From owner-chemistry@ccl.net Tue Apr 11 04:48:01 2006 From: "Barry Hardy barry.hardy^tiscalinet.ch" To: CCL Subject: CCL: CFP: Discussions between Bench Scientists & Modellers on Discovery Tools Message-Id: <-31480-060411044211-20828-EjjkVOMaJJhYl8vZB4KiOw(~)server.ccl.net> X-Original-From: Barry Hardy Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Tue, 11 Apr 2006 10:41:25 +0200 Mime-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy]^[tiscalinet.ch] In our eCheminfo Community of Practice InterAction Meeting running October 16-19 at Bryn Mawr College (Philadelphia) we will be having presentations and discussions on the latest developments in virtual screening, docking, structure-based drug design, AMDE, predictive toxicology, and metabolomics, as applied to drug discovery. We are including a day (October 18) specifically to hold short presentations and discussions between bench scientists & modellers on the experiences of the experimentalists in using modelling and informatics methods and tools, including difficulties and failings found in methods, suggestions for improvements in methods supporting reaction and analytical planning and analysis, and knowledge sharing of tips and tricks of what practices work and when and how. The emphasis will be on the pragmatic application of methods and tools to chemistry problems. The InterAction Meeting format followed is that of short presentations and posters, with 50% of the time reserved for individual Q&As and panel discussions. If interested in being considered for a speaker slot in this program, please submit to me: a) as soon as possible a title with name, organisation, address, and phone and email address contact information for proposed presentation, and any key points you would like to address and discuss b) a 300 word abstract covering main points to be addressed, sent to me no later than April 21. You are also welcome to contact me via email to discuss. And please consider forwarding this call to colleagues in the lab! best regards Barry Hardy, PhD eCheminfo Community of Practice Manager http://echeminfo.colayer.net/ +41 61 851 0170 From owner-chemistry@ccl.net Tue Apr 11 05:44:01 2006 From: "Roger Kevin Robinson r.robinson : imperial.ac.uk" To: CCL Subject: CCL: Ghz to g cm2 Message-Id: <-31481-060411053917-12752-pp8Ev+FSnO+OYJOaOQAMvw a server.ccl.net> X-Original-From: Roger Kevin Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 11 Apr 2006 10:38:11 +0100 MIME-Version: 1.0 Sent to CCL by: Roger Kevin Robinson [r.robinson _ imperial.ac.uk] Hi, There is a page on the CCCBDB which allows you to convert between different rotational constants. I normally use it to convert rotational constants from Ghz from a guassian log file to g cm2. However its down at the moment, it would be useful if I could do this myself so I could add to a program to do it automatically does anyone know what the relationship between these units is or point me to where I could find out as im having trouble locating the answer. Thanks Roger From owner-chemistry@ccl.net Tue Apr 11 10:38:01 2006 From: "Daniel Jana dfjana,+,gmail.com" To: CCL Subject: CCL:G: Ghz to g cm2 Message-Id: <-31482-060411074302-8137-bvUGZXQ54wNX6W7bCBH09w/a\server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 11 Apr 2006 11:43:47 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana[A]gmail.com] Roger Kevin Robinson r.robinson : imperial.ac.uk wrote: > There is a page on the CCCBDB which allows you to convert between > different rotational constants. > I normally use it to convert rotational constants from Ghz from a > guassian log file to g cm2. However its down at the moment, it would be > useful if I could do this myself so I could add to a program to do it > automatically does anyone know what the relationship between these units > is or point me to where I could find out as im having trouble locating > the answer. > Hi, I'm not a specialist on the matter but looking at the formula used at the site you mentioned (using Google cache) I managed to get to an Excel worksheet that does the job for you. From there on it's just playing with the factor between constants. You just have to change the value of B (in GHz) and it'll do the rest. You can get it from: http://mrna.ist.utl.pt/~jana/RotConst.xls I must mention (once again) that I'm not a specialist so I can't garantee that it really works (though based on the website it should). Try with a couple of constants you know are right (one from Gaussian you already have changed) and check the result. If it works, great. If it doesn't contact me and I'll check what the problem is. Hope it helps, Daniel Jana From owner-chemistry@ccl.net Tue Apr 11 11:35:00 2006 From: "Andrew D. Fant fant%x%pobox.com" To: CCL Subject: CCL: Free QSAR (CoMFA) software Message-Id: <-31483-060411113321-20496-KdzIrYpOt9ShTJchp6vsRw:_:server.ccl.net> X-Original-From: "Andrew D. Fant" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 11 Apr 2006 11:33:11 -0400 MIME-Version: 1.0 Sent to CCL by: "Andrew D. Fant" [fant{:}pobox.com] jz7(!)duke.edu wrote: > > Does anyone know any free programs that can do QSAR analysis (using > CoMFA)? Sybyl does this but it is not free. > To the best of my knowledge, Tripos owns at least one patent on CoMFA and so there aren't any free (beer or speech) implementations of it. -- Andrew Fant | And when the night is cloudy | This space to let Molecular Geek | There is still a light |---------------------- fant/a\pobox.com | That shines on me | Disclaimer: I don't Boston, MA | Shine until tomorrow, Let it be | even speak for myself From owner-chemistry@ccl.net Tue Apr 11 12:46:01 2006 From: "Wayne Steinmetz WES04747 ~~ pomona.edu" To: CCL Subject: CCL: Free QSAR (CoMFA) software Message-Id: <-31484-060411124346-13439-ZdXMSSfp7aPmcudTjUCBFg=server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 11 Apr 2006 09:41:11 -0700 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747===pomona.edu] CoMFA is a patented procedure. You require SYBYL. Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-607-7726 Email: wsteinmetz!A!pomona.edu WWW: pages.pomona.edu/~wsteinmetz -----Original Message----- > From: owner-chemistry!A!ccl.net [mailto:owner-chemistry!A!ccl.net] Sent: Tuesday, April 11, 2006 7:36 AM To: Wayne Steinmetz Subject: CCL: Free QSAR (CoMFA) software Sent to CCL by: "Andrew D. Fant" [fant{:}pobox.com] jz7(!)duke.edu wrote: > > Does anyone know any free programs that can do QSAR analysis (using > CoMFA)? Sybyl does this but it is not free. > To the best of my knowledge, Tripos owns at least one patent on CoMFA and so there aren't any free (beer or speech) implementations of it. -- Andrew Fant | And when the night is cloudy | This space to let Molecular Geek | There is still a light |---------------------- fant\a/pobox.com | That shines on me | Disclaimer: I don't Boston, MA | Shine until tomorrow, Let it be | even speak for myselfhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. From owner-chemistry@ccl.net Tue Apr 11 14:28:00 2006 From: "John McKelvey jmmckel||attglobal.net" To: CCL Subject: CCL: Free QSAR (CoMFA) software Message-Id: <-31485-060411140218-6918-KDD471WTE2od5dBgnMkIbw**server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 11 Apr 2006 13:55:50 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel],[attglobal.net] Just curious, Is Graham Richard's SOMFA related to this issue? John McKelvey Wayne Steinmetz WES04747 ~~ pomona.edu wrote: >Sent to CCL by: "Wayne Steinmetz" [WES04747===pomona.edu] >CoMFA is a patented procedure. You require SYBYL. > >Wayne E. Steinmetz >Carnegie Professor of Chemistry >Woodbadge Course Director >Chemistry Department >Pomona College >645 North College Avenue >Claremont, California 91711-6338 >USA >phone: 1-909-621-8447 >FAX: 1-909-607-7726 >Email: wsteinmetz^-^pomona.edu >WWW: pages.pomona.edu/~wsteinmetz > > >-----Original Message----- > > >>From: owner-chemistry^-^ccl.net [mailto:owner-chemistry^-^ccl.net] >> >> >Sent: Tuesday, April 11, 2006 7:36 AM >To: Wayne Steinmetz >Subject: CCL: Free QSAR (CoMFA) software > >Sent to CCL by: "Andrew D. Fant" [fant{:}pobox.com] >jz7(!)duke.edu wrote: > > >>Does anyone know any free programs that can do QSAR analysis (using >>CoMFA)? Sybyl does this but it is not free. >> >> >> > >To the best of my knowledge, Tripos owns at least one patent on CoMFA >and so >there aren't any free (beer or speech) implementations of it. > > > From owner-chemistry@ccl.net Tue Apr 11 16:24:00 2006 From: "Andrew D. Fant fant ~ pobox.com" To: CCL Subject: CCL: Free QSAR (CoMFA) software Message-Id: <-31486-060411154552-4524-8Hxaj6RkNhTbtqnaMziqjw : server.ccl.net> X-Original-From: "Andrew D. Fant" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 11 Apr 2006 15:45:46 -0400 MIME-Version: 1.0 Sent to CCL by: "Andrew D. Fant" [fant::pobox.com] John McKelvey jmmckel||attglobal.net wrote: > Sent to CCL by: John McKelvey [jmmckel],[attglobal.net] > Just curious, > > Is Graham Richard's SOMFA related to this issue? > First off, let me say that I am NOT an attorney and that anyone who takes my half-informed rambling as legal advice needs the head examined. As I understand it, the Tripos CoMFA patent (US 5307287 for those who are willing to risk the liability of having read it) essentially is about a grid alignment and evaluation of molecular properties with PLS fitting across a series. For those who speak patent, there are 90 claims made, with several sub-claims in each section. At one point, I heard someone claim that this patent essentially shut down any 3D method for QSAR that was grid-based. I am not sure if that is the case. At the very least, it claims to cover lattice-based methods, but I would be interested to see if an adaptive-grid method might not be novel enough to escape coverage. Skimming the SoMFA paper from J. Med Chem, it appears that the lack of probe interaction energies (claims 19-20), the use of Self-Organizing Maps instead of PLS fitting and the use of PCA in the analysis may be how it avoids that patent. If anyone really cares about my amateur opinion, I'll read up on it over the long weekend (yay Patriot's Day) and give a followup. Andy -- Andrew Fant | And when the night is cloudy | This space to let Molecular Geek | There is still a light |---------------------- fant]-[pobox.com | That shines on me | Disclaimer: I don't Boston, MA | Shine until tomorrow, Let it be | even speak for myself From owner-chemistry@ccl.net Tue Apr 11 19:57:00 2006 From: "Vorpagel, Erich R Erich.Vorpagel : pnl.gov" To: CCL Subject: CCL: MSCF 2007 Call for Proposals Message-Id: <-31488-060411173525-3455-fwbd616JxCCIVBSj8pwLhQ---server.ccl.net> X-Original-From: "Vorpagel, Erich R" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Tue, 11 Apr 2006 12:55:37 -0700 MIME-version: 1.0 Sent to CCL by: "Vorpagel, Erich R" [Erich.Vorpagel_-_pnl.gov] Greetings CCL Team, Would you please post this announcement for a call for proposals on your ccl.net server? Thank you. ------------------- MSCF 2007 Call-for-Proposals in Environmental Molecular Science Computational Grand-Challenge Applications ________________________________________________________________________ __________ Richland, WA - The Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory announces the 2007 Call-for-Proposals (for allocations of computer time) for Computational Grand-Challenge Applications (CGCA) in environmental molecular science research areas that address the environmental problems and research needs facing the U.S. Department of Energy (DOE) and the Nation. This call includes research applications in biology, chemistry, climate and subsurface science and is open to all research entities regardless of research funding source. Computer allocations for CGCAs are for three years, with the computer allocation appropriate for the scope of research to be performed. A Letter-of-Intent is due May 15, 2006 with final proposals due June 30, 2006. Announcement of awards are expected September 15, 2006. Further information on the CGCA Call-for-Proposals is available at http://mscf.emsl.pnl.gov. The MSCF houses an 11.8 Teraflop HP Linux Itanium2 Cluster with 1960 processors. The MSCF also supports some widely used computational chemistry codes, including the Molecular Science Software Suite (MS3) designed to take advantage of the HP cluster. We seek applications of Grand-Challenge scientific research that require a large number of processors and a significant portion of this computational resource. The EMSL (http://www.emsl.pnl.gov) is a user research facility funded by the Office of Biological and Environmental Research in the DOE. As a National Scientific User Facility, the mission of the EMSL is to provide integrated experimental and computational resources for discovery and technological innovation in the environmental molecular sciences to support the needs of DOE and the Nation. As a research organization, the EMSL provides scientific resources to attain a molecular-level understanding of the physical, chemical and biological processes needed to solve critical environmental problems, educate young scientists, and advance molecular sciences to meet the demanding environmental challenges of the future. Both computational and experimental resources are available to users at "no cost." ------------------- Regards, Erich R. Vorpagel, Ph.D. Chief Scientist Manager Computational Grand-Challenge and Pilot Projects MSCF Visualization and User Services Group Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory P. O. Box 999, MS: K8-91 3335 Q Ave. Phone: 509-376-0751 Richland, WA 99352 FAX: 509-376-0420 Email: erich.vorpagel%pnl.gov Web: http://mscf.emsl.pnl.gov/ From owner-chemistry@ccl.net Tue Apr 11 21:41:00 2006 From: "Ricky Shen hxhgxy2^_^163.com" To: CCL Subject: CCL:G: Cube file Message-Id: <-31489-060411214004-3120-UBYGUH3eSeYoR1xe8OMhUQ!A!server.ccl.net> X-Original-From: "Ricky Shen" Date: Tue, 11 Apr 2006 21:40:03 -0400 Sent to CCL by: "Ricky Shen" [hxhgxy2[*]163.com] Hi, I want to calculate a Cube file using Gaussian 98, but it give a error message and the cube file is not archived. Gaussian version: G98 a11 OS:Redhat Linux 9.0 Compiler: pgf77,pgf90 the error message: PGFIO-F-217/formatted read/unit=5/attempt to read past end of file. File name = /localtmp/Gau-16205.inp formatted, sequential access record = 12 In source file dencub.f, at line number 366 Can you help me to resolve the problem? From owner-chemistry@ccl.net Tue Apr 11 22:34:00 2006 From: "Anatoli Korkin a_korkin::yahoo.com" To: CCL Subject: CCL: MM "clean-up" of the periodic guess structures Message-Id: <-31490-060411223142-27536-+ybpW+XdPKBbkNKIEMN4BA[]server.ccl.net> X-Original-From: "Anatoli Korkin" Date: Tue, 11 Apr 2006 22:31:41 -0400 Sent to CCL by: "Anatoli Korkin" [a_korkin*|*yahoo.com] Dear CCLers, Can you help with an advice on a program/module for "clean-up" of initial periodic structures? In some of my projects they are rather big. I believe the best way to do such "cleaning" before using the "heavy guns" such as DFT for further geometry optimization, is to apply classical molecular mechanics energy optimizer with an explicit list of atoms connectivities. For molecules such option is available in a few programs, I know Materials Studio has it, but I am not aware of any for the periodic systems. For someone who is a good programmer it may be easy to write such a program, but not for me. Hopwever, If someone is interested in joining one of our projects where we have need for this function by writing such program, we can check if there is an overlap of the research interests and mutual benefit. Thank you for your consideration. I am not at CCL list, thus writing or copying your message to me will be very much appreciated. Best regards, Anatoli korkin a_korkin-(|)-yahoo.com