id: <-33913-070327122756-385-LDunhSfTTEZ+CigbSnRioQ|*|server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 27 Mar 2007 10:25:52 -0400 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Geoffrey Hutchison [geoffh^^^pitt.edu] Dear Dr. Felix, Well, if Open Babel has a problem (e.g., not reading your PREP file), please feel free to report it to us! http://sourceforge.net/tracker/?atid=428740&group_id=40728&func=browse We don't have many examples of PREP files, so it's entirely possible that there's a bug in the PREP import routines. So please submit a bug report and include your example file and I'll see that it's fixed ASAP for the 2.1 release. Cheers, -Geoff ------------------------------------------- Geoff Hutchison Assistant Professor, starting Sep. 2007 University of Pittsburgh, Department of Chemistry 219 Parkman Avenue Pittsburgh, PA 15260 On Mar 27, 2007, at 3:15 AM, M. Felix majuma_._krypton.ch.pwr.wroc.pl wrote: > > Sent to CCL by: "M. Felix" [majuma(-)krypton.ch.pwr.wroc.pl] > > Dear CCL users, > > recently I decided to model NADPH in Tinker 4.2 using Amber94 > force field. > Unfortunately, this FF does not suppport parameters for NADPH. They > are available on http://pharmacy.man.ac.uk/amber/ as an add-on to > the original Amber package. Does anyone know how to convert these > PREP and FRCMOD files to the format suitable for Tinker? > > I discovered that Open Babel has the ability to read PREP files, > but I cannot convert them to any other format. For example: > > babel -iprep nadph.prp -oxyz foo.xyz > > gives: > 0 molecules converted > > > Any help will be appreciated. > > M. Felix > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > From owner-chemistry@ccl.net Tue Mar 27 15:04:00 2007 From: "Eduardo edulsa#,#quimica.ufpr.br" To: CCL Subject: CCL: CCL : Program to generate z-matrix Message-Id: <-33914-070327143506-15355-Pb0G1G1it9Xbsq47c8Upew-#-server.ccl.net> X-Original-From: Eduardo Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 27 Mar 2007 14:36:29 -0300 MIME-Version: 1.0 Sent to CCL by: Eduardo [edulsa,quimica.ufpr.br] Dear Viji molden (http://www.cmbi.ru.nl/molden/molden.html) is free (and its source code is avaliable by default). Enjoy with Regards Eduardo Viji shankaran chat2viji:_:gmail.com wrote: > Sent to CCL by: "Viji shankaran" [chat2viji(-)gmail.com] > > Dear friends, > > > can anyone help me out in finding a program to generate z-matrix(internal coordinates) in C or fortran? > > Thakns in advance, > > Viji Shankaran.> > > -- Eduardo Lemos de Sa Associated Professor at Chemistry Department Universidade Federal do Parana Dep. Quimica, P. Box 19081, 81531-990 Curitiba PR / Brazil phone: +55(41)33613300 fax : +55(41)33613186 From owner-chemistry@ccl.net Tue Mar 27 23:29:00 2007 From: "Qian Wang xie.wang,gmail.com" To: CCL Subject: CCL: geometry optimization problem: why lower level geometry is more close to experimental results? Message-Id: <-33915-070327232203-28951-wsqHhLf0JCwkeWHKwZ2CXQ(~)server.ccl.net> X-Original-From: "Qian Wang" Content-Type: multipart/alternative; boundary="----=_Part_25379_25175693.1175048863604" Date: Tue, 27 Mar 2007 22:27:43 -0400 MIME-Version: 1.0 Sent to CCL by: "Qian Wang" [xie.wang..gmail.com] ------=_Part_25379_25175693.1175048863604 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all, I am optimizing a molecule with 10 atoms. Surprisely, the optimized geometry > from HF/6-31G is more close to experimental X-ray structure than optimized geometry from MP2/6-31G* is. Could anyone suggest a possible reason why higher level of calculation does not work better in this case? Thanks in advance! Qian ------=_Part_25379_25175693.1175048863604 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all,

I am optimizing a molecule with 10 atoms. Surprisely, the optimized geometry from HF/6-31G is more close to experimental X-ray structure than optimized geometry from MP2/6-31G* is. Could anyone suggest a possible reason why higher level of calculation does not work better in this case?

Thanks in advance!

Qian
------=_Part_25379_25175693.1175048863604--