From mbdtsnm@hpf.ch.man.ac.uk Mon Feb 20 09:51:25 1995 Received: from nessie.mcc.ac.uk for mbdtsnm@hpf.ch.man.ac.uk by www.ccl.net (8.6.9/930601.1506) id JAA26048; Mon, 20 Feb 1995 09:10:38 -0500 Received: from hpg.ch.man.ac.uk (actually mchhpg.ch.man.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Mon, 20 Feb 1995 11:19:50 +0000 From: Nathaniel (noj) Malcolm Message-Id: <14079.9502201119@hpg.ch.man.ac.uk> Subject: Non-Aqueous Solvation To: chemistry@ccl.net Date: Mon, 20 Feb 95 11:19:35 GMT Mailer: Elm [revision: 70.85] Hi all, this is a (hopefully) brief reply to those who asked for a summary of the info that i recieved from my last posting. I requested any info on non-aqueous solvation of neutral species. Unfortunately the seven or so replies that i got where all from people wanting the same info, and not a single pointer to a single paper. My literature seaches have also been fairly unproductive, there is plenty of data as i said for ions (mainly Y.Marcus and friends) and for the process of transfer of solutes from non-aqueous solvents to water (or other solvents) . Very little has turned , mainly just for one, specific solute and solvent combinations. As i am trying to paramatrize a solvation model for solvents other than water none of this is much use. So to those who asked for my summary i'm sorry but there isn't one, to any one with knowledge of this area, this sort of stuff is definitely of interest to many people,so please send comments to me and i will summarise anything for the list (if i get anything this time ). thanks NOJ Noj.Malcolm@man.ac.uk From dmit@nmr1.ioc.ac.ru Mon Feb 20 12:00:13 1995 Received: from nmr1.ioc.ac.ru for dmit@nmr1.ioc.ac.ru by www.ccl.net (8.6.9/930601.1506) id LAA29354; Mon, 20 Feb 1995 11:19:46 -0500 Received: from [193.124.3.49] by nmr1.ioc.ac.ru with SMTP (WG7Jv1.07b+CWRU/BIOCv1.93) id AA1773 ; Mon, 20 Feb 95 19:19:43 MST Date: Mon, 20 Feb 95 19:19:31 +0300 From: "Dmitry E. Dmitriev" Message-Id: <80007.dmit@nmr1.ioc.ac.ru> X-Minuet-Version: Minuet1.0_Beta_17A Reply-To: X-POPMail-Charset: IBM 8-Bit To: chemistry@ccl.net Subject: Summary: cavity sizes in crowns Dear Netters: Several days ago, I posted a question on calculating cavity sizes in crown ethers. Many thanks to all responders. Special thanks to Patrick Bultinck for his kindly answer with many references. Dmitry Original message was: ---------------------------------------------------------- Dear Netters! I'm looking for references to algorithms or programs which are used to calculate cavity sizes in crown ethers. Also, I would like to know about molecular modelling packages, which can be estimate this parameter. Thanks in advance. Dmitry ============================================================================ Dmitry E. Dmitriev, ** E-mail: dmit@nmr1.ioc.ac.ru NMR Centre Moscow ** ***************** N.D. Zelinsky Inst. of Org. Chem., ** tel : 7 (095) 135 90 94 Russian Academy of Sciences ** fax : 7 (095) 135 53 28 ============================================================================ **************************************************************************** James Crabbe wrote: DeskTop Molecular Modeller is a modeling program for PCs that calculates distances, volumes and areas. It should be appropriate for what you describe. It is available from Oxford University Press for about 250 pounds stirling. Contact Mrs. Janet Caldwell, Oxford Electronic Publishing, Oxford University Press, Walton Street, Oxford OX2 6DP for details. Telephone : +44 865 56767. James Crabbe. **************************************************************************** David White wrote: Have you considered using solid angles? (White, D; Taverner, B.C.; Leach, P.G.L.; Coville, N.J. J. Comput. Chem. 14 (1993) 1042). If so, I have a program which can be used to calculate solid angles and from those data you can deduce the cavity size. I think R D Hancock has done some work in this area. You may want to do and author search on him. David White **************************************************************************** * * * * David White * Man is the best computer we can put * * Postdoctoral Research Associate * aboard a spacecraft -- and the only * * Beckman Institute * one that can be mass produced with * * (217) 244-1733 * unskilled labour * * (217) 244-8371 (fax) * Werner von Braun * * * * **************************************************************************** Patrick Bultinck wrote: About all quantum chemical packages will do, off course you will first have to work in into the field of Quantum Chemistry of Macrocyclic Chemistry. These are some references to articles in which programs of all sort were used to do the calculations. May I ask to PLEASE send a summary of ALL answers you received since I've been working in QCMC bussiness for 1.5 years now, and will be for about 3 years to come ! Attatched to this letter you will find the following : a list of references arranged as follows : Number in my DBase, "Abbreviation in my DB", "Authors", "Title", "Journal", "Volume and year", "Issue (*=3Dnot relevant)", "Class (theory, calculation, or experiment)", "Specific (e.g. ab initio, MMx)", "Keywords (e.g. name of compound)". 25,"ADA92","K.R. Adam L.F. Lindoy","Computer modelling of Metal-Containing Macrocyclic Ligand Systems-the Present and the Future", "BOOK : Crown Compounds toward future applications","1992", "ISBN 1-56081-024-6 (anorg. 2336 en 2321)","69-79","Theory","ab initio semi-empirical","crown-complex" 54,"HAY93","B.P. Hay","Methods for molecular mechanics modeling of coordination compounds","COORDINATION CHEMISTRY REVIEW","1993 (126)","*", "177-236","Theory","Molecular mechanics","bidentate-complex crown-complex" 56,"HAN90","R.D. Hancock","Molecular mechanics calculations and Metal Ion recognition","ACCOUNTS OF CHEMICAL RESEARCH","1990 (23)","*","253-257", "Calculation","Molecular mechanics","crown-complex" 57,"REN93","R. Rencsok T.A. Kaplan J.F. Harrison","Electronic structure of Li(9-crown-3)2 : A molecule with a Rydberg-type ground state", "JOURNAL OF CHEMICAL PHYSICS","1993 (98)","12","9758-9764", "Calculation","ab initio","crown-complex" 58,"WAR69","L.G. Warner D.H. Busch","The stereoisomers of a Macrocyclic Nickel (II) Complex containing six asymmetric centers. Factors determining the stabilities of configurations and conformations","JOURNAL OF THE AMERICAL CHEMICAL SOCIETY","1969 (91)","15","4092-4101","Calculation", "molecular mechanics","crown-complex" 65,"ROD78","L.J. Rodriguez G.W. Liesegang M.M Farrow N. Purdie E.M. Eyring","Kinetic studies of complexation of divalent Strontium, Barium, Lead and mercury cations by aqueous 15-crown-5 and 18-crown-6", "JOURNAL OF PHYSICAL CHEMISTRY","1978 (82)","6","647-650","Experiment", "kinetics","crown-complex" 66,"LAM80","J.D. Lamb R.M. Tzatt C.S. Swain J.J. Christensen", "A systematic study of the effect of macrocycle ring size and donor atom type on the log K, DH, and TDS of reactions at 25=A1C in methanol of mono- and divalent cations with crown ethers","JOURNAL OF THE AMERICAN CHEMICAL SOCIETY","1980 (102)","2","475-479","Experiment","thermodynamics", "crown-complex" 67,"HAN85","S.V. Hannongbua B.M Rode","Quantum-chemical investigations on the interaction of alkaline-Earth-Metal ions with Macrocyclic Compounds","INORGANIC CHEMISTRY","1985 (24)","*","2577-2580","Calculation", "ab initio","crown-complex" 276,"THO94","M.A. Thompson E.D. Glendening D. Feller","The nature of K+/crown ether interactions: a hybrid quantum chemical mechanical-molecular mechanical study.","JOURNAL OF PHYSICAL CHEMISTRY","98 (1994)","*", "10465-10476","Calculation","ab initio molecular mechanics", "crown-complex" 280,"GLE94","E.D. Glendening D. Feller M.A. Thompson", "An ab initio investigation of the structure and alkali metal cation selectivity of 18-crown-6","JOURNAL OF THE AMERICAN CHEMICAL SOCIETY", "116 (1994)","*","10657-10669","Calculation","ab initio","crown crown-complex" 285,"HAM88","T.W. Hambley","Steric contributions to the thermodynamics of electron transfer in Cobalt(III) Haxammine complexes","INORGNANIC CHEMISTRY" "27 (1988)","*","2496-2501","Calculation","Molecular Mechanics", "ethylenediamine-complex 1,3-propanediamine-complex crown-complex" 288,"THO84","V.J. Th=9Am J.C.A. Boeyens G.J. McDougall R.D. Hancock","Origin of the high ligand fiels strength and macrocyclic enthalpy of nitrogen-donor macrocycles.","JOURNAL OF THE AMERICAN CHEMICAL SOCIETY","106 (1984)","*","3198-3207","Calculation","Molecular Mechanics", "crown-complex" 289,"SEI91","E.T. Seidl H.F. Schaefer III","A new configuration of 12-crown-4","JOURNAL OF PHYSICAL CHEMISTRY","95 (1991)","*","3589-3590", "Calculation","Ab initio","12-crown-4 crown" I forgot a reference, and even one of the most interesting for you ! L.P. Trigub, S.V. Krutius and Y.A. Kruglyak, "A package of programs for theoretical conformational analysis of macrocyclic molecules", Journal of Structural Chemistry, Vol. ? (1984), page 642 The authors are Russian, or at least from somewhere in the former USSR ! I think I could come up with their address... Patrick |-----------------------------------------------------------------------| | C-C Patrick Bultinck | | / \ Dept. Inorganic & Physical Chemistry | | C-O O-C Section Quantum Chemistry | | | | University of Ghent | | C-O O-C Krijgslaan 281 (S-3) | | \ / 9000 Gent | | C-C Belgium | | Tel. Int'l code/32/9/264.44.44 | | Macrocycles Fax. Int'l code/32/9/264.49.83 | | Quantum Chemical E-mail : Patrick.Bultinck@rug.ac.be | | Calculations | |-----------------------------------------------------------------------| ============================================================================ Dmitry E. Dmitriev, ** E-mail: dmit@nmr1.ioc.ac.ru NMR Centre Moscow ** ***************** N.D. Zelinsky Inst. of Org. Chem., ** tel : 7 (095) 135 90 94 Russian Academy of Sciences ** fax : 7 (095) 135 53 28 ============================================================================ From san@mbu.iisc.ernet.in Mon Feb 20 12:07:17 1995 Received: from sangam.ncst.ernet.in for san@mbu.iisc.ernet.in by www.ccl.net (8.6.9/930601.1506) id LAA29212; Mon, 20 Feb 1995 11:11:04 -0500 From: Received: from soochak.ncst.ernet.in (soochak.ncst.ernet.in [144.16.11.100]) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with ESMTP id VAA09709 for ; Mon, 20 Feb 1995 21:40:39 +0530 Received: from iisc.ernet.in (iisc.iisc.ernet.in [144.16.64.3]) by soochak.ncst.ernet.in (8.6.8.1/8.6.5) with SMTP id VAA27527 for ; Mon, 20 Feb 1995 21:37:38 +0530 Received: from vigyan.UUCP by iisc.ernet.in (ERNET-IISc/SMI-4.1) id AA16703; Mon, 20 Feb 95 21:45:30+0530 Date: Mon, 20 Feb 95 21:45:30+0530 Message-Id: <9502201615.AA16703@iisc.ernet.in> Received: by vigyan.iisc.ernet.in (smail2.3) id AA26073; 20 Feb 95 21:38:30 EST (Mon) To: vigyan!chemistry@ccl.net Subject: summary of data analysis of protein structures hi! here is the summary of responses I got this time for my query on data analysis of protein crystal structures. I am grate ful to all who responded especially erich baur who wants to have regular communuication with me. However, I have not been able to contact him personally because my mails to him are bouncing back. Through this medium, I apologise to him for my failure in this regard and assure that I shall keep try untill my mail stop bouncing back. My special thanks to K. Stewarts and Dr. Phillipe for the references. your's cordially sandeep kumar san@mbu.iisc.ernet.in P.S. I will welcome futher comments and suggestions. **********START of SUMMRY********************************************* From: tbi.univie.ac.at!erich.bauer (Erich Bauer) Message-Id: <9502091923.AA00383@renoir> Subject: Re: CCL:data analysis of protein crystal structure To: san@mbu.iisc.ernet.in Date: Thu, 9 Feb 1995 20:23:02 +0100 (MEZ) Cc: san@mbu.iisc.ernet.in In-Reply-To: <9502091622.AA16267@iisc.ernet.in> from "san@mbu.iisc.ernet.in" at Feb 9, 95 09:52:49 pm X-Mailer: ELM [version 2.4 PL2] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Length: 8528 Status: R san@mbu.iisc.ernet.in > > Hi! hi, > About Ten or fifteen days back I posted a query regarding the > personal experiences of the people involved in the data analysis of > the crystal structures of biomolecules esp. proteins. I am sorry to > state that my query evoked only two responses. > one of the advices that came my way was about the selection of dataset. > I agree with the responder that this is a problem. dear sandeep, i got the message. Interestingly, i am at the moment concerned with the same questions. Being new to CCL and PDB I am, however not experienced in these fields. I will try to give you some hints from what I learned on the subjects during the last months. Not all of it is on my mind right now, but, if you agree, we can stay in touch and post ideas whenever they come to our minds. It makes no sense to bother ALL CCLers with that. ( If you don't, just send an email saying "OH NO , NOT yOU AGAIN, STOP, PLEASE STOP !!", i won't feel insulted.) > I have found out that in PDB there is a directory called user_group > which contains different useful subdirectories. One of them call > subset_list contains the list of PDB entries for proteins which > have been selected using some criteria. one of the list is from > Jane Richardson's lab for different structural motifs. Another from > Chris Sander's lab lists the proteins with less than 30% sequence > homology. I hope tihs information is very useful to the people involved > in this area. it is, indeed. if you need the original references, how to obtain such datasets: @Article{Hobohm:91a, author = "Uwe Hobohm and Michael Scharf and Reinhard Schneider and Chris Sander", title = "Selection of representative protein data sets", journal = "Protein Science", year = "1992", volume = "1", OPTnumber = "", pages = "409 - 417", OPTnote = "eb00", OPTannote = "P-DB" } @Article{Boberg:92a, author = "Jorma Boberg and Tapio Salakoski and Mauno Vihinen", title = "Selection of a Representative Set of Structures from Brookhaven Protein Data Bank", journal = "Proteins", year = "1992", volume = "14", OPTnumber = "", pages = "265 - 276", OPTnote = "eb00", OPTannote = "P-DB" } If you want, I can send you the ftp sites to obtain the newest datasets. ( i would have to gather the papers from home ... ) The whole subject seems to be a little bit involved: If you want to choose data f.i. for secondary structure prediction, you should try to avoid ( rare ) data from membrane proteins. So you have to focus on let's say globular proteins. If you do so, you put in additional information that in turn has been taken from the knowledge of tertiary structur to classify the protein. This can be repeated at any level of description ( certain class of proteins, certain folds,domains etc...) and i don't see any REAL answer to that problem. > I renew my request to the people involved in data analysis > to come forward and share their experiences with one another. I may > also be useful to the outsiders also as it can give them a glimpse > of current situation in this important field. I am basically interested > in discussing how statistics can be exploited to shed some light on the > hidden principles and properties of protein structures which are being If you need programms for data analysis, i might be able to point you to. For the reasons mentioned above and as only a very restricted set of structure proteins and some enzxymes are being crystallized from pharma, meds etc. PDB itself is a strongly selected dataset. > diposited in the databanks. What all can we learn from data analysis? > I am sure the are many more protein motifs still left undiscovered in Most pdb files contain classification for secondary structures. Several programs for optimisation and displaing structures are of different opinion. I am presently doing an exhaustive search in *.pdb and we are looking at all kind of representations for measures, f.i. not only the values of bond-angles, plantwists etc. but also higher moment and norms etc. etc. ( my boss is mathematican, he probably knows which representations make sense on what ) > these PDB files. There may be answers hidden in these files which could > tell us why protein secondary structure prediction is still inaccurate. This question could serve as a basis for a newsgroup or a mail-reflector on its own. I can provide you SOME impressions right away, for more please don't hesitate to ask fori, most of the subject is still obsured to me, comments are welcome. 1) The matter is related with experimental data exploitation and with the subject of global optimisation: probably it is non local interactions, f.i. neighbouring of other domains that enable/disable formation of secondary structure that, in turn are only the local outcome of non-local problem. ( Several attemp have made with more global approaches: then we have a problem of tromendous high dimension even for small molecules. ( we are working on a global optimization packege that might do well for medium sized molecules, however accuracy of potential functions might be much to poor ) ). 2) One could try to predict molecule's structure with force filed calculations: too slow even for small molecules. ( paramatrisation of MD programs takes a LOOOOOOOOOOOOOOOOOOOONG time. only large companies, consortia etc. ( BIOSYM/SanDiego) can cope with that.) 3) MD is, in principle just an inadequate method. why shold f.i. 2 H behave differently in the same distance from each other when they have a different ditance along the backbone? 4) if you work with ab initio-methods to fit data, they take an even LOOOOOO OOOOOOOOOOOOOOOOOOOOOOOOOnger time to fit fro small molecules. 5) Measured data are not very accurate, sometimes the complete topology is wrong as X-RAY pictures have to be interpreted and sometimes people need much experience and intuition to guess the right folding pattern. ( Sometimes they have to remove one or the other .pdb file as results turn out to be TOTALLY wrongi as I was told. Not to talk about the errors that are not being detected and noone can prove ... ) 6) SecStr prediction is basicly heuristics with neural nets etc, based on mentioned before datasets.. helices f.i. are often considered a hydrophobic nucleation site - somtimes they are however strongly influenced by long range interactions. > Only things we need to do is to be frank and informally discuss the > various problems one generally encounters when taking up such a project. > How best one can cope with it. I will even welcome sharing of latest > litrature on the subjects amongst the people involved in such projects. fine. On what topics ? if you want , I can send you my literature list i read during the last months. there is also a mail-server, where you can send your sequence and they send it back within some hours with sec.str. prdiction. > yours' cordially > sandeep kumar > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: san@mbu.iisc.ernet.in > -- Original Sender From: Address: san@mbu.iisc.ernet.in > CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator > MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 > Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search > http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV > your's sincerelly erich -- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | namenet : Erich Bornberg - Bauer | ------------------------------------------------------------ | snailnet: Inst. f. theor. Chem., | Inst. fuer Mathematik | | : Waehringerstr. 17/308 | Strudlhofg. 4 | ------------------------------------------------------------ | : Univ. Wien, A - 1090, Vienna / Austria | ------------------------------------------------------------ | voicenet: *43-1-40 480 - 667, 677| (nonet yet, try drums)| | faxnet : 402 85 25 | ( --- " --- ) | | internet: erich@tbi.univie.ac.at | erich@cma.univie.ac.at| ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ project: making every problem NP-complete ... From: bioinfo.ernet.in!sangeeta Message-Id: <9502112000.AA03278@bioinfo.bioinfo.ernet.in> Content-Type: text Apparently-To: san@mbu.iisc.ernet.in Status: R Hello Sandeep! Extremely sorry for not responding earlier to your discussion. Actually I was busy preparing the manuscript of a paper. How are you ? Have you received any responses so far? The point that you have raised, about the relevance of the three dimensional structures predicted from crystal structure data analysis to experimental biologists is quite an important one. So many methods have been developed so far for predicting the sec. structures and many more may be still coming up. I think what is more important from the experimental point of view is the tertiary structure of proteins. So the efforts have to be concentrated on making more efficient and effective use of the crystal structure data for predicting tertiary structures. I personally feel that given a sufficiently large data set of highly resolved structures, one can get a lot of information on the tert. structures (thus, the size of data set and quality of structures being the limiting factors). In today's world of networks and high performance computing, the tools using cellular automata theory and neural networks can definitle can be exploited to derive biologically significant structures. My thoughts may sound too optimistic but then that is what I sincerely feel. I would welcome further discussion on this topic. What else? How's your work going on? Do write. I would have relatively less hectic time next week, hopefully. Also send me the responses from others. Bye for now. -Sangeeta.11 Feb. '95. From: cmda.abbott.com!STEWARTK Received: from randb.pprd.abbott.com (randb.abbott.com) by abtlabs.abbott.com with SMTP id AA20723 (5.65c/IDA-1.4.4 for ); Sat, 11 Feb 1995 12:49:58 -0600 Received: from DECNET-MAIL (STEWARTK@CMDA) by RANDB.PPRD.Abbott.Com (PMDF V4.3-13 #5551) id <01HMX9NS5Y688YZ76E@RANDB.PPRD.Abbott.Com>; Sat, 11 Feb 1995 12:52:49 -0600 (CST) Date: Sat, 11 Feb 1995 12:52:49 -0600 (CST) Subject: Re: CCL:data analysis of protein crystal structure To: san@mbu.iisc.ernet.in Message-Id: <01HMX9NS7K1U8YZ76E@RANDB.PPRD.Abbott.Com> X-Vms-To: RANDB::IN%"san@mbu.iisc.ernet.in" Mime-Version: 1.0 Content-Transfer-Encoding: 7BIT Status: R Sandeep: Here are some 1994 references in the area of Protein Structure Analysis: Protein Science 3, 1927-1937, 1994 FASAB J 8, 1237-1239 and 1240-1247, 1994 FEBS Letters 355, 213-219, 1994 CABIOS 10, 545-546, 1994 J. Mol. Biol. 242, 321-329, 1994 Curr. Opinion in Struct. Biol., 4 422-428, 1994 Proteins: Struct. Funct. Genet., 19, 222-229, 1994 Proteins: Struct. Funct. Genet., 19, 85-97 and 165-173 J. Mol. biol. 239, 306-314, 1994. Of course, all publications by Chris Sander and Janet Thornton are important in this area. Tom Blundell is also a researcher whose name comes to mind for important work in this area. Kent Stewart Department of Structural Biology Abbott Laboratories Chicago, IL, USA From: biosym.com!youkha (Philippe Youkharibache) Message-Id: <9502091857.AA15243@iris75.biosym.com> To: Subject: Re: CCL:data analysis of protein crystal structure Status: R Sandeep, I do not have the refs at hand, right now. however check in particular the work from Manfred Sippl Steve Bryant who derive residue base force fields for threading and in the longer term protein folding prediction, from statistical analysis of known protein structures Good luck Philippe ************************************************************************** Dr. Philippe Youkharibache e-mail: youkha@biosym.com Biosym Technologies Inc. 9685 Scranton Road tel: (619) 546 5562 San Diego, CA 92121 fax: (619) 458 0136 ************************************************************************** From: athe.wustl.edu!toni (Toni Kazic) Message-Id: <9502091953.AA14776@athe.wustl.edu> To: san@mbu.iisc.ernet.in In-Reply-To: <9502091622.AA16267@iisc.ernet.in> (san@mbu.iisc.ernet.in) Subject: Re: CCL:data analysis of protein crystal structure Status: R Dear Sandeep, I am not directly involved in that area, but I strongly encourage you in asking such straightforward and practical questions. There is too much special-casing and not enough analysis! Good luck, Toni Toni Kazic Institute for Biomedical Computing Washington University From: "William T. Winter" Subject: Re: CCL:data analysis of protein crystal structure To: san@mbu.iisc.ernet.in In-Reply-To: <9502091622.AA16267@iisc.ernet.in> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: R > state that my query evoked only two responses. Thiis board is still viewed by many as quantum chemistry and hence is probably not widly followe by protein crystallographers.Subscribe to bionet.xtallography on you nearest internet newstand and send them your request. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dr. William T. Winter Phone: (315)470-6876 315 Baker Lab FAX: (315)470-6856 SUNY-ESF Internet: wtwinter@mailbox.syr.edu Syracuse, NY 13210-2786 ******************end of summary************************************ From qfsaulo@usc.es Mon Feb 20 13:51:49 1995 Received: from uscmail.usc.es for qfsaulo@usc.es by www.ccl.net (8.6.9/930601.1506) id NAA02742; Mon, 20 Feb 1995 13:44:04 -0500 Received: by uscmail.usc.es (5.67b/1.34) id AA06918; Mon, 20 Feb 1995 19:46:50 +0100 Date: Mon, 20 Feb 1995 19:46:50 +0100 From: qfsaulo@usc.es (Saulo Vazquez Rodriguez) Message-Id: <199502201846.AA06918@uscmail.usc.es> To: chemistry@ccl.net Subject: Gaussian Quadrature Formulas Dear netters, I want to use the gaussian quadrature method for integral evaluation. I would greatly appreciate bibliografic information about this subject. Thanks in advance. Saulo Vazquez (qfsaulo@usc.es) From thep@risc1.lrm.fi.cnr.it Mon Feb 20 15:51:29 1995 Received: from risc1.lrm.fi.cnr.it for thep@risc1.lrm.fi.cnr.it by www.ccl.net (8.6.9/930601.1506) id PAA04858; Mon, 20 Feb 1995 15:22:39 -0500 Received: by risc1.lrm.fi.cnr.it (AIX 3.2/UCB 5.64/4.03) id AA29153; Mon, 20 Feb 1995 21:12:36 +0100 From: thep@risc1.lrm.fi.cnr.it (Pornthep Sompornpisut) Message-Id: <9502202012.AA29153@risc1.lrm.fi.cnr.it> Subject: help for Molscript (thanks) To: chemistry@ccl.net Date: Mon, 20 Feb 1995 21:12:36 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 508 Dear Colleagues, This is my message I posted on 17.02.95 > Dear Colleagues, > > Could anyone inform me how to get the program MOLSCRIPT? > Is the program available via ftp? > > Thanks in advance > Pornthep Many thanks again to the following persons who kindly gave me the information about the program MolScript. Brian W. Beck Jan Labanowski Harald Lanig Robert F. Setlik Rolf-Dietrich Stigler If there are many people interested the answers, I'll summarize to the net. Your sincerely, Pornthep From cmao771@charon.cc.utexas.edu Mon Feb 20 17:51:28 1995 Received: from hpcf.cc.utexas.edu for cmao771@charon.cc.utexas.edu by www.ccl.net (8.6.9/930601.1506) id RAA07178; Mon, 20 Feb 1995 17:16:18 -0500 Received: from charon.cc.utexas.edu by hpcf.cc.utexas.edu (5.0/SMI-SVR4) id AA23324; Mon, 20 Feb 1995 16:16:18 +0600 Received: by charon.cc.utexas.edu (5.61/CRI-80.1) id AA44648; Mon, 20 Feb 95 16:16:15 -0600 From: Bersuker Message-Id: <9502202216.AA44648@charon.cc.utexas.edu> Subject: MO LCAO with fractional charges To: chemistry@ccl.net (Computational Chemistry List) Date: Mon, 20 Feb 95 16:16:13 CST X-Mailer: ELM [version 2.3 PL11] content-length: 972 Dear Netters: We have a non-trivial problem. Developing a method of semiempirical fragmentary MO LCAO calculations, we encounter the necessity to calculate the electronic structure of molecular systems with FRACTIONAL CHARGES. So far, we couldn't find any existing method which can be easily adapted to include fractional charges; to our knowledge, all the known methods are reasonably assuming that the number of electron is integer. Could anybody help us with suggestions or hints? We promise to generalize the replies for the CCL. -- * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Isaac B. Bersuker | E-mail: Welch 3.140 | cmao771@charon.cc.utexas.edu (prefered) Dept. of Chemistry | bersuker@eeyore.cm.utexas.edu Univeristy of Texas at Austin | Phone: (512) 471-4671 Austin, TX 78712 | Fax: (512) 471-8696 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *