From owner-chemistry@ccl.net Fri Oct 29 03:16:01 2010 From: "George Lawrence geoe2]-[hotmail.com" To: CCL Subject: CCL: Thank You Message-Id: <-43031-101027053156-2630-HUxe212LcWIrK3mOVXVbIA(_)server.ccl.net> X-Original-From: "George Lawrence" Date: Wed, 27 Oct 2010 05:31:55 -0400 Sent to CCL by: "George Lawrence" [geoe2..hotmail.com] Thank you all fo your responses, it has been very helpful. Regards George From owner-chemistry@ccl.net Fri Oct 29 04:25:00 2010 From: "Matt Segall matt.segall{}optibrium.com" To: CCL Subject: CCL: New Paper: Making Priors a Priority Message-Id: <-43032-101029042158-6597-lSavQdbgNqz9rAZl5pJVWQ_+_server.ccl.net> X-Original-From: "Matt Segall" Date: Fri, 29 Oct 2010 04:21:57 -0400 Sent to CCL by: "Matt Segall" [matt.segall---optibrium.com] A new paper, "Making Priors a Priority" addresses a key challenge the community needs to address to get the most out of the predictive models we build. Just published on-line in J. Comp. Aided Mol. Design (DOI 10.1007/s10822-010-9388- 7), the paper discusses the question, "How useful will a model be in making a decision in a practical context?" To answer this requires an understanding of the prior probability distribution (the prior) and hence prevalence of negative outcomes due to the property being assessed. The full paper can be downloaded from the Springer website at http://www.springerlink.com/content/x15h763770611316/ or a free preprint is available from the Optibrium on-line community at http://www.optibrium.com/community/publications/110-making-priors-a-priority. From owner-chemistry@ccl.net Fri Oct 29 08:46:00 2010 From: "wuxiao xiaowu759]~[hotmail.com" To: CCL Subject: CCL: oplsaa force field parameter of EPON862 containing -CH2- group linked to two phenyl Message-Id: <-43033-101029050344-14555-/XuwdWNfG2AtSUTC08/R8A[*]server.ccl.net> X-Original-From: wuxiao Content-Type: multipart/alternative; boundary="_23880ecb-b330-467e-8084-b4315de4033f_" Date: Fri, 29 Oct 2010 17:03:32 +0800 MIME-Version: 1.0 Sent to CCL by: wuxiao [xiaowu759 a hotmail.com] --_23880ecb-b330-467e-8084-b4315de4033f_ Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 8bit Dear CCLers, I want to simulate an epoxy resin, EPON862, using oplsaa force field in gromacs. In the molecules, there are -CH2- group which are linked to two phenyl. In the parameter file of oplsaa force field, I can not find the suitable atom type for the C atoms. Instead, I had tried the opls_149 (CH3, toluene) or opls_148(CH2, ethyl benzene), which led to fatal errors. One of possible solution to my problem can be creating new atom type for -CH2-, but it is very hard work to optimize the parameters. So, have you happened to simulate/find such a similar molecule(there are -CH2- group which are linked to two phenyl) in the format of oplsaa force field? If yes, please kindly give me the references. Thanks a lot! yours sincerely, Chaofu Wu, Dr. --_23880ecb-b330-467e-8084-b4315de4033f_ Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: 8bit
Dear CCLers,
  I want to simulate an epoxy resin, EPON862, using oplsaa force field in gromacs. In the molecules, there are -CH2- group which are linked to two phenyl. In the parameter file of oplsaa force field, I can not find the suitable atom type for the C atoms. Instead, I had tried the opls_149 (CH3, toluene) or opls_148(CH2, ethyl benzene), which led to fatal errors. One of possible solution to my problem can be creating new atom type for -CH2-, but it is very hard work to optimize the parameters. So, have you happened to simulate/find such a similar molecule(there are -CH2- group which are linked to two phenyl) in the format of oplsaa force field? If yes, please kindly give me the references. Thanks a lot! 
yours sincerely,
Chaofu Wu, Dr.
--_23880ecb-b330-467e-8084-b4315de4033f_-- From owner-chemistry@ccl.net Fri Oct 29 09:21:00 2010 From: "Vincent Leroux vincent.leroux : loria.fr" To: CCL Subject: CCL: New Paper: Making Priors a Priority Message-Id: <-43034-101029075818-11483-o+NvvOKiLTeair8dvFt/Jg-$-server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 29 Oct 2010 13:58:08 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux=loria.fr] Dear Matt Segall, You forgot to mention that you actually wrote this paper. Just imagine how this mailing list would look like if every scientist out there would advertise his/her last paper. Plus you dare call an "on-line community" part of the website of the commercial company you work for. By looking at the forum seems like "community" might be a little bit to big a word to describe it, but it is for sure a more adequate place for your post ;-) If it was a Science or Nature paper about computational chemistry, I would be happy to get the opportunity to discuss with the authors here, but well, even if your paper might be interesting we are still far from there... "How useful will a model be in making a decision in a practical context?". I want to know too! Two nice corporate keywords "making a decision" and "practical context" for the price of one: well done! Congratulations for "Making Priors a Priority". Awesome title! "To answer this requires an understanding of the prior probability distribution (the prior) and hence prevalence of negative outcomes due to the property being assessed.": sure this is right! May I add: "It also requires an understanding of the present probability distribution (the present) and hence actual significance of the property being assessed, and an understanding of the future probability (the prospect) that things will still make some kind of sense, provided that prior of present did". Oh wait, I did not read the paper yet, maybe it is in the conclusion already, just before the usual "These interesting questions will be investigated in future works" that could be called "Making Presents Presentable" and "Prospecting Prospects". Regards, VL Le 29/10/10 10:21, Matt Segall matt.segall{}optibrium.com a écrit : > Sent to CCL by: "Matt Segall" [matt.segall---optibrium.com] > A new paper, "Making Priors a Priority" addresses a key challenge the community > needs to address to get the most out of the predictive models we build. Just > published on-line in J. Comp. Aided Mol. Design (DOI 10.1007/s10822-010-9388- > 7), the paper discusses the question, "How useful will a model be in making a > decision in a practical context?" To answer this requires an understanding of > the prior probability distribution (the prior) and hence prevalence of > negative outcomes due to the property being assessed. > > The full paper can be downloaded from the Springer website at > http://www.springerlink.com/content/x15h763770611316/ or a free preprint is > available from the Optibrium on-line community at > http://www.optibrium.com/community/publications/110-making-priors-a-priority.> > > From owner-chemistry@ccl.net Fri Oct 29 09:56:00 2010 From: "Chaofu Wu xiaowu759===hotmail.com" To: CCL Subject: CCL: oplsaa force field parameter of EPON862 Message-Id: <-43035-101029050721-21425-uzlduPO5zokyq9rb93Gyew]*[server.ccl.net> X-Original-From: "Chaofu Wu" Date: Fri, 29 Oct 2010 05:07:20 -0400 Sent to CCL by: "Chaofu Wu" [xiaowu759||hotmail.com] Dear CCLers, I want to simulate an epoxy resin, EPON862, using oplsaa force field in gromacs. In the molecules, there are -CH2- group which are linked to two phenyl. In the parameter file of oplsaa force field, I can not find the suitable atom type for the C atoms. Instead, I had tried the opls_149 (CH3, toluene) or opls_148(CH2, ethyl benzene), which led to fatal errors. One of possible solution to my problem can be creating new atom type for -CH2-, but it is very hard work to optimize the parameters. So, have you happened to simulate/find such a similar molecule(there are -CH2- group which are linked to two phenyl) in the format of oplsaa force field? If yes, please kindly give me the references. Thanks a lot! yours sincerely, Chaofu Wu, Dr. From owner-chemistry@ccl.net Fri Oct 29 18:05:01 2010 From: "Shirley Peng speng]-[chemcomp.com" To: CCL Subject: CCL: CCG announces the new version of PSILO Message-Id: <-43036-101029153136-32268-PVNF/iyjTmpGFtZT4jiivg _ server.ccl.net> X-Original-From: "Shirley Peng" Date: Fri, 29 Oct 2010 15:31:35 -0400 Sent to CCL by: "Shirley Peng" [speng(-)chemcomp.com] CHEMICAL COMPUTING GROUP ANNOUNCES THE NEW VERSION OF THEIR PROTEIN STRUCTURE DATABASE SYSTEM: PSILO MONTREAL, Canada October 29, 2010 Chemical Computing Group (CCG) is happy to announce the release of PSILO version 2010.09. PSILO is a protein structure database system that allows for an integrated repository of proprietary and non-proprietary structural data. With PSILO, experimental and computational macromolecular structural data can be registered, annotated, tracked and shared across organizational departments. PSILO provides powerful bioinformatics and cheminformatics searches with analysis and visualization capabilities through a standard web browser interface. Some of the new and enhanced capabilities in PSILO 2010.09 are: * 3D searches for protein-ligand and protein-protein interactions * Faster pocket similarity searching * Automatic protein kinase annotation to identify the hinge, HRD motif, G-loop, etc., regions PSILOs simple yet powerful Google-like search bar allows researchers to apply multiple combinations of text, sequence, 2D substructure and 3D geometry to their search criteria. Were pleased to announce PSILO 2010.09, a product with superior capabilities than competing protein structure databases in the market mentioned Paul Labute, president and CEO of CCG. With PSILOs new powerful 3D search, researchers can now query structural data directly from standard sketchers, facilitating searches for common contacts and other motifs in the protein structure database added Paul. PSILO 2010.09 comes with a faster and enhanced pocket similarity search. It automatically maintains a pocket database with an annotated ligand environment. Paul Labute said, PSILO can search for and score similar binding pockets in dissimilar proteins, allowing organizations to identify cases of convergent evolution and off-target binding, recognizing potential side effects or new possible therapeutic areas. Another addition in the 2010.09 version is the automatic performance of bioinformatics annotations for all deposited structures: assignment of domain identifiers, Gene Ontology terms, SCOP classes, antibody CDR regions, kinase domain regions and BLAST neighbors. For additional information about PSILO please contact: info|-|chemcomp.com About Chemical Computing Group Chemical Computing Group (CCG) is a leading supplier of software solutions for Life Sciences. CCG has been in business since 1994, always providing state of the art applications in Drug Discovery to Pharmaceutical, Biotech and Academic researcher. CCGs products and services are used by biologists, medicinal chemists and computational chemists throughout the world. Chemical Computing Group has a proven track record in scientific innovation, consistently producing releases and upgrades for all their products. CCG has a very strong reputation for collaborative scientific support, maintaining support offices in both Europe and North America. CCG headquarter is in Montreal, Canada. For more information visit: www.chemcomp.com For additional information please contact: Raul Alvarez Senior Marketing Manager (514) 393-1055 ralvarez|-|chemcomp.com From owner-chemistry@ccl.net Fri Oct 29 20:21:01 2010 From: "Eric Scerri scerri.:.chem.ucla.edu" To: CCL Subject: CCL: question on Born-Oppenheimer approx. Message-Id: <-43037-101029202000-2771-bFQrZCGGMdMn51hbM5GiaQ{=}server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-27-853188524 Date: Fri, 29 Oct 2010 17:20:33 -0700 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Eric Scerri [scerri*o*chem.ucla.edu] --Apple-Mail-27-853188524 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit Dear CCL'ers For many years now a few theoretical chemists (Primas, Woolley, Sutcliffe) have claimed that there is something significant going on in connection with the Born-Oppenheimer approximation. They claim that applying the approximation amounts to writing the structure of a molecule in 'by hand' rather than the structure being inherent in the quantum formalism. They cite examples such as C2H5OH and CH3OCH3 which share the same Hamiltonian and conclude that structure cannot therefore be deduced > from QM in an ab initio fashion. Some philosophers of chemistry have taken this a good deal further as a sign that chemistry (molecular structure) cannot be strictly reduced to quantum mechanics. Some even claim that there is 'emergence' taking place. Most chemists I have discussed this issue with claim that these philosophers and even the theoretical chemists mentioned above are reaching incorrect conclusions. Most chemists claim that structure does really exist as a matter of fact and that we could in principle solve the Schrodinger equation without fixing the position of the nuclei by solving the equation for every conceivable arrangement and would thereby recover the inherent structure. I would be interested in comments and have a follow-up question if there is any interest in this topic. all the best, eric scerri Eric Scerri, The Periodic Table, Its Story and Its Significance, Oxford University Press, 2007 http://www.oup.com/us/catalog/general/subject/Chemistry/?view=usa&ci=9780195305739 --Apple-Mail-27-853188524 Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable

Dear = CCL'ers

For many years now a few theoretical = chemists (Primas, Woolley, Sutcliffe) have claimed that there is = something significant going on in connection with the Born-Oppenheimer = approximation.  

They claim that applying = the approximation amounts to writing the structure of a molecule in 'by = hand' rather than the structure being inherent in the quantum formalism. =  

They cite examples such as C2H5OH and = CH3OCH3 which share the same Hamiltonian and conclude that structure = cannot therefore be deduced from QM in an ab initio fashion. =  

Some philosophers of chemistry have = taken this a good deal further as a sign that chemistry (molecular = structure) cannot be strictly reduced to quantum mechanics.  Some = even claim that there is 'emergence' taking place. =  

Most chemists I have discussed this = issue with claim that these philosophers and even the theoretical = chemists mentioned above are reaching incorrect conclusions.  Most = chemists claim that structure does really exist as a matter of fact and = that we could in principle solve the Schrodinger equation without fixing = the position of the nuclei by solving the equation for every conceivable = arrangement and would thereby recover the inherent structure. =  

I would be interested in comments and = have a follow-up question if there is any interest in this topic.   =    

all the best,
eric = scerri



Eric Scerri, The Periodic Table, Its Story and Its Significance, = Oxford University Press, 2007

=


= --Apple-Mail-27-853188524-- From owner-chemistry@ccl.net Fri Oct 29 23:11:00 2010 From: "N. Sukumar nagams%x%rpi.edu" To: CCL Subject: CCL: question on Born-Oppenheimer approx. Message-Id: <-43038-101029230855-22986-OIx7Prv3tRih/ECs50966w[#]server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Fri, 29 Oct 2010 23:09:10 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams^_^rpi.edu] I would say that the question of THE inherent structure is ill-defined (unless you care to specify what you mean). Do you mean the lowest total energy state of a specified number of electrons and specified nuclei? Or do you mean the lowest energy structure of a specified 2D formula (such as C2H5OH or CH3OCH3) or 2D structure? Or do you mean the most probable instantaneous configuration at a given temperature? In general, there are Born-Oppenheimer-like structures that can be thought of as being preferentially populated in a statistical ensemble at a given temperature. (C2H5OH and CH3OCH3 only share the same total single-molecule Hamiltonian). Dr. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research http://reccr.chem.rpi.edu/ -------------------------- "It is nice to know that the computer understands the problem. But I would like to understand it too." -- Eugene P. Wigner ==============Original message text=============== On Fri, 29 Oct 2010 20:20:33 EDT "Eric Scerri scerri.:.chem.ucla.edu" wrote: Dear CCL'ers For many years now a few theoretical chemists (Primas, Woolley, Sutcliffe) have claimed that there is something significant going on in connection with the Born-Oppenheimer approximation. They claim that applying the approximation amounts to writing the structure of a molecule in 'by hand' rather than the structure being inherent in the quantum formalism. They cite examples such as C2H5OH and CH3OCH3 which share the same Hamiltonian and conclude that structure cannot therefore be deduced > from QM in an ab initio fashion. Some philosophers of chemistry have taken this a good deal further as a sign that chemistry (molecular structure) cannot be strictly reduced to quantum mechanics. Some even claim that there is 'emergence' taking place. Most chemists I have discussed this issue with claim that these philosophers and even the theoretical chemists mentioned above are reaching incorrect conclusions. Most chemists claim that structure does really exist as a matter of fact and that we could in principle solve the Schrodinger equation without fixing the position of the nuclei by solving the equation for every conceivable arrangement and would thereby recover the inherent structure. I would be interested in comments and have a follow-up question if there is any interest in this topic. all the best, eric scerri Eric Scerri, The Periodic Table, Its Story and Its Significance, Oxford University Press, 2007 http://www.oup.com/us/catalog/general/subject/Chemistry/?view=usa&ci=9780195305739 ===========End of original message text===========