From owner-chemistry@ccl.net Thu Sep 22 07:32:25 2005 From: "CCL" To: CCL Subject: CCL: W:Report Message-Id: <-29263-050922073124-31603-yMAUgaInZno5pHj3b3+iyA%a%server.ccl.net> X-Original-From: "Wendy Anne Warr" Sent to CCL by: "Wendy Anne Warr" [wendy%a%warr.com] --Replace strange characters with the "at" sign to recover email address--. Chemical Information and Computation 2005, Number 1 Report on the 229th ACS National Meeting and Exposition Our report on the Spring 2005 National Meeting of the American Chemical Society, held in San Diego, went to press in August. Apart from the usual news section, covering about 70 companies, this 160-page report, with colour graphics, carries transcripts of all the presentations given in the award symposium honouring Peter Willett as winner of the COMP Award for Computers in Chemical and Pharmaceutical Research, plus transcripts of papers on the future of scientific publishing, safe exchange of chemical information, ADME, molecular mechanics and simulation, and drug discovery. The last of the 34 transcripts records the open meeting of the ACS committees on ACS Publications and CAS. The line up of speakers includes Steve Bachrach, Pieter Bolman, Bob Clark, Tim Clark, Jason Cole, Simon Coles (Southampton), John Delaney, Ren Deplanque, Jonathan Essex, Johnny Gasteiger, Steve Heller, Chris Lipinski, Larry Marnett, Brian Masek, Peter Murray-Rust, Anthony Nicholls, Marc Nicklaus, Tudor Oprea, Stephen Pickett, Henry Rzepa, Mark Seierstad, Bill Town, Andrea Twiss-Brooks, Eric Vangrevelinghe, Hugo Villar, Wendy Warr, Peter Willett, Ann Wolpert, and others. The full contents list is available at http://warr.com/morepubs.html. Wendy From owner-chemistry@ccl.net Thu Sep 22 10:37:21 2005 From: "CCL" To: CCL Subject: CCL: Re: overalying samll molecules Message-Id: <-29264-050922103330-30535-Rvre4mP3Un5ZbAo6rjMoiw.@.server.ccl.net> X-Original-From: Michel Petitjean Date: Thu, 22 Sep 2005 15:44:35 +0200 (MEST) Sent to CCL by: Michel Petitjean [ptitjean...@...itodys.jussieu.fr] --Replace strange characters with the "at" sign to recover email address--. To: Subject: CCL: Re: overalying samll molecules Yes there is: freeware CSR downloadable from http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR > Hi, > I am trying to overlaying the 3D structures of two small molecules one > which is not peptide. Is there any free software I can do this? > Thanks in advance for any help. > Regards, > > pedro Michel Petitjean, Email: petitjean..@..itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean..@..ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html From owner-chemistry@ccl.net Thu Sep 22 12:04:16 2005 From: "CCL" To: CCL Subject: CCL: W:subscribe Message-Id: <-29276-050922101908-29563-u/JqU7wOnvd/VKuOXwe3Bw*o*server.ccl.net> X-Original-From: "Alexandre A. VARNEK" Sent to CCL by: "Alexandre A. VARNEK" [l.cci*o*chimie.u-strasbg.fr] --Replace strange characters with the "at" sign to recover email address--. subscribe From owner-chemistry@ccl.net Thu Sep 22 12:04:11 2005 From: "CCL" To: CCL Subject: CCL: input structure creation/editing Message-Id: <-29272-050922064558-28880-yYe1GfABltLLr2SCVvIS7g|a|server.ccl.net> X-Original-From: john furr Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 22 Sep 2005 06:45:52 -0400 MIME-Version: 1.0 Sent to CCL by: john furr [john.furr|a|gmail.com] --Replace strange characters with the "at" sign to recover email address--. Dynamol has a molecular editor. Not sure if that is what you are looking for or not? http://www.dynamol.com On 9/21/05, CCL wrote: > Dear CCLers, > > which program running under GNU/Linux would you recommend for the creation > and editing of the input structures > for the quantum-chemical calculations? Molden is good for inputs using > Z-matrices, but is very inconvenient for the free-hand "fine-tuning" of the > guess structures, say for the transition states. Ghemical is not bad but its > development seem to be stopped. > Something as simple as the editor built-in in WebMO would be good... > > Thank you. > > > Best regards, > Konstantin Ivanov From owner-chemistry@ccl.net Thu Sep 22 12:04:10 2005 From: "CCL" To: CCL Subject: CCL: input structure creation/editing Message-Id: <-29265-050921224731-23454-ff9BL2kuStsaNs+uyOfqNA[#]server.ccl.net> X-Original-From: Luciano Costa Content-Type: multipart/alternative; boundary="----=_Part_4582_14856885.1127353806715" Date: Wed, 21 Sep 2005 22:50:06 -0300 MIME-Version: 1.0 Sent to CCL by: Luciano Costa [ltcnikit[#]gmail.com] --Replace strange characters with the "at" sign to recover email address--. ------=_Part_4582_14856885.1127353806715 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Ivanov, you can use gview (gaussian viewer) for linux. On 9/21/05, CCL wrote: > > Dear CCLers, > which program running under GNU/Linux would you recommend for the > creation and editing of the input structures > for the quantum-chemical calculations? Molden is good for inputs using > Z-matrices, but is very inconvenient for the free-hand "fine-tuning" of t= he > guess structures, say for the transition states. Ghemical is not bad but = its > development seem to be stopped. > Something as simple as the editor built-in in WebMO would be good... > Thank you. > Best regards, > Konstantin Ivanov > -- ### Luciano Tavares da Costa ### ## MSc. Eng. Qu=EDmico ## 100 % Linux ############################# ------=_Part_4582_14856885.1127353806715 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Ivanov,

you can use gview (gaussian viewer) for linux. 

On 9/21/05, CCL <owner-chemistry[#]ccl.net> wr= ote:
Dear CCLers,=
 
which program running under GNU/Linux would you recommend for the= creation and editing of the input structures
for the quantum-chemical calculations? Molden is good for inputs using Z-matrices, but is very inconvenient for the free-hand "fine-tuning" of the guess structures, say for the transition states. Ghemical is not bad but its development seem to be stopped.
Something as simple as the editor built-in in WebMO would be good...
 
Thank you.
 
 
Best regards,
   Konstantin Ivanov



--
### Luciano Tavares da = Costa ###
##       MSc. Eng. Qu=EDmico
= ##       100 % Linux
#####################= ######## ------=_Part_4582_14856885.1127353806715-- From owner-chemistry@ccl.net Thu Sep 22 12:04:11 2005 From: "CCL" To: CCL Subject: CCL: overlaying small molecules Message-Id: <-29269-050922001519-21464-IyYvZceRebjWImuKK6BqgQ * server.ccl.net> X-Original-From: Dr Seth Olsen Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 22 Sep 2005 13:44:31 +1000 MIME-Version: 1.0 Sent to CCL by: Dr Seth Olsen [s.olsen1 * uq.edu.au] --Replace strange characters with the "at" sign to recover email address--. Hi Pedro, In this case you're probably not likely to find something that will do it automatically for you. However, there is capacity in the programs I mentioned (MMTK and Scientific python modules) to allow you to write a script that should do this. You would have to write the script but the good news is that the learning curve for python scripting is almost non-existent and it will bring you much advantage in the long term. Cheers, Seth ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1 * uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms ----- Original Message ----- > From: CCL Date: Thursday, September 22, 2005 8:03 am Subject: CCL: overlaying small molecules > > Sent to CCL by: Pedro Antonio Reche > [reche^_^research.dfci.harvard.edu] > --Replace strange characters with the "at" sign to recover email > address--. > > Dear Rajan, > Thanks for the email. The 3D structures I want overlay correspond > to a > peptide ( 9 residues) and that of a compound that it is supposed > simulate the structure of the peptide. The structures are in PDB > format. Any help welcome! > > pedro > > On Sep 21, 2005, at 5:56 PM, Rajan Vatassery wrote: > > > Dear Pedro, > > I think this would depend on the type of input file you are > using. if > > it is something as simple as a GAMESS input, or some other > electronic> structure calc where bonds aren't explicitly marked, > then simply > > combining the two coordinates should work. > > however, i have a feeling that your problem is a bit more > complex than > > my interpretation of it from your email. i'd be glad to help you > if you > > clarify your problem and maybe some of your background (so i > don't > > speak > > beneath your level). otherwise, good luck > > raj > > > > > > > > On Wed, 2005-09-21 at 09:50, CCL wrote: > >> Sent to CCL by: Pedro Antonio Reche > >> [reche!=!research.dfci.harvard.edu] > >> > >> --Replace strange characters with the "at" sign to recover email > > >> address--. > >> > >> Hi, > >> I am trying to overlaying the 3D structures of two small > molecules one > >> which is not peptide. Is there any free software I can do this? > >> Thanks in advance for any help. > >> Regards, > >> > >> pedro > >> > >> > >> > >> -= 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>> > >> Send your subscription/unsubscription requests to: > >> CHEMISTRY-REQUEST * ccl.net>> > >> If your is mail bouncing from ccl.net domain due to spam > filters, > >> please>> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+-+-+-+-+- > >> +-+ > >> > >> > >> > > > > > > -= 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> > Send your subscription/unsubscription requests to: CHEMISTRY- > REQUEST * ccl.net > HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, > please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Thu Sep 22 12:04:12 2005 From: "CCL" To: CCL Subject: CCL: W:problem with SCIPCM Message-Id: <-29266-050922083635-21677-yMAUgaInZno5pHj3b3+iyA;;server.ccl.net> X-Original-From: "Soto Delia" Sent to CCL by: "Soto Delia" [sotodelia;;hotmail.com] --Replace strange characters with the "at" sign to recover email address--. I need your help I`m trying to make a optimization with SCIPCM but I have the next problem WARNING! Serious error in surface integrals. Nuclear flux = 317.76 Qnuc = 336.00 Error in int = 0.00 It is probable that some of the solute is outside the cavity and/or parts of the cavity surface cannot be reached from the origin. Try more integration points or a different set of integration origins. Surface Problems in SciFoc Error termination via Lnk1e in /home/g03/l502.exe What I can do? Tanks Delia sotodelia;;hotmail.com From owner-chemistry@ccl.net Thu Sep 22 12:04:12 2005 From: "CCL" To: CCL Subject: CCL: [CCL]: Re: overalying samll molecules Message-Id: <-29271-050922103553-30726-PSdynCfptnDCkWeF/srY3A[*]server.ccl.net> X-Original-From: Michel Petitjean Date: Thu, 22 Sep 2005 16:35:50 +0200 (MEST) Sent to CCL by: Michel Petitjean [ptitjean[*]itodys.jussieu.fr] --Replace strange characters with the "at" sign to recover email address--. To: Subject: [CCL]: Re: overalying samll molecules Yes there is: freeware CSR downloadable from http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR > Hi, > I am trying to overlaying the 3D structures of two small molecules one > which is not peptide. Is there any free software I can do this? > Thanks in advance for any help. > Regards, > > pedro Michel Petitjean, Email: petitjean[*]itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean[*]ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html From owner-chemistry@ccl.net Thu Sep 22 12:04:11 2005 From: "CCL" To: CCL Subject: CCL: input structure creation/editing Message-Id: <-29267-050921234823-6002-6luLcmXK8k2VadO2OsR0oQ{:}server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Date: Wed, 21 Sep 2005 20:08:09 -0700 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren{:}delsci.com] --Replace strange characters with the "at" sign to recover email address--. > which program running under GNU/Linux would you recommend for > the creation and editing of the input structures for the > quantum-chemical calculations? PyMOL has a fragment based builder specifically oriented towards "hand" tweaking. You can for instance drag atoms around in the plane of the screen, rotate torsions, and move or rotate fragments delimited by two or more "joint" atoms. You'll definitely want a late-model beta for this, which has a slightly more intuitive (but not necessarily easy) builder user interface. Start by clicking the "Builder" button and try to work from there. GNU/Linux buids available -- simply untar, run ./setup.sh, and launch with ./pymol.com http://delsci.com/beta Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren{:}delsci.com > -----Original Message----- > From: owner-chemistry{:}ccl.net [mailto:owner-chemistry{:}ccl.net] > Sent: Wednesday, September 21, 2005 2:01 PM > To: Warren DeLano > Subject: CCL: input structure creation/editing > > Dear CCLers, > > which program running under GNU/Linux would you recommend for > the creation and editing of the input structures for the > quantum-chemical calculations? Molden is good for inputs > using Z-matrices, but is very inconvenient for the free-hand > "fine-tuning" of the guess structures, say for the transition > states. Ghemical is not bad but its development seem to be stopped. > Something as simple as the editor built-in in WebMO would be good... > > Thank you. > > > Best regards, > Konstantin Ivanov > From owner-chemistry@ccl.net Thu Sep 22 12:04:16 2005 From: "CCL" To: CCL Subject: CCL: multi-reference CI Message-Id: <-29278-050922035634-12892-uKxuO21mT4w7naKs8bEBYw : server.ccl.net> X-Original-From: Frank Neese Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Thu, 22 Sep 2005 10:15:03 +0200 Mime-Version: 1.0 Sent to CCL by: Frank Neese [neese : mpi-muelheim.mpg.de] --Replace strange characters with the "at" sign to recover email address--. Dear Jeny, our ORCA program supports various flavors of approximate MR-CI methods and is easy to use. It is freely available from our website. Future versions will significantly expand the MRCI functionality and will also include CASSCF. http://ewww.mpi-muelheim.mpg.de/bac/index_en.php (go to "download area") Frank From owner-chemistry@ccl.net Thu Sep 22 12:04:16 2005 From: "CCL" To: CCL Subject: CCL: overalying samll molecules Message-Id: <-29277-050922001522-21511-NoVL6820ztFLVAa9994j6w]"[server.ccl.net> X-Original-From: Dr Seth Olsen Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 22 Sep 2005 13:41:26 +1000 MIME-Version: 1.0 Sent to CCL by: Dr Seth Olsen [s.olsen1]"[uq.edu.au] --Replace strange characters with the "at" sign to recover email address--. Hi Pedro, MMTK (with perhaps additional bits from Scientific Python) can do this, I believe, and should be sufficiently flexible that you could overlay to maximize site-to-site least squares or simply match centre of mass and higher rotational moments. The only difficulty is that you'll have to write the script. Molekel might be able to do it if you choose a set of atoms on each molecule and then print the current configuration - but I'm not sure. Cheers, Seth ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1]"[uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms ----- Original Message ----- > From: CCL Date: Thursday, September 22, 2005 0:50 am Subject: CCL: overalying samll molecules > > Sent to CCL by: Pedro Antonio Reche > [reche!=!research.dfci.harvard.edu] > --Replace strange characters with the "at" sign to recover email > address--. > > Hi, > I am trying to overlaying the 3D structures of two small molecules > one > which is not peptide. Is there any free software I can do this? > Thanks in advance for any help. > Regards, > > pedro > > > > -= 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> > Send your subscription/unsubscription requests to: CHEMISTRY- > REQUEST]"[ccl.net > HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, > please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Thu Sep 22 12:04:15 2005 From: "CCL" To: CCL Subject: CCL: a solvation model with the ONIOM? Message-Id: <-29275-050921233756-440-LDunhSfTTEZ+CigbSnRioQ()server.ccl.net> X-Original-From: ying xiong Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=gb2312 Date: Thu, 22 Sep 2005 10:37:49 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: ying xiong [xiongying96()yahoo.com.cn] --Replace strange characters with the "at" sign to recover email address--. Dear sir, Can a solvation model (e.g. PCM) be used with the ONIOM calculation to account for the bulk solvent effects ? Ying Xiong yxiong()mail.ccnu.edu.cn ___________________________________________________________ 雅虎免费G邮箱－中国第一绝无垃圾邮件骚扰超大邮箱 http://cn.mail.yahoo.com From owner-chemistry@ccl.net Thu Sep 22 12:04:11 2005 From: "CCL" To: CCL Subject: CCL: multi-reference CI Message-Id: <-29268-050922001523-21533-9JUtfnUunPL3G2OzvntyQw""server.ccl.net> X-Original-From: Dr Seth Olsen Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 22 Sep 2005 13:38:15 +1000 MIME-Version: 1.0 Sent to CCL by: Dr Seth Olsen [s.olsen1""uq.edu.au] --Replace strange characters with the "at" sign to recover email address--. Hi Jeny, Molpro, Columbus, Gamess, NWChem. Cheers, Seth ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1""uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms ----- Original Message ----- > From: CCL Date: Thursday, September 22, 2005 4:36 am Subject: CCL: multi-reference CI > > Sent to CCL by: jz7|-|duke.edu > > --Replace strange characters with the "at" sign to recover email > address--. > > Dear all, > > Which program can do the multi-reference CI calculation? I checked the > most popular Gaussian program. The manual only mentions the direct CI. > What other programs should I check? > > Thanks a lot! > Jeny > > > > -= 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> > Send your subscription/unsubscription requests to: CHEMISTRY- > REQUEST""ccl.net > HOME Page: http://www.ccl.net | Jobs Page: > http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, > please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > > From owner-chemistry@ccl.net Thu Sep 22 12:04:15 2005 From: "CCL" To: CCL Subject: CCL: Cleaning up dusty deck fortran and converting to C/C++ Message-Id: <-29273-050922003204-30437-UBYGUH3eSeYoR1xe8OMhUQ[A]server.ccl.net> X-Original-From: "Perry E. Metzger" Content-Type: text/plain; charset=us-ascii Date: Wed, 21 Sep 2005 23:37:05 -0400 MIME-Version: 1.0 Sent to CCL by: "Perry E. Metzger" [perry[A]piermont.com] --Replace strange characters with the "at" sign to recover email address--. > I have some old fortran I would like to convert to C.. Have used F2C > on an example code, which had me go back and clean up the fortran > first.. not a bad thing. > > Are there any utilities that would take a dusty fortran deck and clean > it up on its own... i.e. remove unused variables, and the like, for > example? I have a 40,000 line F77 code I would like also to run in C. Speaking as someone who was initially trained in computer science, not chemistry, you are very unlikely to get decent/maintainable results this way. Fortran, especially old Fortrans like Fortran 77, lacks the ability to create real data structures and the ability to do recursion. There is no point in translating such code except if you simply want to run it unchanged and maintain the code in Fortran (i.e. if you're using f2c as a pure compiler) -- you will ultimately save enormous amounts of time rewriting it, even for very large programs. I've seen many efforts in my Computer Science professional career in which people attempted to keep old code alive at all costs -- and in each case, it ended up costing far more human labor and far more money than a straight rewrite would cost. Rewriting, using the original code as a model and as a mechanism for validating regression tests, is often a superior solution. You say in a later message that your primary issue is that you aren't that familiar with C. I can't speak for your particular case, but the average chemist is a smart person with a substantial ability to handle abstraction and a capacity to deal with detail. Learning another programming language idiomatically is not nearly as difficult for a person in such a situation as attempting to keep the old code going will be, and you will gain substantial advantages from using idiomatic C code, such as being able to do proper dynamic allocation, linked lists, trees, recursive algorithms, etc. The only provisio I give is that C is a very sharp instrument -- it lacks run time checks. You have to learn to be disciplined to use it well. Sadly, the more appropriate languages for this sort of work have become desperately unpopular... Perry From owner-chemistry@ccl.net Thu Sep 22 12:04:11 2005 From: "CCL" To: CCL Subject: CCL: Gaussian Error Message-Id: <-29270-050922015428-3509-tqD63KfbOd+OfIRRplXydg#server.ccl.net> X-Original-From: "Dr. K. Selvaraj" Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 22 Sep 2005 10:11:02 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Dr. K. Selvaraj" [kselva#cata.ncl.res.in] --Replace strange characters with the "at" sign to recover email address--. Dear Dr. Sarah I have seen your query in mailing list about gaussian error through internet. I also face the same. I am new to G98W and trying to optimise a simple Si-cluster with net negative chrages. The error message is as follows "Warning! Spurious integrated density: NE= 68 NElCor= 0 Integral= 67.87825 Tolerance=1.00D-03 Consistency failure #2 in CalDSu. Error termination via Lnk1e in C:\G98W\l502.exe." Could you please suggest me if there is any hint to fix this. Also I need to know if there is any mailing list for G98W users? I would appreciate your help in this. best regards Selvaraj ----------------------------------- Dr. K. Selvaraj Scientist, Catalysis Division National Chemical Laboratory Pashan Road, Pune - 411 008, INDIA Phone (Off) : 020-25893300 Extn 2262 Phone & Fax : 020-25893761 (Cata. Off) email: kselva#cata.ncl.res.in www.ncl-india.org ***************************************************************** This email is virus free by TrendMicro Inter Scan Security Suite. ***************************************************************** From owner-chemistry@ccl.net Thu Sep 22 12:04:15 2005 From: "CCL" To: CCL Subject: CCL: overlaying small molecules Message-Id: <-29274-050921234830-6045-+oDO7YHSS+xBWwf2EYRiIg[-]server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Date: Wed, 21 Sep 2005 20:00:55 -0700 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren[-]delsci.com] --Replace strange characters with the "at" sign to recover email address--. > >> I am trying to overlaying the 3D structures of two small > molecules one > >> which is not peptide. This is something PyMOL can do. It is easiest if you start with two separate pdb files. Once they're open in PyMOL, select Pair Fitting from the Wizard menu and then just click on pairs of atoms to superimpose, starting each pair with the atom from the mobile object. Once you have 3+ pairs, click "Fit Pairs" to do the superposition. You can then save out the translated molecule as pdb or mol. > Is there any free software I can do this? PyMOL is free to evaluate (no registration required) and free period if you compile from the open source code. Latest beta d/l's from http://delsci.com/beta Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren[-]delsci.com > -----Original Message----- > From: owner-chemistry[-]ccl.net [mailto:owner-chemistry[-]ccl.net] > Sent: Wednesday, September 21, 2005 4:27 PM > To: Warren DeLano > Subject: CCL: overlaying small molecules > > > Sent to CCL by: Pedro Antonio Reche > [reche^_^research.dfci.harvard.edu] > > --Replace strange characters with the "at" sign to recover > email address--. > > Dear Rajan, > Thanks for the email. The 3D structures I want overlay > correspond to a peptide ( 9 residues) and that of a compound > that it is supposed simulate the structure of the peptide. > The structures are in PDB format. Any help welcome! > > pedro > > On Sep 21, 2005, at 5:56 PM, Rajan Vatassery wrote: > > > Dear Pedro, > > I think this would depend on the type of input file you > are using. if > > it is something as simple as a GAMESS input, or some other > electronic > > structure calc where bonds aren't explicitly marked, then simply > > combining the two coordinates should work. > > however, i have a feeling that your problem is a bit more > complex than > > my interpretation of it from your email. i'd be glad to > help you if you > > clarify your problem and maybe some of your background (so i don't > > speak > > beneath your level). otherwise, good luck > > raj > > > > > > > > On Wed, 2005-09-21 at 09:50, CCL wrote: > >> Sent to CCL by: Pedro Antonio Reche > >> [reche!=!research.dfci.harvard.edu] > >> > >> --Replace strange characters with the "at" sign to recover email > >> address--. > >> > >> Hi, > >> I am trying to overlaying the 3D structures of two small > molecules one > >> which is not peptide. Is there any free software I can do this? > >> Thanks in advance for any help. > >> Regards, > >> > >> pedro > >> > >> > >> > >> -= 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>> > >> Send your subscription/unsubscription requests to: > >> CHEMISTRY-REQUEST[-]ccl.net>> > >> If your is mail bouncing from ccl.net domain due to spam filters, > >> please>> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > >> +-+ > >> > >> > >> > > > > > > -= 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> > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST[-]ccl.net> > If your is mail bouncing from ccl.net domain due to spam > filters, please> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > > From owner-chemistry@ccl.net Thu Sep 22 15:00:38 2005 From: "CCL" To: CCL Subject: CCL: overlaying small molecules Message-Id: <-29280-050922144054-1261-71EBbKw9gZXJCGnbax6J1Q*_*server.ccl.net> X-Original-From: "Gunda Tam醩" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=response Date: Thu, 22 Sep 2005 20:42:01 +0200 MIME-Version: 1.0 Sent to CCL by: "Gunda Tam醩" [tgunda2005*_*puma.unideb.hu] --Replace strange characters with the "at" sign to recover email address--. Mol2mol can do it (it is not freeware but shareware). Several options are available, such as - All atoms are selected with equal weighting (1 for each atom); - All heavy atoms are selected, no hydrogens are regarded; - All atoms are considered, the weight factor is 2 for heavy atoms, 1 for hydrogens; - The atoms previously selected from the graphics window are considered only (residues, chains, or a peptide/DNS backbone). - For arbitrary selections an atom list can be inputted. See at : http://web.interware.hu/frenzy/mol2mol Dr. Tamas E. Gunda tgunda {at} puma.unideb.hu ----- Original Message ----- > From: "CCL" To: "Gunda, Tamas E " Sent: Wednesday, September 21, 2005 16:50 Subject: CCL: overalying samll molecules > > Sent to CCL by: Pedro Antonio Reche [reche!=!research.dfci.harvard.edu] > > --Replace strange characters with the "at" sign to recover email address--. > > Hi, > I am trying to overlaying the 3D structures of two small molecules one which is not peptide. Is there any free > software I can do this? > Thanks in advance for any help. > Regards, > > pedro From owner-chemistry@ccl.net Thu Sep 22 13:57:20 2005 From: "CCL" To: CCL Subject: CCL: 3rd FlexX Docking Workshop: Location updated Message-Id: <-29279-050922135639-2703-Tixf4Kam84fPqpXBXzr6kg.:.server.ccl.net> X-Original-From: Carsten Detering Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 22 Sep 2005 19:56:19 +0200 MIME-Version: 1.0 Sent to CCL by: Carsten Detering [detering.:.biosolveit.de] --Replace strange characters with the "at" sign to recover email address--. Dear CCLers: News on BioSolveIT's FlexX Docking Workshop (Nov. 10-11): * Venue: caesar (www.caesar.de) in Bonn, Germany. * The agenda is set up. The Workshop Website: http://www.biosolveit.de/workshops/2005 Registration: http://www.biosolveit.de/workshops/2005/registration.html Read more: General Information: The workshop will give in-depth knowledge in the docking program FlexX, and will put special emphasis on the latest version, Release 2. It is designed for novices as well as advanced users of FlexX. The participants must have at least basic knowledge of Unix operating systems. Because this workshop is dedicated to hands-on training, every participant will have the opportunity to practice the acquired knowledge on individual, brand new workstations. This is why the number of participants is limited. So register now to ensure your spot in this reputable workshop. There are only few spots left! The Venue: caesar The Center of Advanced European Studies and Research (www.caesar.de) is in Germany's former capital Bonn (www.bonn.de). It is located in a beautiful and stylish new building. Three major airports are conveniently located (CGN, DUS, FRA). The Agenda: * Nov. 9th: You are cordially invited to a reception and dinner. * Nov 10th: 8:30 - 9:30 (1) Getting Started 9:30 - 10:30 (2) The Workflow Picture 10:45 - 11:15 (3) Overview over the Environment 11:15 - 12:30 (4) Ligand Preparation 13:30 - 14:30 (5) Receptor Preparation 14:45 - 16:15 (6) Docking Procedure 16:45 - 17:45 (7) Extension Modules with Emphasis on FlexX-Pharm * Nov 11th: 8:30 - 10:00 (8) Configuration / Transforms 10:15 - 11:15 (9) Scripting / Parallelization 11:30 - 12:30 (10) Parameter Tuning 13:30 - 15:00 (11) Scoring 15:15 - 16:15 (12) FlexX with Sybyl Note that the agenda may still be subject to minor changes. Comments by previous participants: * "This is great! I will now be able to use FlexX more versatilely" * "The provided material is extremely helpful!" * "It was great to see FlexV in action, I had never even heard of it before." * "I would definitely recommend this workshop to a colleague!" * "The material provided is a very useful supplement to the User Guide and to rework the course material" * "I can highly recommend this workshop. After doing this course I feel I can use FlexX much better now." Learn to improve your knowledge in one of the best docking tools on the market. We will see you in Bonn in November! -the developers of FlexX From owner-chemistry@ccl.net Thu Sep 22 15:38:36 2005 From: "CCL" To: CCL Subject: CCL: Cleaning up dusty deck fortran and converting to C/C++ Message-Id: <-29281-050922152357-8511-jrCl9C53LzcYN7C5MMvWgg : server.ccl.net> X-Original-From: "Shobe, David" content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 22 Sep 2005 15:21:18 -0400 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe : sud-chemieinc.com] --Replace strange characters with the "at" sign to recover email address--. Sent to CCL by: "Perry E. Metzger" [perry[A]piermont.com] > Sadly, the more appropriate languages for this sort of work have become > desperately unpopular... I gotta ask: what languages would you consider most appropriate for this sort of work (computational chemistry calculations)? --David Shobe, Ph.D., M.L.S. S黡-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry : ccl.net [mailto:owner-chemistry : ccl.net] Sent: Wednesday, September 21, 2005 11:37 PM To: Shobe, David Subject: CCL: Cleaning up dusty deck fortran and converting to C/C++ Sent to CCL by: "Perry E. Metzger" [perry[A]piermont.com] --Replace strange characters with the "at" sign to recover email address--. > I have some old fortran I would like to convert to C.. Have used F2C > on an example code, which had me go back and clean up the fortran > first.. not a bad thing. > > Are there any utilities that would take a dusty fortran deck and clean > it up on its own... i.e. remove unused variables, and the like, for > example? I have a 40,000 line F77 code I would like also to run in C. Speaking as someone who was initially trained in computer science, not chemistry, you are very unlikely to get decent/maintainable results this way. Fortran, especially old Fortrans like Fortran 77, lacks the ability to create real data structures and the ability to do recursion. There is no point in translating such code except if you simply want to run it unchanged and maintain the code in Fortran (i.e. if you're using f2c as a pure compiler) -- you will ultimately save enormous amounts of time rewriting it, even for very large programs. I've seen many efforts in my Computer Science professional career in which people attempted to keep old code alive at all costs -- and in each case, it ended up costing far more human labor and far more money than a straight rewrite would cost. Rewriting, using the original code as a model and as a mechanism for validating regression tests, is often a superior solution. You say in a later message that your primary issue is that you aren't that familiar with C. I can't speak for your particular case, but the average chemist is a smart person with a substantial ability to handle abstraction and a capacity to deal with detail. Learning another programming language idiomatically is not nearly as difficult for a person in such a situation as attempting to keep the old code going will be, and you will gain substantial advantages from using idiomatic C code, such as being able to do proper dynamic allocation, linked lists, trees, recursive algorithms, etc. The only provisio I give is that C is a very sharp instrument -- it lacks run time checks. You have to learn to be disciplined to use it well. Sadly, the more appropriate languages for this sort of work have become desperately unpopular... Perry From owner-chemistry@ccl.net Thu Sep 22 16:24:11 2005 From: "CCL" To: CCL Subject: CCL: Knowledge Management in R&D; optimising productivity in knowledge creation, capture, retrieval and transfer Message-Id: <-29282-050922144745-6195-hSeqCdGRdtsQeb5E4Ov3nw]~[server.ccl.net> X-Original-From: Barry Hardy Content-Type: multipart/alternative; boundary="=====================_18486321==_.ALT" Date: Thu, 22 Sep 2005 19:50:10 +0200 Mime-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy]~[tiscalinet.ch] --Replace strange characters with the "at" sign to recover email address--. --=====================_18486321==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed For those of you interested in the management of chemical information in a drug discovery context and increasingly as the industry moves over to collaborative eR&D-based support systems, enterprise ELNs and NL-processing - and at the same time needs to start thinking more and more about strategic knowledge management - you should find reading further below interesting. Barry At our InnovationWell Autumn InterAction meetings (Philadelphia, USA, October 11,12) and (Basel, Switzerland, November 9,10) we are having two interesting day long meeting sessions discussing key strategies, issues and novel solutions with regards to Knowledge Management in Life Science R&D. (list of presentations is enclosed below). Further information on these sessions and others in drug discovery and life science product development is available through the InnovationWell website and members' list (complete the SignUp at http://innovationwell.net/) with abstracts and news also posted on the Ferryman Blog (http://barryhardy.blogs.com/theferryman/). Look forward to seeing you in Philadelphia or Basel! best regards Barry Hardy Community of Practice Manager Douglas Connect, Switzerland +41 61 851 0170 (office) Knowledge Management in R&D, optimising productivity in knowledge creation, capture, retrieval and transfer InnovationWell InterAction Meeting Session, Philadelphia, USA, 12 October 2005 Presenters and Discussion Leaders: The ABCD Project, a Framework for Knowledge Management, Peter Gates (Johnson and Johnson) Enabling Collaboration in a Virtual and Global Drug Discovery R&D Environment : Collaboration - it doesn't just "happen", John Barrett, Principal (ITI Associates) Global Information Integration in R&D, Scott Starry, Senior Product Manager (Symyx IntelliChem) Knowledge Management Case Study Analysis of a Collaborative Life Science R&D Environment, Jeff Spitzner, CSO (Rescentris) An Interactive Environment for Multiparameter Optimization and Knowledge Management, James H Wikel, CTO (Coalesix) Measuring Knowledge Management via Social Network Analysis, Bonnie Montano (Georgetown University) Natural Language Processing for Knowledge Extraction in the Life Sciences, Rosemary Polsky-Newman, VP, Corporate Development (ExerGen Biosciences) Managing Knowledge in Breast Cancer: Converting Clinical, Molecular and Imaging Data into Knowledge, Michael Liebman (Windber Research Institute) Legal Issues in a Knowledge Sharing Environment, James M. Kanagy, Director e-Commerce and Business Method Patents (GlaxoSmithKline) Enterprise Electronic Lab Notebook Case Studies, Rudy Potenzone (CambridgeSoft) Analysis based on Molecular Diversity, Steve Boyer (IBM) InnovationWell Meeting Session, Basel, Switzerland, 9 November 2005 Presenters and Discussion Leaders: ABCD and Combinatorial Library Design, Alan Gibbs (Johnson and Johnson) Assembly, Distribution and Retrieval of Biological Information in Drug Discovery, Kim Henrick, Macromolecular Structure Database (MSD) group leader (European Bioinformatics Insititute) Molecular Architecture to Prepare Structures with Desired Properties: The Integration of Databases and Software into the Day-to-Day Practice of a Medicinal Chemist, Ulrich Jordis (Vienna University of Technology) Ontologies: Real Applications in Pharma, Steve Gardner, CTO (Biowisdom) Pharmaceutical Development and the use of Electronic Lab Notebooks, Michael Swartz, VP, Knowledge Management (CambridgeSoft) Global Information Integration in R&D, Pierre Allemand, Director, Business Development (Symyx AG) Strategic Knowledge Management in Life Science Research, Victor Newman (The Knowledgeworks) Aggregation, Filtering and Alerting of Scientific Information from Multiple Sources, Mark Sharp (Corpora) Global Roll Out of an Electronic Notebook at Schering AG, Rolf Jautelat (Schering AG) Registration to attend the meetings or to access virtually is available through the InnovationWell website at http://innovationwell.net/ or through contacting Nicki Douglas (nicki.douglas at douglasconnect.com) Barry Hardy, PhD Douglas Connect, Switzerland +41 61 851 0170 (office) www.douglasconnect.com --=====================_18486321==_.ALT Content-Type: text/html; charset="us-ascii" For those of you interested in the management of chemical information in a drug discovery context and increasingly as the industry moves over to collaborative eR&D-based support systems, enterprise ELNs and NL-processing - and at the same time needs to start thinking more and more about strategic knowledge management  - you should find reading further below interesting.

Barry

At our InnovationWell Autumn InterAction meetings (Philadelphia, USA, October 11,12) and (Basel, Switzerland, November 9,10) we are having two interesting day long meeting sessions discussing key strategies, issues and novel solutions with regards to Knowledge Management in Life Science R&D.  (list of presentations is enclosed below).  Further information on these sessions and others in drug discovery and life science product development is available through the InnovationWell website and members' list (complete the SignUp at http://innovationwell.net/) with abstracts and news also posted on the Ferryman Blog (http://barryhardy.blogs.com/theferryman/). 

Look forward to seeing you in Philadelphia or Basel!

best regards
Barry Hardy
Community of Practice Manager
Douglas Connect, Switzerland
+41 61 851 0170 (office)


Knowledge Management in R&D, optimising productivity in knowledge creation,
capture, retrieval and transfer

InnovationWell InterAction Meeting Session, Philadelphia, USA, 12 October 2005

Presenters and Discussion Leaders:
The ABCD Project, a Framework for Knowledge Management, Peter Gates (Johnson and Johnson)
Enabling Collaboration in a Virtual and Global Drug Discovery R&D Environment : Collaboration - it doesn抰 just "happen", John Barrett, Principal (ITI Associates)
Global Information Integration in R&D, Scott Starry, Senior Product Manager (Symyx IntelliChem)
Knowledge Management Case Study Analysis of a Collaborative Life Science R&D Environment, Jeff Spitzner, CSO (Rescentris)
An Interactive Environment for Multiparameter Optimization and Knowledge Management, James H Wikel, CTO (Coalesix)
Measuring Knowledge Management via Social Network Analysis, Bonnie Montano (Georgetown University)
Natural Language Processing for Knowledge Extraction in the Life Sciences, Rosemary Polsky-Newman, VP, Corporate Development (ExerGen Biosciences)
Managing Knowledge in Breast Cancer: Converting Clinical, Molecular and Imaging Data into Knowledge, Michael Liebman (Windber Research Institute)
Legal Issues in a Knowledge Sharing Environment, James M. Kanagy, Director e-Commerce and Business Method Patents (GlaxoSmithKline)
Enterprise Electronic Lab Notebook Case Studies, Rudy Potenzone (CambridgeSoft)
Analysis based on Molecular Diversity, Steve Boyer (IBM)

InnovationWell  Meeting Session, Basel, Switzerland, 9 November 2005

Presenters and Discussion Leaders:
ABCD and Combinatorial Library Design, Alan Gibbs (Johnson and Johnson)
Assembly, Distribution and Retrieval of Biological Information in Drug Discovery, Kim Henrick, Macromolecular Structure Database (MSD) group leader (European Bioinformatics Insititute)
Molecular Architecture to Prepare Structures with Desired Properties: The Integration of Databases and Software into the Day-to-Day Practice of a Medicinal Chemist, Ulrich Jordis (Vienna University of Technology)
Ontologies: Real Applications in Pharma, Steve Gardner, CTO (Biowisdom)
Pharmaceutical Development and the use of Electronic Lab Notebooks, Michael Swartz, VP, Knowledge Management (CambridgeSoft)
Global Information Integration in R&D, Pierre Allemand, Director, Business Development (Symyx AG)
Strategic Knowledge Management in Life Science Research, Victor Newman (The Knowledgeworks)
Aggregation, Filtering and Alerting of Scientific Information from Multiple Sources, Mark Sharp (Corpora)
Global Roll Out of an Electronic Notebook at Schering AG, Rolf Jautelat (Schering AG)


Registration to attend the meetings or to access virtually is available through the InnovationWell website at http://innovationwell.net/ or through contacting Nicki Douglas (nicki.douglas at douglasconnect.com)


Barry Hardy, PhD
Douglas Connect, Switzerland
+41 61 851 0170 (office)
www.douglasconnect.com

--=====================_18486321==_.ALT-- From owner-chemistry@ccl.net Thu Sep 22 16:25:50 2005 From: "CCL" To: CCL Subject: CCL: Applying the Semantic Web to Drug Discovery and Development; Web Services Message-Id: <-29283-050922144955-7381-o80D67vVBtiLxWnyey+vTg : server.ccl.net> X-Original-From: Barry Hardy Content-Type: multipart/alternative; boundary="=====================_18469486==_.ALT" Date: Thu, 22 Sep 2005 19:49:53 +0200 Mime-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy : tiscalinet.ch] --Replace strange characters with the "at" sign to recover email address--. --=====================_18469486==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed At our InnovationWell Autumn InterAction meetings (Philadelphia, USA, October 11,12) and (Basel, Switzerland, November 9,10) we are progressing our InnovationWell "Applying the Semantic Web to Drug Discovery and Development" program with two sessions concentrating on Web Services. Generally we will not particularly concentrate on the IT and technical aspects of the semantic web (although they certainly will not be ignored :!) - rather the InnovationWell approach is more to engage in discussions on how to advance key business issues in drug discovery, development and safety incorporating practices, processes and technologies that enable innovation and progress in the life science and healthcare sectors. (That said we have some very good technical people presenting in these web services sessions!) Look forward to seeing you in Philadelphia or Basel. best regards Barry Hardy InnovationWell Community of Practice Manager http://innovationwell.net/ Douglas Connect, Switzerland +41 61 851 0170 (office) Applying the Semantic Web to Drug Discovery and Development Applications of Web-based Services in Drug Discovery Pharmaceutical research is under challenge to improve the choice, quality and safety of lead candidates. There is a clear need for an open discussion and an awareness of the requirements for a much more complex knowledge management and knowledge transfer between academic, government and commercial interests. The semantic web has the potential to make significant contributions to the drug discovery of the future but is at this time at an early development stage and there are only a few public tools for the data mining and sharing of chemical information. Just a few years ago, the only imaginable way of doing in silico drug design - or, indeed, any cheminformatics research - was to use in-house and commercial software and databases. New developments in Web services however are offering today's researchers additional resources. Although cheminformatics admittedly lags far behind bioinformatics (where an enormous wealth of data and software is literally a click away), we are beginning to see some chemical resources in open access. A goal for this program on "Web-based Services in Drug Design" is to present some of the possibilities of web-based tools and data and to lead into discussions on how can web services work for both the academic world and industry, while maintaining commercial, ip and security concerns? What potential impact could they have on discovery productivity? What are the best sustainable business models that can be applied to such services? How significant are the benefits of increased upstream and downstream knowledge flow due to services based on ontology frameworks? What are the key current hindrances to be overcome for the integration of web services into drug discovery in the chemical information area? InterAction Meeting Session "Applications of Web-based Services in Drug Discovery" Joint InnovationWell and eCheminfo Meetings http://innovationwell.net/ and http://eCheminfo.com/ Philadelphia, USA, 11 October 2005 chaired by Marc Nicklaus (National Institutes of Health) Presenters & Discussion Leaders: A Web-based Chemoinformatics System for Drug Discovery, Brett Tounge (Johnson & Johnson Pharmaceutical Research & Development, LLC) Web enabling technology for the design, enumeration, optimization and tracking of compound libraries, Brad Feuston (Merck) Web-Based Services of the National Cancer Institute's CADD Group, Marc Nicklaus (NIH) ZINC web services - providing 3D structures of purchasable compounds for virtual screening to humans and machines, John Irwin (UCSF) Pubchem, Steve Bryant (NCBI) Search-and-query Information System for the Study and Discovery of Novel Agents in the Treatment of Cancer, David Covell (National Cancer Institute) High-performance Applications Based on Web Services: It's Not an Oxymoron. The Use of Web Services in the ABCD Drug Discovery Platform, Dmitrii Rassokhin (Johnson & Johnson Pharmaceutical Research & Development, LLC) Basel, Switzerland, 10 November 2005 chaired by Kim Henrick (European Bioinformatics Institute) Presenters & Discussion Leaders: Investigating chemical trends in the context of ligand-protein complexes by using on-line data analysis directly on the web, Dimitris Dimitropoulos (European Bioinformatics Institute) The Representation of Chemical Structures and its Application to Property Prediction, Johann Gasteiger (Universitaet Erlangen-Nuernberg) Open Archives as a Route for the Capture, Dissemination and Access to Chemical Information, Simon Coles (University of Southampton) Identification of biological units in protein crystals, Eugene Krissinel (European Bioinformatics Institute) SWISS-MODEL Server and Repository: Web based resources for comparative protein structure modeling and their application in drug discovery, Torsten Schwede (University of Basel) Further information on this program and others and on registration to attend the meetings or to access virtually is available through the InnovationWell and eCheminfo websites. Barry Hardy, PhD Douglas Connect, Switzerland +41 61 851 0170 (office) www.douglasconnect.com --=====================_18469486==_.ALT Content-Type: text/html; charset="us-ascii"
At our InnovationWell Autumn InterAction meetings (Philadelphia, USA, October 11,12) and (Basel, Switzerland, November 9,10) we are progressing our InnovationWell "Applying the Semantic Web to Drug Discovery and Development" program with two sessions concentrating on Web Services.

Generally we will not particularly concentrate on the IT and technical aspects of the semantic web (although they certainly will not be ignored :!) - rather the InnovationWell approach is more to engage in discussions on how to advance key business issues in drug discovery, development and safety incorporating practices, processes and technologies that enable innovation and progress in the life science and healthcare sectors.  (That said we have some very good technical people presenting in these web services sessions!)

Look forward to seeing you in Philadelphia or Basel.

best regards
Barry Hardy
InnovationWell Community of Practice Manager
http://innovationwell.net/
Douglas Connect, Switzerland
+41 61 851 0170 (office)


Applying the Semantic Web to Drug Discovery and Development

Applications of Web-based Services in Drug Discovery
Pharmaceutical research is under challenge to improve the choice, quality and safety of lead candidates. There is a clear need for an open discussion and an awareness of the requirements for a much more complex knowledge management and knowledge transfer between academic, government and commercial interests. The semantic web has the potential to make significant contributions to the drug discovery of the future but is at this time at an early development stage and there are only a few public tools for the data mining and sharing of chemical information.

Just a few years ago, the only imaginable way of doing in silico drug design - or, indeed, any cheminformatics research - was to use in-house and commercial software and databases. New developments in Web services however are offering today抯 researchers additional resources. Although cheminformatics admittedly lags far behind bioinformatics (where an enormous wealth of data and software is literally a click away), we are beginning to see some chemical resources in open access.

A goal for this program on "Web-based Services in Drug Design" is to present some of the possibilities of web-based tools and data and to lead into discussions on how can web services work for both the academic world and industry, while maintaining commercial, ip and security concerns? What potential impact could they have on discovery productivity? What are the best sustainable business models that can be applied to such services? How significant are the benefits of increased upstream and downstream knowledge flow due to services based on ontology frameworks? What are the key current hindrances to be overcome for the integration of web services into drug discovery in the chemical information area?
        
InterAction Meeting Session "Applications of Web-based Services in Drug Discovery"
Joint InnovationWell and eCheminfo Meetings
http://innovationwell.net/ and http://eCheminfo.com/

Philadelphia, USA, 11 October 2005
chaired by Marc Nicklaus (National Institutes of Health)

Presenters & Discussion Leaders:
A Web-based Chemoinformatics System for Drug Discovery, Brett Tounge (Johnson & Johnson Pharmaceutical Research & Development, LLC)
Web enabling technology for the design, enumeration, optimization and tracking of compound libraries, Brad Feuston (Merck)
Web-Based Services of the National Cancer Institute抯 CADD Group, Marc Nicklaus (NIH)
ZINC web services - providing 3D structures of purchasable compounds for virtual screening to humans and machines, John Irwin (UCSF)
Pubchem, Steve Bryant (NCBI)
Search-and-query Information System for the Study and Discovery of Novel Agents in the Treatment of Cancer, David Covell (National Cancer Institute)
High-performance Applications Based on Web Services: It's Not an Oxymoron. The Use of Web Services in the ABCD Drug Discovery Platform, Dmitrii Rassokhin (Johnson & Johnson Pharmaceutical Research & Development, LLC)


Basel, Switzerland, 10 November 2005
chaired by Kim Henrick (European Bioinformatics Institute)

Presenters & Discussion Leaders:
Investigating chemical trends in the context of ligand-protein complexes by using on-line data analysis directly on the web, Dimitris Dimitropoulos (European Bioinformatics Institute)
The Representation of Chemical Structures and its Application to Property Prediction, Johann Gasteiger (Universitaet Erlangen-Nuernberg)
Open Archives as a Route for the Capture, Dissemination and Access to Chemical Information, Simon Coles (University of Southampton)
Identification of biological units in protein crystals, Eugene Krissinel (European Bioinformatics Institute)
SWISS-MODEL Server and Repository: Web based resources for comparative protein structure modeling and their application in drug discovery, Torsten Schwede (University of Basel)


Further information on this program and others and on registration to attend the meetings or to access virtually is available through the InnovationWell and eCheminfo websites.


Barry Hardy, PhD
Douglas Connect, Switzerland
+41 61 851 0170 (office)
www.douglasconnect.com

--=====================_18469486==_.ALT-- From owner-chemistry@ccl.net Thu Sep 22 16:59:50 2005 From: "CCL" To: CCL Subject: CCL: Cleaning up dusty deck fortran and converting to C/C++ Message-Id: <-29284-050922164115-10282-2Qergr/O4i9bYJNCuk4H3w:_:server.ccl.net> X-Original-From: "Marcus Martin" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 22 Sep 2005 13:55:29 -0600 MIME-Version: 1.0 Sent to CCL by: "Marcus Martin" [marmart:_:sandia.gov] --Replace strange characters with the "at" sign to recover email address--. On Sep 21, 2005, at 9:37 PM, CCL wrote: > Speaking as someone who was initially trained in computer science, not > chemistry, you are very unlikely to get decent/maintainable results > this way. Fortran, especially old Fortrans like Fortran 77, lacks the > ability to create real data structures and the ability to do > recursion. There is no point in translating such code except if you > simply want to run it unchanged and maintain the code in Fortran > (i.e. if you're using f2c as a pure compiler) -- you will ultimately > save enormous amounts of time rewriting it, even for very large > programs. Actually, I believe a reason has recently appeared as the new gcc 4 build from GNU has unfortunately removed the old g77 functionality and replaced it with a Fortran 95 compiler which appears (in some of my very preliminary tests) to produce code that is not as memory efficient as the old code. > I've seen many efforts in my Computer Science professional career in > which people attempted to keep old code alive at all costs -- and in > each case, it ended up costing far more human labor and far more money > than a straight rewrite would cost. Rewriting, using the original code > as a model and as a mechanism for validating regression tests, is > often a superior solution. Alas, I have also seen some very high profile cases where old Fortran codes were discarded in favor of new "object orientated C++" codes that still have yet to match the old "legacy" codes they were supposed to replace. Good or bad code can be written in many languages. Besides, rewriting 200,000 lines of Fortran into a new language while simultaneously changing all of the data structures is a pretty darn big task that doesn't result in any publications. If I were ever to replace my Fortran code with C I would initially translate and then begin changing some of the data structures as desired within the new framework. Arrays are still the most efficient data structure for many tasks, but it would be nice to have a few linked lists and some memory allocation once in a while. Plus, if a machine has a complier it certainly has a C compiler so portability is very good for ANSI C codes. Marcus ------------------------------------------------------------------- Marcus G. Martin Senior Member of Technical Staff Multiscale Computational Materials Methods Sandia National Laboratories PO Box 5800 MS 1110 Albuquerque NM 87185-1110 v. 505 284-6355 f. 505 845-7442 http://www.cs.sandia.gov/marcusmartin/ http://towhee.sourceforge.net ------------------------------------------------------------------- Marcus G. Martin Senior Member of Technical Staff Multiscale Computational Materials Methods Sandia National Laboratories PO Box 5800 MS 1110 Albuquerque NM 87185-1110 v. 505 284-6355 f. 505 845-7442 http://www.cs.sandia.gov/marcusmartin/ http://towhee.sourceforge.net From owner-chemistry@ccl.net Thu Sep 22 23:40:59 2005 From: "CCL" To: CCL Subject: CCL: multi-reference CI Message-Id: <-29286-050922195329-8774-V2krR9zCct+W7wrobbVq0A-#-server.ccl.net> X-Original-From: "Robert Gdanitz" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 22 Sep 2005 19:08:01 -0400 MIME-Version: 1.0 Sent to CCL by: "Robert Gdanitz" [gdanitz-#-ncat.edu] --Replace strange characters with the "at" sign to recover email address--. Then there is Amica, http://gdanitz.hec.utah.edu/amica, for explicit correlated (r12-) MR-CI(SD) and ACPF like methods, but one can also perform the corresponding traditional calculations (i.e. without linear r12-terms). The input is (by chance) similar to the one of NWChem. Robert Gdanitz --- "Success is the ability to go from one failure to another with no loss of enthusiasm" Winston Churchill From owner-chemistry@ccl.net Thu Sep 22 23:40:59 2005 From: "CCL" To: CCL Subject: CCL: PCM-ONIOM input ? Message-Id: <-29285-050922205508-12057-ojeTGSJ58dQiffzb3z0E2Q{=}server.ccl.net> X-Original-From: ying xiong Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=gb2312 Date: Fri, 23 Sep 2005 08:54:59 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: ying xiong [xiongying96{=}yahoo.com.cn] --Replace strange characters with the "at" sign to recover email address--. Dear sir， >That is posible to do PCM/ONIOM, you can see >the gaussian manual: >http://www.gaussian.com/iops.htm >in Overlay 5/94 >good luck Thank for for your help! I try it, but I failed. I get the following information: --------------------------------------------------# oniom(B3LYP/sto-3g:amber=softfirst) geom=connectivity scrf=(pcm,solv ent=water) IOp(5/94=0) ------------------------------------------------- No SCRF with ONIOM. Error termination via Lnk1e in /usr/local/g03/l1.exe at Fri Sep 23 02:02:22 2005. Could you please give me an example on how to set the input for PCM/ONIOM ? ___________________________________________________________ 雅虎邮箱超强增值服务－2G超大空间、pop3收信、无限量邮件提醒 http://cn.mail.yahoo.com