From noy@einstein.sc.mahidol.ac.th Thu Nov 13 01:32:43 1997 Received: from einstein.sc.mahidol.ac.th for noy@einstein.sc.mahidol.ac.th by www.ccl.net (8.8.3/950822.1) id BAA23152; Thu, 13 Nov 1997 01:12:02 -0500 (EST) Received: (from noy@localhost) by einstein.sc.mahidol.ac.th (8.7.6/8.7.3) id NAA23169 for chemistry@www.ccl.net; Thu, 13 Nov 1997 13:02:35 -0700 From: "Dr. Teerakiat Kerdcharoen" Message-Id: <199711132002.NAA23169@einstein.sc.mahidol.ac.th> Subject: geometry of poly(p-phenylene vinylene) To: chemistry@www.ccl.net Date: Thu, 13 Nov 1997 13:02:35 -0700 (GMT+7) Content-Type: text Dear allied scientists, I am doing molecular modeling research on some type of polymers. I would like to get experimental geometry of PPV (poly p-phenylene vinylene) either monomer or oligomers if the x-ray data of full polymer might not be available. Other relevant informations, i.e. derivatives of PPV are very much appreciated. Thank you for your kind answers in advance, Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen, Ph.D. Profession: Lecturer and Information Technology Consultant Address: Department of Physics, Mahidol University, Bangkok 10400 Phone: 2461381 FAX 2461381 Homepage: http://einstein.sc.mahidol.ac.th/noy/ Research: Computer Aided Molecular Design (CAMD) ----------------------------------------------------------------------------- From jsl@virgil.ruc.dk Thu Nov 13 07:32:48 1997 Received: from emma.ruc.dk for jsl@virgil.ruc.dk by www.ccl.net (8.8.3/950822.1) id GAA24269; Thu, 13 Nov 1997 06:35:20 -0500 (EST) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by emma.ruc.dk (8.8.5/8.8.5) with ESMTP id MAA12267; Thu, 13 Nov 1997 12:41:16 +0100 (MET) Received: from VIRGIL/MAILQUEUE by virgil.ruc.dk (Mercury 1.21); 13 Nov 97 12:35:01 +0100 Received: from MAILQUEUE by VIRGIL (Mercury 1.21); 13 Nov 97 12:34:53 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "E. Lewars" Date: Thu, 13 Nov 1997 12:34:52 +0100 Subject: CCL:EHM TODAY--OPINIONS CC: chemistry@www.ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <12E8ED4951@virgil.ruc.dk> Wed, 1997 Nov 12, E. Lewars: > Subj: Extended Hueckel Today--opinions > > Hello, What do people out there in netland think of the *current* status of the > extended Hueckel method that was popularized by Roald Hoffmann, starting > ca. 1963? It was, I think, the first generally applicable method, in the > sense that it was not limited to planar pi electron arrays and could in > principle perform geometry optimizations. Is it the general view that it is > essentially obsolete, having been displaced by more sophisticated methods like > MNDO and its decendants AM1 and PM3? Does it have some advantages over AM1 > and PM3? EHM does have one fundamental advantage over AM1, PM3 and other NDO-type theories: It is based on a proper treatment of atomic orbital (AO) overlap and thus includes terms that are neglected in NDO theories. For example, the repulsion between closed shells is a second order overlap effect, that is not reproduced by NDO theories. This leads to situations where EHM is superior to NDO theory. e.g., Tetrahedron 39, 3345 (1983). Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From ticky@soma.niif.spb.su Thu Nov 13 09:32:49 1997 Received: from doors.ptc.spbu.ru for ticky@soma.niif.spb.su by www.ccl.net (8.8.3/950822.1) id IAA24765; Thu, 13 Nov 1997 08:52:13 -0500 (EST) Received: from soma.niif.spb.su (soma.phys.spbu.ru [193.125.196.76]) by doors.ptc.spbu.ru (8.8.5/8.7.3/OL.cf-2.3) with SMTP id QAA04118 for ; Thu, 13 Nov 1997 16:51:36 +0300 (MSK) Received: by soma.niif.spb.su (SMI-8.6/SMI-SVR4) id QAA03092; Thu, 13 Nov 1997 16:51:27 +0300 Date: Thu, 13 Nov 1997 16:51:27 +0300 (MSK) From: "T.G. Shinkevich" To: CHEMISTRY@www.ccl.net Subject: about summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers I asked you for help in my research. Of course, I will summarise all of the mail I receive. Thanks a lot for the messages I have received. Yours sincerely postgraduate student of The Chemical Department of St.Petersburg State University Timothy Shinkevich. E-mail: ticky@soma.phys.spbu.ru From jeremy@med.usyd.edu.au Thu Nov 13 09:37:07 1997 Received: from blackburn.med.su.oz.au for jeremy@med.usyd.edu.au by www.ccl.net (8.8.3/950822.1) id JAA25155; Thu, 13 Nov 1997 09:24:12 -0500 (EST) Received: (jeremy@localhost) by blackburn.med.su.oz.au (8.6.11/8.6.4) id BAA01224 for chemistry@www.ccl.net Fri, 14 Nov 1997 01:24:27 +1100 From: Jeremy R Greenwood Message-Id: <199711131424.BAA01224@blackburn.med.su.oz.au> Subject: Re: CCL:logP and solubility for Amino Acids and peptides To: chemistry@www.ccl.net Date: Fri, 14 Nov 1997 01:24:25 +1100 (EST) In-Reply-To: from "Wang Arthur" at Nov 13, 97 12:25:08 pm X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCL: Wang Arthur asked: > We are currently on a project of de novo protein design. A set of scales > which describe the hydrophobicities of the natural amino acids is what we > badly need. > (2) LogP values for the 20 natural amino acids and oligopeptides (up to > buta- or pentapeptides). I ask, while we're on the subject: It seems the accurate de novo determination of LogP for novel amino acids and zwitterionic analogues is by no means an easy task. Suggestions and references gratefully received and summarised. Jeremy Greenwood Department of Pharmacology University of Sydney From oliver@mpi-sb.mpg.de Thu Nov 13 11:32:52 1997 Received: from mpi-sb.mpg.de for oliver@mpi-sb.mpg.de by www.ccl.net (8.8.3/950822.1) id KAA25637; Thu, 13 Nov 1997 10:38:54 -0500 (EST) Received: from mpii-ol.ag1.mpi-sb.mpg.de (mpii-ol.ag1.mpi-sb.mpg.de [139.19.10.174]) by mpi-sb.mpg.de (8.8.8/8.8.8) with ESMTP id QAA03687 for ; Thu, 13 Nov 1997 16:36:31 +0100 (MET) Received: from mpii-ol (localhost.mpi-sb.mpg.de [127.0.0.1]) by mpii-ol.ag1.mpi-sb.mpg.de (8.8.8/8.8.8) with ESMTP id QAA11369 for ; Thu, 13 Nov 1997 16:36:36 +0100 (MET) Message-Id: <199711131536.QAA11369@mpii-ol.ag1.mpi-sb.mpg.de> X-Mailer: exmh version 1.6.9 8/22/96 To: chemistry@www.ccl.net Subject: ab-initio calculation of UV/VIS-spectra Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Thu, 13 Nov 1997 16:36:35 +0100 From: Oliver Kohlbacher Dear CLLers, what possibilities do exist to predict UV/VIS spectra of aromatic compounds? To my understanding, it should be possible to predict them from the orbital energies obtained by a CI calculation. How difficult is this task? And how to get intensities? Thanks for any advice, Oliver -- ---- Oliver Kohlbacher (oliver@mpi-sb.mpg.de) Max-Planck-Institut fuer Informatik, Im Stadtwald, 66121 Saarbruecken Tel.: 0681-9325-505 Fax: 0681-9325-199 From Steve.Bowlus@sandoz.com Thu Nov 13 12:32:52 1997 Received: from gatekeeper.sandoz.att.nl for Steve.Bowlus@sandoz.com by www.ccl.net (8.8.3/950822.1) id LAA26008; Thu, 13 Nov 1997 11:40:58 -0500 (EST) From: Received: by gatekeeper.sandoz.att.nl; id RAA18092; Thu, 13 Nov 1997 17:40:56 +0100 (MET) X400-Originator: Steve.Bowlus@sandoz.com X400-Recipients: CHEMISTRY@www.ccl.net X400-MTS-Identifier: [/PRMD=SANDOZ/ADMD=400NET/C=CH/;0034700007856872000002] X400-Content-Type: P2-1988 (22) Message-ID: <0034700007856872000002*@MHS> To: Subject: Re: CCL:Examples for Main Chain Flexible Docking Date: Thu, 13 Nov 1997 17:43:37 +0100 ---------------------------- Forwarded with Changes --------------------------- From: Steve Bowlus at USPAC01M Date: 11/12/97 7:58AM To: chemistry-request@www.ccl.net at INTERNET1 Subject: Re: CCL:Examples for Main Chain Flexible Docking ------------------------------------------------------------------------------- A recent example of large shifts upon ligand binding is adenylosuccinate synthase. Compare the apoenzyme (1ade, 1adi from PDB) with ligated/inhibited enzyme (1juy, 1gin, for example; there are a number of structures deposited) sb _______________________________________________________________________________ Subject: CCL:Examples for Main Chain Flexible Docking From: chemistry-request@www.ccl.net at INTERNET1 Date: 11/12/97 10.17 AM Dear CCLers: We are studying main chain flexibility in protein-protein or protein-ligand docking. We would like to find some examples where protein main chain conformation changes significantly when binds with other molecule. Could someone give me a few examples? Thanks in advance. Luhua Lai ----------------------------------------- Luhua Lai Institute of Physical Chemistry & Department of Chemistry Peking University Beijing 100871 CHINA Phone: 86-10-62751490 Fax: 86-10-62751725 E-mail: lai@ipc.pku.edu.cn ----------------------------------------- -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: lai@csb0.IPC.PKU.EDU.CN -- Original Sender From: Address: lai@ipc.pku.edu.cn CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html From Steve.Bowlus@sandoz.com Thu Nov 13 12:39:45 1997 Received: from gatekeeper.sandoz.att.nl for Steve.Bowlus@sandoz.com by www.ccl.net (8.8.3/950822.1) id LAA25954; Thu, 13 Nov 1997 11:35:59 -0500 (EST) From: Received: by gatekeeper.sandoz.att.nl; id RAA22198; Thu, 13 Nov 1997 17:35:48 +0100 (MET) X400-Originator: Steve.Bowlus@sandoz.com X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=SANDOZ/ADMD=400NET/C=CH/;0034700007856875000002] X400-Content-Type: P2-1988 (22) Message-ID: <0034700007856875000002*@MHS> To: , Subject: CCL:logP and solubility for Amino Acids and peptides Date: Thu, 13 Nov 1997 17:38:34 +0100 ---------------------------- Forwarded with Changes --------------------------- From: chemistry-request@www.ccl.net at INTERNET1 Date: 11/13/97 6:33AM To: Steve Bowlus at USPAC01M *To: chemistry@www.ccl.net at INTERNET1 Subject: CCL:logP and solubility for Amino Acids and peptides ------------------------------------------------------------------------------- A literature search concerning Z-scales and Svante Wold (spelling?) should provide some leading references for (1), and probably references relating to (2), since the scales include that information, if I recall correctly. Several years ago (1991-1994?), Tripos did an application note on this topic. You might try contacting them. The presentation was given by Wally Reiher (are you out there, Wally?). sb _______________________________________________________________________________ Subject: CCL:logP and solubility for Amino Acids and peptides From: chemistry-request@www.ccl.net at INTERNET1 Date: 11/13/97 6.33 AM Dear CCLer We are currently on a project of de novo protein design. A set of scales which describe the hydrophobicities of the natural amino acids is what we badly need. So, would you please kindly provide any clue for the following issues: (1) Any paper describing such a set of scales (2) LogP values for the 20 natural amino acids and oligopeptides (up to buta- or pentapeptides). (3) Solubilities for these amino acids and oligopeptides. I will surely put back the summary. Meanwhile, please receive my best wishes. Arthur _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ Arthur Wang Doctoral Candidate _/ _/ Molecular Design Lab _/ _/ Institute of Physical Chemistry, Peking University _/ _/ Beijing 100871, P.R.China _/ _/ _/ _/ E-mail: arthur@ipc.pku.edu.cn _/ _/ Tel: 86-10-62751490 Fax: 86-10-62751725 _/ _/ WWW: http://www.ipc.pku.edu.cn/moldes/arthur/home.html _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: arthur@csb0.IPC.PKU.EDU.CN -- Original Sender From: Address: arthur@csb0.IPC.PKU.EDU.CN CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html From ostell@object.nlm.nih.gov Thu Nov 13 13:33:01 1997 Received: from ncbi.nlm.nih.gov for ostell@object.nlm.nih.gov by www.ccl.net (8.8.3/950822.1) id MAA26353; Thu, 13 Nov 1997 12:46:03 -0500 (EST) Received: from object.nlm.nih.gov (object [130.14.25.153]) by ncbi.nlm.nih.gov (8.8.8/8.8.8) with SMTP id MAA02533; Thu, 13 Nov 1997 12:46:01 -0500 (EST) Received: by object.nlm.nih.gov id MAA03018; Thu, 13 Nov 1997 12:45:55 -0500 Date: Thu, 13 Nov 1997 12:45:55 -0500 From: ostell@object.nlm.nih.gov (Jim Ostell) Message-Id: <199711131745.MAA03018@object.nlm.nih.gov> To: Gerald.Loeffler@univie.ac.at Subject: CCL:Sequence Classes and CORBA Servers Cc: biowidgets-consortium@fruitfly.BDGP.Berkeley.EDU, javachem@wag.caltech.edu, bioobjects@ebi.ac.uk, chemistry@www.ccl.net, lifesciences@omg.org Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-MD5: +OSDcimnkZG0lSnZYEUcBA== A Few Comments from NCBI There has been quite a lot a traffic recently starting from Gerald Loeffler's innocent question about object oriented class libraries for interfaces to sequence data and leading to questions of NCBI's position on CORBA and the OMG. The discussion ranged over at least three major topics: How do I get programmatic access to data and tools today? Will a particular technology solve our problems? Will people actually use it (or will it really happen)? These are often conflated together and well mixed with passion and politics in discussions, which is why I tend to avoid them by email. Since NCBI's opinion has been asked, I will attempt to say something on these three topics in case it helps. Note that all three answers represent only our own tools and opinions and are not intended as a comprehensive discussion of the subject. 1) How do I get programmatic access to data and tools today? Interfaces to our network servers are provided either as linkable network client libraries in the NCBI toolkit (1), or as WWW URLs which you can use from any WWW library (like www perl for example). These provide all the capabilities Loeffler requested; get a sequence based on an id, get a bunch of sequences based on a query, do a blast search, get an alignment, etc. A small demo program, seqget.c, from the toolkit demo directory that takes a sequence id, fetches the sequence, and prints it in a variety of formats. There are URLs documented on our web site that do all this as well (see "Linking to Entrez" (2) for example). These are not only designed to be used as hot links in web documents, but directly for querying the system from software. For the vast majority of our system usage these provide a sufficient interface and they are extensively used by outside sites. 2) Will a particular technology solve our problems? None of the above was done in C++, JAVA, or CORBA, which were specified in Loeffler's original request, although the specific capabilities he requested are available in our tools. At NCBI we are very conservative about our choices of technologies, since we do not want to be at their mercy as they change. Our network servers support more than 40,000 unique users a day, running millions of queries, so we must be careful in our approach. We prefer to focus on the task of integrating biomedical information, doing alignments, building maps, and so on, not on following an evolving technology. Currently for us this means C code and relational databases as appropriate. The ASN.1 specification was originally intended to be implemented as C++ but that language was not very portable until the last couple years. Now that it is, we have in fact embarked on a C++ version of the toolkit. This may serve as a more object oriented view of our tools, and clearly it is being informed by our experiences of the last seven years. However it has to be a part time project given the pressure on our resources. Over the years various computer technologies have arisen. At one time some people suggested adopting relational databases would enable interoperoperability. Then it was object oriented databases, PERL, TCL, SmallTalk, and others. We, like others, are very dependent on some of these technologies, but their adoption has not lead to deep or widespread interoperability. This is only partly because different technologies are appropriate in different environments. The biggest reason is because the research domain of molecular biology is extremely diverse and fluid. Once one moves beyond the simplest view of the data (eg. a FASTA file) it is very difficult to find agreements that suit everyone's needs over time, even within a single development group. Finding ways to exchange very simple objects is not limited by the technology choice. The technology with by far the greatest impact that we have recently adopted for NCBI production services is the WWW. Part of the reason it has been so successful compared with other technologies, is that you do not have to agree on much in the way of content for the technology to be effective. You do not have to be much of a programmer to do useful things with it. It has clearly demonstrated its utility and widespread viability. As such we have put serious resources into supporting web interfaces, and to using the web as a way of exchanging data, such as the query and BLAST URLs I described above. Note that use of the WWW to provide network connectivity does not restrict access to GUI interfaces. We explicitly provide URLs that can be used for direct data access. The advantage of using web technology itself is that we get the advantages of all the support it is getting. Vendors are even changing their operating systems to make them work efficiently with it, and more capabilities are being added to web servers which we are exploiting as they become well established. Of course all the content presented this way is being driven by the same NCBI toolkit that supported the older client/servers. So I am trying to make two points here: One is that technologies come and go in the computer industry. Only a few have a massive and long lasting impact. Even those go through a considerable shakeout period. We try to restrict our efforts to such well established, central technologies, and we try to do it at least late in their shakeout stage. We try to maximize our time spent on biological issues, and minimize our time spent on sorting out computer technologies. The second point is that no matter what technology you choose, you have to do something with it. NCBI has created a corpus of tools that provide the infrastructure for popular and important tools as standalone programs on many platforms and as internet client/servers. The same routines now provide the backend power for the WWW servers. Our infrastructure enables us to make effective use of the technology. Should a single distributed object approach emerge from the current technology turmoil as persuasively useful as the WWW has, we would put the same infrastructure behind it. 3) Will people actually use it (or will it really happen)? In my opinion, JAVA is a promising technology but is clearly in the early shakeout stages. Our strategy here is to make our OO move to C++ while bearing in mind the principles behind JAVA. When and if JAVA settles down we will be in a better position to take advantage of it. CORBA is much more established and NCBI has been a member of OMG since the very first meeting years ago. We ended up building our own client/server because no products were available. Now that products are available, we find them to be very heavyweight systems. In our experience, the relatively coarse granular interactions that make practical sense on the internet require a relatively light weight server and www servers fill the bill nicely. For our own purposes, we do not see any advantage to paying the technology cost of going to CORBA. In addition to connectivity, CORBA also offers an interface definition language, IDL, and there is something to be said for that. IDL can also be used as a data definition language although that is not its primary intent. NCBI uses ASN.1, which is primarily a data definition language, and this is how we define and encode data for our network services (be they client/server or web based) when our own tools provide the interface at the network. Programmers using our clients then do not actually read and write ASN.1 directly, they use C code functions which return C structures to them. CORBA is most commonly used the same way. The programmer does not read and write IDL encoded information. The CORBA compiler generates stub functions in C, C++, SmallTalk, or JAVA, and the programmer uses those. However, IDL also defines the interfaces as well (the access functions). When one is working with complex objects like annotated sequences or contigs of annotated sequences or genome assemblies of contigs, one must be careful with the default implementation of the interfaces generated by CORBA in order to make efficient use of bandwidth. In order to agree on interfaces to a data model, one must first agree on a data model. Assuming that agreement is reached, then one must select interfaces that both take into account the practical aspects of available technology, such as mentioned above, as well as providing both sufficient generality and sufficient specificity to be widely useful. As the developers of the Standard Template Libraries for C++ will attest, this is non-trivial for even objects as simple and well understood as strings and lists. At NCBI we elected to define the data model to provide a unifying framework, but let the interfaces develop in response to our real time needs to provide services to working biologists. The reasoning was that if we could develop real tools like Entrez, BLAST, Sequin, and others, as sets of routines developed by many different people that interoperate closely, we would have the basis for a set of proven useful interfaces. At this point, I would say we have very good ideas about a relatively coarse granular interface to our services, and you can see that in the Entrez and BLAST interfaces. We have surfaced these interfaces in a number of ways, including ASN.1, URLs, function call libraries, etc. However, our experience is that interfaces into the underlying structures themselves are much more difficult to standardize and legitimate needs of complicated tools like editors are very difficult to generalize. We have some better ideas about this now that we have built Sequin and the second generation Entrez as message passing components. We are beginning discussions here about trying to capture some of that hindsight into C++ class libraries. But we certainly consider it premature for us to be proposing standard interfaces at this level that we ourselves would be willing to use. We are certainly not ready to propose such interfaces for others. It is very obvious to us from our own usage that finding ever more powerful and flexible ways to use our web servers is benefiting the biomedical community at lots of levels, from end users, to web page builders, to programmers. We continue to put heavy resources there and to watch developments such as fastcgi programs and the use of XML as a data description language as obviously beneficial improvements. We are watching technologies like JAVA and CORBA but feel it is premature for us to make a production commitment to them at this time. Given the uncertainty regarding CORBA as the long term technology of choice and our own skepticism about the utility of defining community interface standards except at very simple levels right now, we do not see the OMG standards process as the most effective path forward for NCBI at this time. From our own perspective we need to satisfy ourselves that we have a workable solution to our own interface needs. While we have not made a point of going out and proselytizing our technical approaches, we have always welcomed visitors who are seriously interested in learning what we are doing or making use of the tools we can offer. We are happy to share our experiences and have offered workshops and talks at scientific meetings or at NCBI, and are certainly willing to do so again. Jim Ostell, Ph.D. Chief, Information Engineering Branch NCBI 1) NCBI Toolkit =96 linkable C libraries for many platforms Anonymous ftp from ncbi.nlm.nih.gov In toolkit/ncbi_tools Current network Entrez interface is ncbi/cdromlib/accentr.h Current BLAST interface (network or standalone) ncbi/tools/blast.h Examples of usage in ncbi/demo Hardcopy documentation (real old..sorry) by request from toolbox@ncbi.nlm.nih.gov 2) URL access =96 NCBI home page =96 http://www.ncbi.nlm.nih.gov/ Linking to Entrez =96 = http://www.ncbi.nlm.nih.gov/Entrez/Linking.html Linking to BLAST =96 on our anonymous ftp site, look in blast/blasturl/README From martin@qtp.ufl.edu Thu Nov 13 14:32:53 1997 Received: from qtp.ufl.edu for martin@qtp.ufl.edu by www.ccl.net (8.8.3/950822.1) id NAA26604; Thu, 13 Nov 1997 13:34:09 -0500 (EST) Received: from visi2.qtp.ufl.edu by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id NAA21252; Thu, 13 Nov 1997 13:34:06 -0500 Received: by visi2.qtp.ufl.edu (SMI-8.6/SMI-SVR4) id NAA13138; Thu, 13 Nov 1997 13:34:05 -0500 Date: Thu, 13 Nov 1997 13:34:05 -0500 Message-Id: <199711131834.NAA13138@visi2.qtp.ufl.edu> From: Charles & To: Oliver Kohlbacher Cc: chemistry@www.ccl.net Subject: CCL:ab-initio calculation of UV/VIS-spectra In-Reply-To: <199711131536.QAA11369@mpii-ol.ag1.mpi-sb.mpg.de> References: <199711131536.QAA11369@mpii-ol.ag1.mpi-sb.mpg.de> Oliver Kohlbacher writes: > > what possibilities do exist to predict UV/VIS spectra of > aromatic compounds? To my understanding, it should be possible > to predict them from the orbital energies obtained by a > CI calculation. How difficult is this task? > And how to get intensities? > The easiest way to do this is to use ZINDO or MOPAC. The ZINDO package has been parameterized to reproduce UV/VIS spectra for organic and transition metal compounds using a singles CI. I think you can purchase this through Hypercube. It is fairly easy. Intensities are harder to model, but ZINDO maybe provide reasonable results. Ab initio spectra are much harder to obtain because of the computational requirements for accutate calculations. I would think that you could obtain crude UV/VIS spectra using Gaussian with the CASSCF+MP2 option, but this is hard to run on anything but relatively small systems (i.e. no more than say 10 pi orbitals). The Guassian CIS option may work, but I doubt it will be better than ZINDO. You might also try ACES, which using a type of coupled cluster + equations of motion approach, but, again, this will require a lot of disk space and memory. Chuck Martin -- -------------------------------------- Dr. Charles H. Martin Quantum Theory Project 362 Williamson Hall PO Box 118435 University of Florida Gainesville, Florida 32611-8435 Fax: (352) 392-8722 Email: martin@qtp.ufl.edu Web: www.cat.syr.edu/~cmartin/hv -------------------------------------- From martin@qtp.ufl.edu Thu Nov 13 14:40:50 1997 Received: from qtp.ufl.edu for martin@qtp.ufl.edu by www.ccl.net (8.8.3/950822.1) id NAA26708; Thu, 13 Nov 1997 13:58:03 -0500 (EST) Received: from visi2.qtp.ufl.edu by qtp.ufl.edu (SMI-8.6/SMI-SVR4) id NAA21363; Thu, 13 Nov 1997 13:57:04 -0500 Received: by visi2.qtp.ufl.edu (SMI-8.6/SMI-SVR4) id NAA13159; Thu, 13 Nov 1997 13:57:02 -0500 Date: Thu, 13 Nov 1997 13:57:02 -0500 Message-Id: <199711131857.NAA13159@visi2.qtp.ufl.edu> From: Charles & To: CCL Cc: Josi Santiago Duca Subject: CCL:average structures On the topic of average structures for semi-flexible systems I would tend to agree with Rick Venable that you can not really describe a flexible structure (such as a torsional motion or a semi-flexible polyene chain) using something like an "average structure." There are techniques, however, which using averages from MD simulations to describe such systems, but they require some work to get at the information you want. If you are trying to observe a "floppy" structure, then you may wish to condier the type of experiment which probes the structure. For example, Karl Freed and Graham Flemming have examined some cases of flexible amino acid chains in solution and considered how to explain the experimentally observed flouresence decay of a TYR group in a floppy environment. Essentially, one runs a long time simulation, then constructs the experimental time correlation function from a "basis set expansion" of the "space of correlation functions." The basis set expansion describes the chain, essentially, as as a collection of beads of moving under the influence of random forces, and the correlations which correct for the non-randomness. The basis functions are correlation functions for the EQUILIBRIUM distribution function, and can thus be obtained from an very good equlibirum simulation. Using these methods of non-equlibirum statistical mechanics, one can obtain any non-equlibirum property, or correlation function, (i.e. like a response to an applied field) by a an expansion in the basis set of equilibrium correlation functions. (Note that if the chain is VERY flexible, then the ends will bump into each other, introducing what is termed an excluded volume interaction. This complicates the approach described above.) Again, this is a non-convetional way of describing "average strucrues" and is not really available in any standard package. But perhaps it will provide some new ways of thinking about the problem. Some of the references for this can be found on: http://rainbow.uchicago.edu/~freed.html With Best Regards Chuck Martin -- -------------------------------------- Dr. Charles H. Martin Quantum Theory Project 362 Williamson Hall PO Box 118435 University of Florida Gainesville, Florida 32611-8435 Fax: (352) 392-8722 Email: martin@qtp.ufl.edu Web: www.cat.syr.edu/~cmartin/hv -------------------------------------- From tvd@msi.com Thu Nov 13 16:32:55 1997 Received: from bioc1.msi.com for tvd@msi.com by www.ccl.net (8.8.3/950822.1) id PAA27349; Thu, 13 Nov 1997 15:44:41 -0500 (EST) Received: by bioc1.msi.com (5.64/0.0) id AA12346; Thu, 13 Nov 97 12:41:55 -0800 Received: from biff.msi.com(146.202.0.225) by bioc1.msi.com via smap (V2.0) id xma012344; Thu, 13 Nov 97 12:41:28 -0800 Received: from win95-pc.msi.com by biff.biosym.com (4.1/SMI-4.1) id AA17792; Thu, 13 Nov 97 12:40:24 PST Message-Id: <3.0.32.19971113124624.00778748@146.202.0.225> X-Sender: tvd@146.202.0.225 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Thu, 13 Nov 1997 12:46:26 +0000 To: CHEMISTRY@www.ccl.net From: Ton van Daelen Subject: Cerius2 SDK training workshop, Dec 1-2, Philadelphia Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCLers - This workshop might be of interest to some of you. Regards - Ton Software Developer's Kit Training Workshop Molecular Simulations will be offering a two day workshop on the Cerius2 software developer's kit (SDK) at Silicon Graphics Computer System's (near) Philadelphia office on December 1-2. This event is aimed at scientists and programmers developing chemistry applications. Both novices and expert users of MSI products are invited. The course is limited to 20 participants. The first day will cover the basics of code development using the SDK. Attendees will learn how to add a graphical front-end to in-house codes to facilitate the process of setting up a calculation and analyzing results. On the second day attendees can work on a realistic application in collaboration with MSI's SDK training staff. This is a very practically oriented workshop targeted towards delivering a working interface to an external program by the end of the course. Monday, December 1, 10am-5pm Cerius2 architecture SDK tool set User interface design Command processing API subsystems: Algorithms Data model Plotting Tables Graphics Packaging and distribution Tuesday, December 2, 9am-4pm Scripting capabilities in Cerius2 Debugging Fortran, C and C++ SDK code Integrating Quantum and MM applications Writing customized descriptors Mini project on topic of choice A sign up sheet can be found at MSI's web site: http://www.msi.com/info/training/training_sdk.html Ton van Daelen, Ph.D. Product Manager Software Developer's Kit __o E: tvd@msi.com _`\<,_ Molecular Simulations, Inc P: -1-619-546-5329 (*)/ (*) 9685 Scranton Road F: -1-619-458-0136 /\/\/\/\/\/\ San Diego, CA 92121 W: http://www.msi.com Check out What's New in SDK on the SDK web pages at http://www.msi.com/support/sdk/ The example application library now contains new SDK applications dealing with plotting, trajectory animation, and conformational searching. From boufer@cennas.nhmfl.gov Thu Nov 13 17:32:54 1997 Received: from cennas.nhmfl.gov for boufer@cennas.nhmfl.gov by www.ccl.net (8.8.3/950822.1) id QAA27617; Thu, 13 Nov 1997 16:41:11 -0500 (EST) Received: from localhost (boufer@localhost) by cennas.nhmfl.gov (8.8.5/8.8.5) with SMTP id QAA15463 for ; Thu, 13 Nov 1997 16:41:12 -0500 (EST) Date: Thu, 13 Nov 1997 16:41:11 -0500 (EST) From: Ahmed Bouferguene X-Sender: boufer@cennas To: chemistry@www.ccl.net Subject: Advice for purchasing PC Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, Our department is interested in purchasing some PCs to be used for numerical computation~(in physics and chemistry) and graphical representations. However, we do not have a thorough experience with PCs and we would like to have your comments about a good configuration and of course about any good software that would be worth to have. Thanks all. Ahmed Bouferguene