From hutschka@quantix.u-strasbg.fr Thu Mar 14 04:16:16 1996 Received: from quantix.u-strasbg.fr for hutschka@quantix.u-strasbg.fr by www.ccl.net (8.7.1/950822.1) id DAA29671; Thu, 14 Mar 1996 03:52:45 -0500 (EST) From: Received: by quantix.u-strasbg.fr (AIX 3.2/UCB 5.64/4.03) id AA33904; Thu, 14 Mar 1996 09:54:21 +0100 Date: Thu, 14 Mar 1996 09:54:21 +0100 Message-Id: <9603140854.AA33904@quantix.u-strasbg.fr> To: chemistry@www.ccl.net Subject: SUMARY : G92 ECP and F functions Cc: hutschka@quantix.u-strasbg.fr Hello, Two weeks ago I posted a question to the list. Here is the sumary of the answers I got : My question was : I had troubles with trying to optimize a geometry with g92 (RevE.2). I'm trying to optimize a geometry at the HF level using the Berny algorithm. A RECP describe the core electrons of the metal and it contains G,S-G,P-G,D-G,F-G components. The basis set associated with this RECP is a [3s,3p,2d,2f] GTF basis set. I've no troubles to perform single point calculations but the optimization lead to the following error message : ------ RHF calculation of E ------ Compute integral first derivatives. ... and contract with generalized density number 0. Use density number 0. RysSet: KIntrp= 2534 KCalc= 0 KAssym= 2170 L702 exits ... SP integral derivatives will be done elsewhere. Compute integral first derivatives. Integral derivatives from FoFDir, PRISM(SPDF). MinBra= 0 MaxBra= 3 MinLOS=-1 MaxLOS=-1 MinRaf= 0 MaxRaf= 3 MinLRy= 4. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E=1 JSym2E=1. Fock matrices symmetrized in FoFDir. Use density number 0. MaxL=3 MaxP=3 NDeriv=1 MaxT=77 L709 cannot do derivatives in this basis. Error termination in Lnk1e. ------ The error is arrising from the l709 link I've looked at the code and it cames from the ECPGRD Subroutine wich compute the derivatives of one electron integrals over effective core potentials. I looked at the manual and found nothing... I've tried other tests and my believe is that it is not possible to have F function describing the valence electrons of the metal if you have a ECP (or RECP) for the core and if you intend to optimize a geometry. So my question is : Does anybody know such limitations with g92 and ECP ? More what are the limits in term of component (S,P,D,F) of a basis set for an atom ?. Does anybody know if this problem could be avoided with g94 ?. So any help or comment would be appreciated. I will sumarize for the list. THE ANSWERS ARE : ***************************************************************** >From Kazuo Teraishi : ***************************************************************** I just encountered exactly the same problem with gaussian 94. I think there are some limitations with ECP which are not mentioned in the manual. Another limitation I came accross was the calculation of analytical second derivatives with ECP. E-mail : JDA03546@niftyserve.or.jp ***************************************************************** >From Dr. David Danovich ***************************************************************** What you probably should do is to optimize by Fletcher-Powell (FP) algorithm which does not require derivatives. E-mail : dodik@yfaat.ch.huji.ac.il ****************************************************************** >From Douglas J. Fox (Director of Technical Support) ****************************************************************** The limit is on computing the derivatives of integrals using higher than d functions with ECP's. This is not an aspect of Gaussian 92 that was improved with G94. You can optimize these geometries with OPT=FP which requires only energies and not gradients but it can be too slow if you have a large number of degrees of freedom. E-mail : help@gaussian.com ****************************************************************** ****************************************************************** It's therefore clear that it's not possible to compute analytic derivatives if the basis set of the metal atom describe by an ECP contains higher than d functions. The alternative way to optimize a geometry in this case is to use the FP procedure and thus to choose as small as possible number of degrees of freedom. I thanks all those who answered . Even those wich are not cited here because they send me MIME encoded messages wich our mail did not understand. I hope this sumary will be helpfull. HUTSCHKA Francois. Laboratory of Quantum Chemistry Universite Louis Pasteur STRASBOURG - FRANCE E-Mail : hutschka@quantix.u-strasbg.fr From owner-chemistry@ccl.net Thu Mar 14 12:16:21 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id LAA06856; Thu, 14 Mar 1996 11:49:06 -0500 (EST) Received: from fair1.fairfield.edu for LSTEFFEN@fair1.fairfield.edu by bedrock.ccl.net (8.7.1/950822.1) id LAA23999; Thu, 14 Mar 1996 11:48:53 -0500 (EST) From: Received: from fair1.fairfield.edu by fair1.fairfield.edu (PMDF V4.3-7 #10178) id <01I2BSXMV5JK8YCTQT@fair1.fairfield.edu>; Thu, 14 Mar 1996 11:48:45 EST Date: Thu, 14 Mar 1996 11:48:45 -0500 (EST) Subject: Environmental Science Textbook To: chemistry@ccl.net Message-id: <01I2BSXMXKCI8YCTQT@fair1.fairfield.edu> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT We are developing an intermediate level course in environmental science. I would be interested to know peoples opinions on textbooks available for such a course. The course will stress basic physics and chemistry and it is aimed at Juniors. We have looked at a number of books, for example J. Beard "Chem. Energy and the Inv." (a little to general) and Schwrtzenbach "Env. Org. Chem." (to specific and maybe to high of a level). If there is sufficient response I will post a summary back to the list. Please send replies directly to me: lsteffen@fair1.fairfield.edu Thanks, L. Kraig Steffen Chemistry Fairfield University Fairfield CT 06430 203 254 4000 x 2254 fax: 203 254 4034 email: lsteffen@fair1.fairfield.edu www: http://192.160.244.139/chem/chem.html From rosas@irisdav.chem.vt.edu Thu Mar 14 12:34:51 1996 Received: from irisdav.chem.vt.edu for rosas@irisdav.chem.vt.edu by www.ccl.net (8.7.1/950822.1) id MAA07056; Thu, 14 Mar 1996 12:15:04 -0500 (EST) Received: by irisdav.chem.vt.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id MAA09136; Thu, 14 Mar 1996 12:13:40 -0500 From: "Victor M. Rosas Garcia" Message-Id: <9603141213.ZM9134@irisdav.chem.vt.edu> Date: Thu, 14 Mar 1996 12:13:35 -0500 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: "Geometry is not a stationary point" message... Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi everybody, I currently running some geometry optimizations of some phosphorus-containing rings in MOPAC93. My route card looks like this: PM3 GNORM=0.01 EPS=78.3 CHARGE=1 T=3600.00 EF LET DDMIN=0.0 NOINTER NOLOG and in several cases I get the error message: WARNING -- GEOMETRY IS NOT AT A STATIONARY POINT In the manual says that: "To avoid this message, make sure that the geometry can be optimized, given the optimization flags you have chosen. In particular, if (3N-6) optimization flags are set, and there are no dummy atoms, then it is unlikely that this message will be generated." I guess I hit one of those *unlikely* cases :( So my questions are: a) Do I have to worry about this message? b) Should I reoptimize those geometries to get rid of the error? c) Is it only an artifact because I specified a GNORM=0.01? I'm wondering, because in all cases the final gradient norm is < 1.0 and in most cases is < 0.5 (which I think is pretty good) Any suggestions are welcome. TIA Victor -- ----------------------------------------------------------------------- Victor M. Rosas Garcia * "How can we contrive to be rosas@irisdav.chem.vt.edu * at once astonished at the Virginia Tech doesn't necessarily share * world and yet at home in it?" the opinions you just read. * G. K. Chesterton ----------------------------------------------------------------------- From shenderm@aruba.ccit.arizona.edu Thu Mar 14 13:16:22 1996 Received: from aruba.ccit.arizona.edu for shenderm@aruba.ccit.arizona.edu by www.ccl.net (8.7.1/950822.1) id MAA07172; Thu, 14 Mar 1996 12:25:18 -0500 (EST) Received: (from shenderm@localhost) by aruba.ccit.arizona.edu (8.7.5/8.7.3) id KAA42013; Thu, 14 Mar 1996 10:26:08 -0700 Date: Thu, 14 Mar 1996 10:26:08 -0700 (MST) From: Mark D Shenderovich X-Sender: shenderm@aruba.ccit.arizona.edu To: rosa@risc2.iaif.pa.cnr.it cc: chemistry@www.ccl.net Subject: Re: CCL:AMBER potentials In-Reply-To: <9603051524.AA19415@risc2.iaif.pa.cnr.it> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 5 Mar 1996 rosa@risc2.iaif.pa.cnr.it wrote: > Dear Netters, > > I'd like to know if polysaccharides - polysaccharides > polysaccharides - polypeptides potentials are > available for AMBER. > See the last publication of MacroModel group in JACS,1996,18,2078-2086. Mark Shenderovich. From owner-chemistry@ccl.net Thu Mar 14 13:18:54 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id MAA07465; Thu, 14 Mar 1996 12:46:32 -0500 (EST) Received: from aruba.ccit.arizona.edu for shenderm@aruba.ccit.arizona.edu by bedrock.ccl.net (8.7.1/950822.1) id MAA25258; Thu, 14 Mar 1996 12:46:28 -0500 (EST) Received: (from shenderm@localhost) by aruba.ccit.arizona.edu (8.7.5/8.7.3) id KAA95308; Thu, 14 Mar 1996 10:46:52 -0700 Date: Thu, 14 Mar 1996 10:46:52 -0700 (MST) From: Mark D Shenderovich X-Sender: shenderm@aruba.ccit.arizona.edu To: Chyh-chong Chuang cc: str-nmr@net.bio.net, molmodel@net.bio.net, chemistry@ccl.net Subject: Re: CCL:coupling constant restrain of D-Amino Acid for structural refine. In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 12 Mar 1996, Chyh-chong Chuang wrote: > > Dear Netters: > > Does any one could point me some references about how to use the > measured 3J-na coupling constant of a D-form amino acid as an additional > restrain in nmr structural refinement. > Any suggest/comment will be great appreciated. > > Thanks all Dear Chuang, If you know how to use these coupling constants for L-amino acids, there is no problem with D-amino acids. The only difference is that for D-AA the angle H-N-Ca-H which is used in Karplus equation, is calculated as |phi+60|, and for L-AA it is |phi-60|, where phi is conventional torsional angle around N-Ca bond. Depending on available software, you may calculate expected phi angles and use them as constrains, or you may use exptl. coupling constants as direct constraints in MD simulations. The latter is preferable. See: Mierke & Kessler, Biopolymers, 1993, 33, 1003; Mierke et al., Biopolymers, 1994, 34, 559. Best regards, Mark Shenderovich. From qiang@euch4e.chem.emory.edu Thu Mar 14 14:16:21 1996 Received: from euch4e.chem.emory.edu for qiang@euch4e.chem.emory.edu by www.ccl.net (8.7.1/950822.1) id NAA08201; Thu, 14 Mar 1996 13:22:12 -0500 (EST) From: Received: by euch4e.chem.emory.edu (AIX 3.2/UCB 5.64/4.03) id AA23931; Thu, 14 Mar 1996 13:22:06 -0500 Date: Thu, 14 Mar 1996 13:22:05 -0500 (EST) To: hutschka@quantix.u-strasbg.fr Cc: chemistry@www.ccl.net, hutschka@quantix.u-strasbg.fr Subject: Re: CCL:G:SUMARY : G92 ECP and F functions In-Reply-To: <9603140854.AA33904@quantix.u-strasbg.fr> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Actually, I've extended the ECP integral routines to higher l(to h? if I remeber) values. Actually we have also implemented analytical hessian with ECP into Gaussian9x (x=2,4), which might be avaliable in the future. With this extension, u can calculate analytical hessian with f function (then of course gradient with f function) with DFT, HF, and MP2. (well, f function with MP2.., a little disk-demanding) However, the issume is, is f function crucial to ur geometry?! I guess one should always consider this before doing large calculations. For energetics, sure. But for geometry, according to our experince and literature, is not not critical. Of course, u know ur system the best. Any way, let's hope the code will be released in the near future. On Thu, 14 Mar 1996 hutschka@quantix.u-strasbg.fr wrote: > > Hello, > > Two weeks ago I posted a question to the list. > Here is the sumary of the answers I got : > > My question was : > > I had troubles with trying to optimize a geometry > with g92 (RevE.2). > I'm trying to optimize a geometry at the HF level > using the Berny algorithm. > A RECP describe the core electrons of the metal and it contains > G,S-G,P-G,D-G,F-G components. > The basis set associated with this RECP is a [3s,3p,2d,2f] > GTF basis set. > I've no troubles to perform single point calculations but the > optimization lead to the following error message : > > ------ > RHF calculation of E > ------ > Compute integral first derivatives. > ... and contract with generalized density number 0. > Use density number 0. > RysSet: KIntrp= 2534 KCalc= 0 KAssym= 2170 > L702 exits ... SP integral derivatives will be done elsewhere. > Compute integral first derivatives. > Integral derivatives from FoFDir, PRISM(SPDF). > MinBra= 0 MaxBra= 3 MinLOS=-1 MaxLOS=-1 MinRaf= 0 MaxRaf= 3 MinLRy= 4. > IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E=1 JSym2E=1. > Fock matrices symmetrized in FoFDir. > Use density number 0. > MaxL=3 MaxP=3 NDeriv=1 MaxT=77 > L709 cannot do derivatives in this basis. > Error termination in Lnk1e. > > ------ > > The error is arrising from the l709 link > I've looked at the code and it cames from the ECPGRD Subroutine > wich compute the derivatives of one electron integrals over effective > core potentials. > I looked at the manual and found nothing... > I've tried other tests and my believe is that it is not possible to > have F function describing the valence electrons of the metal > if you have a ECP (or RECP) for the core and if you intend to > optimize a geometry. > So my question is : > Does anybody know such limitations with g92 and ECP ? > More what are the limits in term of component (S,P,D,F) > of a basis set for an atom ?. > Does anybody know if this problem could be avoided with > g94 ?. > So any help or comment would be appreciated. > I will sumarize for the list. > > THE ANSWERS ARE : > > ***************************************************************** > >From Kazuo Teraishi : > ***************************************************************** > > I just encountered exactly the same problem with gaussian 94. > I think there are some limitations with ECP which are not mentioned > in the manual. Another limitation I came accross was the > calculation of analytical second derivatives with ECP. > > E-mail : JDA03546@niftyserve.or.jp > > ***************************************************************** > >From Dr. David Danovich > ***************************************************************** > > What you probably should do is to optimize by Fletcher-Powell (FP) > algorithm which does not require derivatives. > > E-mail : dodik@yfaat.ch.huji.ac.il > > ****************************************************************** > >From Douglas J. Fox (Director of Technical Support) > ****************************************************************** > > The limit is on computing the derivatives of integrals using higher > than d functions with ECP's. This is not an aspect of Gaussian 92 that > was improved with G94. > > You can optimize these geometries with OPT=FP which requires only > energies and not gradients but it can be too slow if you have a large number > of degrees of freedom. > > E-mail : help@gaussian.com > > ****************************************************************** > ****************************************************************** > > It's therefore clear that it's not possible to compute analytic > derivatives if the basis set of the metal atom describe by an ECP > contains higher than d functions. > The alternative way to optimize a geometry in this case is to use > the FP procedure and thus to choose as small as possible number of > degrees of freedom. > I thanks all those who answered . > Even those wich are not cited here because they send me MIME encoded > messages wich our mail did not understand. > I hope this sumary will be helpfull. > > HUTSCHKA Francois. > Laboratory of Quantum Chemistry > Universite Louis Pasteur > STRASBOURG - FRANCE > E-Mail : hutschka@quantix.u-strasbg.fr > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: hutschka@quantix.u-strasbg.fr > -- Original Sender From: Address: hutschka@quantix.u-strasbg.fr > 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 > > ______________________________________________________________ Qiang Cui Dept. of Chem. Emory Univ. 508 Webster Dr. Apt.#2 Atlanta, GA 30322. Decatur, GA 30033. (404)-727-2381 (404)-636-6149 http://tswww.cc.emory.edu/~qcui ______________________________________________________________ From LCHEN@BINAH.CC.BRANDEIS.EDU Thu Mar 14 15:16:27 1996 Received: from binah.cc.brandeis.edu for LCHEN@BINAH.CC.BRANDEIS.EDU by www.ccl.net (8.7.1/950822.1) id OAA10880; Thu, 14 Mar 1996 14:26:42 -0500 (EST) From: Received: from BINAH.CC.BRANDEIS.EDU by BINAH.CC.BRANDEIS.EDU (PMDF V4.3-10 #10451) id <01I2BYO6T7688XDK4N@BINAH.CC.BRANDEIS.EDU>; Thu, 14 Mar 1996 14:26:40 -0500 (EST) Date: Thu, 14 Mar 1996 14:26:40 -0500 (EST) Subject: look for VersaTermPRO To: chemistry@www.ccl.net Message-id: <01I2BYO6TGTE8XDK4N@BINAH.CC.BRANDEIS.EDU> X-VMS-To: IN%"chemistry@www.ccl.net" X-VMS-Cc: LCHEN MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netter, I'm looking for a Mac version of VersaTermPRO program. Thanks in advance. -Lingran ======================== Lingran Chen, Ph.D. Department of Chemistry Brandeis University Waltham MA 02254-9110 USA ======================== From owner-chemistry@ccl.net Thu Mar 14 15:26:05 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id PAA11096; Thu, 14 Mar 1996 15:03:53 -0500 (EST) Received: from ribozyme.vadms.wsu.edu for thompson@ribozyme.vadms.wsu.edu by bedrock.ccl.net (8.7.1/950822.1) id PAA28604; Thu, 14 Mar 1996 15:03:49 -0500 (EST) Received: by ribozyme.vadms.wsu.edu (950413.SGI.8.6.12/930416.SGI) id JAA01241; Thu, 14 Mar 1996 09:58:39 -0800 Date: Thu, 14 Mar 1996 09:58:38 -0800 (PST) From: "Steven M. Thompson" To: PSB general interest , ackerman@hpcc.gov, aday@julian.uwo.ca, adelling@indiana.edu, adrian.smith@veths.no, afagen@nucleus.harvard.edu, alan@reed.edu, allenc@ucmp1.berkeley.edu, attwood@bsm.bioc.ucl.ac.uk, best@zoology.washington.edu, bill@lmc.med.howard.edu, bio-soft@net.bio.net, biomatrix@net.bio.net, bionews@net.bio.net, bioquest@beloit.edu, boone@ese.ogi.edu, brianf@salus.med.uvm.edu, broe@aardvark.ucs.uoknor.edu, brutlag@cmgm.stanford.edu, butler@gcg.com, cfleming@alleg.edu, PSB co-chairs -- Russ Altman , A Keith Dunker , Larry Hunter , Teri Klein , Sharon Surles , chemistry@ccl.net, chod21633@ggr.co.uk, clayton.naeve@stjude.org, cohen@cgl.ucsf.edu, comp-bio@net.bio.net, crip@phar.umich.edu, ctibiol@liverpool.ac.uk, d.waddell@mailbox.uq.oz.au, danj@dev.gdb.ORG, Davison@UH.EDU, devereux@gcg.com, dewittd@pilot.msu.edu, dhusic@esu.edu, dibug@comp.bioz.unibas.ch, dubayc@ohsu.edu, eddy@sequencer.wustl.edu, els@eti.bio.uva.nl, eric-johnson@uiowa.edu, ernest@lenti.med.umn.edu, fuellen@dali.Mathematik.Uni-Bielefeld.DE, fvega@lambda.gene.cinvestav.mx, gaeta@angis.su.oz.au, gary@amanita.biom.cornell.edu, gary@phylo.life.uiuc.edu, gernert@suna.biochem.duke.edu, gilbertd@bio.indiana.edu, gribskov@sdsc.edu, hagen@bscr.uga.edu, havel@ptolemy.med.harvard.edu, higgins@ebi.ac.uk, hsiao@mail.pmf.org.tw, info-gcg@net.bio.net, ingvar.eidhammer@ii.uib.no, inquiry@educom.edu, jcvs@scientia.up.ac.za, Joe@Genetics.Washington.EDU, joef@dnacore.mbp.missouri.edu, johnsoda@etsuserv.east-tenn-st.edu, jrebers@nmu.edu, k-murphy@uiowa.edu, karplus@cse.ucsc.edu, koza@cs.stanford.edu, krishna%bic-mku@dbt.ernet.in, KRobison@nucleus.harvard.edu, levitt@cellbio.stanford.edu, lybrand@proteus.bioeng.washington.edu, lzh@UTKVX.UTCC.utk.edu, mars@parvati.lv-whi.nevada.edu, mary@evl.eecs.uic.edu, mathog@seqaxp.bio.caltech.edu, meir@zoology.washington.edu, mgouy@biomserv.univ-lyon1.fr, michaelw@cs.su.oz.au, miked@visembryo.ucsf.edu, mol-evol@net.bio.net, molmodel@net.bio.net, mount@joplin.biosci.arizona.edu, mpagel@indiana.edu, msssf@ibm.cl.msu.edu, msw@hto-d.usc.edu, oleson@plains.nodak.edu, ooi@kuier.kyoto-u.ae.jp, pak4@cornell.edu, paolo@risc1.ist.unige.it, philstas@vub.ac.be, pmiller@liverpool.ac.uk, pps@iona.cryst.bbk.ac.uk, Susan Jean Johns , rasmol@ggr.co.uk, rdavis@sfsu.edu, rickl@ai.mit.edu, robert.murphy@cmu.edu, robert@TechFak.Uni-Bielefeld.DE, roger_blumberg@brown.edu, schuster@icbr.ifas.ufl.edu, sgilber1@cc.swarthmore.edu, shoop@cs.umn.edu, slezak@llnl.gov, smeinhar@badlands.nodak.edu, Sogin@evol5.MBL.EDU, sspencer@rhino.bocklabs.wisc.edu, sunil@tripos.com, swhite@cc.brynmawr.edu, swolf@koko.csustan.edu, swope@almaden.ibm.com, takagi@ims.u-tokyo.ac.jp, "Steve M. Thompson" , thornton@bsm.bioc.ucl.ac.uk, tim@angis.su.oz.au, tree@ag.Arizona.EDU, ugarkov@olimp.irb.hr, webb@cse.psu.edu, wehart@cs.sandia.gov, woodman@macmail.chem.washington.edu Subject: Pacific Symposium on Biocomputing Education Session CFP Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: QUOTED-PRINTABLE Dear Colleague, Please find enclosed a "Call for Participation" for the upcoming educational issues session to be held as part of the 1997 Pacific Symposium on Biocomputing (PSB '97).=20 We are very excited about this meeting and about our session. We hosted a similar session at PSB '96 that was favorably received and generated a considerable amount of interest. To the best of our knowledge no other meetings on computational approaches to molecular biology provide a forum on educational issues, yet this is and will remain an extremely important and relevant topic in this field.=20 Please take a few minutes to fill out and return the enclosed questionnaire if you didn't do it for us last year. We would especially like your comments regarding what you think are the most important issues in biocomputing education. Plan to submit a paper or poster if you can, but at least mark the meeting on your calendar and consider joining us in Hawaii next year.=20 =09Regards, Susan J. Johns and Steven M. Thompson +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++= +++++ A Call For Participation: BIOCOMPUTING EDUCATION II: FURTHER CHALLENGES AND OPPORTUNITIES=20 "The Workshop Setting" Pacific Symposium on Biocomputing Hawaii - January 6-9, 1997 Ritz Carlton Kapalua on Maui Session Chairs: Susan J. Johns and Steven M. Thompson =09 Center for Visualization, Analysis and Design in the Molecular Sciences (VADMS) Washington State University Pullman, WA 99164-1224 =09 phone: (509) 335-0424 & 335-0533 FAX: (509) 335-9688 & 335-0540 e-mail: prcadams@ribozyme.vadms.wsu.edu thompson@ribozyme.vadms.wsu.edu We invite participation in the 1997 Pacific Symposium in Biocomputing=20 (PSB '97) Educational Issues Session. The PSB '97 Biocomputing Education Session will focus on "the workshop format: How to fund, organize, and implement for success." We particularly want to encourage the submission of manuscripts and poster abstracts covering various aspects of delivering workshops within any subspecialty of biocomputing; however, we do not wish to discourage the submission of general works in all manners of biocomputing education as well. Please refer to our World Wide Web pages on this field for an overview of some of the many resources available (http://ribozyme.vadms.wsu.edu/~vadms/teach.html).=20 At present there is little defined curricula for computational molecular biology. Although specific individuals have developed courses or workshops, educational materials such as textbooks or laboratory exercises are not widely available. In addition to the absence of formal materials, there is also a lack of communication among those of us who are now teaching courses in this domain. Correcting the deficiencies regarding the lack of educational materials and the lack of communication on educational issues represents both a challenge and an opportunity for the community of scientists who are currently doing research in biocomputing.= =20 Recognizing this need for an educational forum, the Pacific Symposium on Biocomputing has once again included our session on biocomputing education as part of its overall program. Our hope is that this session will further serve as an important node with regard to the dissemination of educational materials, information, and approaches in this field.=20 Our session will be structured to encourage the open exchange of information regarding teaching philosophies, teaching materials, and teaching experiences --- "how" to teach biocomputing --- especially using the workshop format, between all participants. It will consist of a poster session plus an hour long discussion forum with a panel consisting of individuals who have presented successful biocomputing workshops. We will also nominate the best paper submitted to our session for possible oral presentation during a general session. The PSB conference co-chairs will select a manuscript from the nominated papers submitted by each session for these oral presentations. We further hope to organize informal discussion groups to be held periodically throughout the conference. We feel that this is particularly important in order to help overcome many participants' inertia regarding intragroup conversation. Submissions: We encourage you to submit full technical papers on biocomputing education, particularly using the workshop format, to be included in a standard refereeing process. Submitted papers will be peer reviewed by at least three independent referees. Those papers that are accepted will be published in an archival proceedings. The papers are restricted to 12 pages; PSB format templates will be provided. We envision that such papers could range from philosophical discussions on biocomputing education to the nuts-and-bolts of particular workshops that are enjoying significant success. As mentioned above, we will select one manuscript >from the accepted papers for possible oral presentation.=20 Authors who do not wish to submit a peer-reviewed paper are encouraged to submit a poster abstract. These abstracts will not be published in the proceedings. However, they will be distributed to all attendees as a separate volume. Furthermore, all abstract authors will have the opportunity to display their posters and/or deliver live computer demonstrations. We also envision that many of the discussion forum panelists will be from this group as well as from those whom have submitted papers. If you have been involved in presenting biocomputing technigues within a workshop format, please indicate in your submission whether you would be interested in serving on this panel.=20 Even if you do not want to submit anything officially to the session, we hope that you will be able to attend and participate in the conference.=20 Bring your outlines, syllabi, laboratory exercises, videotapes, or any=20 other instructional means, as well as your ideas to share among the=20 participants. We want your involvement. =20 General Conference Description: PSB '97 will be held January 6-9, 1997, and will be the 4th consecutive annual meeting (inclusive of HICCS 94-95 biocomputing subsection) devoted to the broad domain of computational biology, with an emphasis in the data-rich area of molecular biology. PSB '96 attracted 145 participants >from throughout the world. PSB is one of the oldest, continously held meetings devoted to the biology/computer science interface and is distinguished from other conferences in this domain by its emphasis on tool development. Please refer to the PSB World Wide Web pages (http://cgl.ucsf.edu/psb/) for an announcement of the upcoming meeting, and the last meeting's announcement, attendee listing, and delivered papers (many available in PostScript format for downloading).=20 Important specific features of this conference are: 1. organization of the meeting is by the participants themselves, who submit proposals for sessions that are then selected by the organizing committee; 2. the chosen session chairs issue calls for papers for their respective sessions and then oversee the review of the submitted papers; 3. invitations to give oral presentations in the various sessions are predicated upon the acceptance of peer-reviewed manuscripts; 4. the accepted papers are published as a hardbound conference proceedings (PSB'96, ISBN 981-02-2578-4); 5. an electronic version of the conference proceedings is also available; 6. live software demonstrations across a broad domain of biology are featured; and 7. an educational issues forum is included within this research meeting. The teaching of computational biology and molecular biology are in their formative stages; this educational forum can play a pivotal role in the development of this field.=20 About 20 proposals for sessions were submitted to the organizing committee for PSB '97; these were pared down to include at least the following six=20 topical areas: =091) intelligent databases for molecular biology;=20 =092) recent developments in visualization;=20 =093) molecular evolution;=20 =094) analysis and prediction of protein structure;=20 =095) new directions in molecular dynamics, including quantum =09=09mechanical/molecular mechanical hybrid systems;=20 =096) educational issues, particularly using the workshop format.=20 Key dates: Immediate =09--=09Return of questionnaire July 1=09=09--=09Manuscripts and poster abstracts due =09=09=09(extensions allowed by arrangement) August 15=09--=09Review process must be finished September 15=09--=09Final, camera ready copy, due +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++= +++++ Pacific Symposium on Biocomputing --- Educational Issues Questionnaire (We sent out a similar questionnaire last year; if you filled it out then, there is no need to repeat the work, unless you want to update some sections --- we have your data on file. Thanks.) Please provide us with the following information: =09Name: =09E-Mail: =09Address: =09=09=09=09=09=09=09=09 =09Telephone:=09=09FAX: General comments on Biocomputing Education: Courses or workshops you are teaching in the broadly defined field of "Biocomputing" and the year such courses or workshops began: A brief statement of your willingness to participate in the 1997 meeting=20 as one: =A7 Who would submit a paper or poster abstract by July 1 describing course= ,=20 workshop, or curriculum issues, and who would subsequently attend the=20 meeting to present the poster or paper (oral paper presentation - if=20 nominated by us and chosen for delivery by PSB organizing committee); =09(yes or no):=20 =09if yes, tentative title, and whether you wish to submit in paper=20 or poster format: =A7 Who would plan to attend the meeting, participate in the panel discussi= on, the software demonstrations, and the poster session on educational issues= ,=20 but who would not submit a paper or poster;=20 =09(yes or no): =A7 Who might or might not attend the meeting, but who would be willing to= =20 review papers. =09(yes or no): Names and addresses of others who might be interested in participating in t= he educational session, especially the names and addresses of possible referee= s: Finally, as there might be some limited funds available to support participants, please indicate whether you would require financial support to attend the meeting. Funds would be absolutely required, =09yes or no: Please e-mail the filled-out questionnaire to: =09 =09=09=09thompson@ribozyme.vadms.wsu.edu or FAX to:=09=09(509) 335-9688=20 or snail-mail to:=09Steve Thompson =09=09=09Washington State University =09=09=09VADMS Center =09=09=09Pullman WA 99164-1224 From dsmith@debye.dasgroup.com Thu Mar 14 17:16:30 1996 Received: from cool95.third-wave.com for dsmith@debye.dasgroup.com by www.ccl.net (8.7.1/950822.1) id QAA12277; Thu, 14 Mar 1996 16:44:02 -0500 (EST) Received: from mailer ([206.31.47.69]) by cool95.third-wave.com (Netscape Mail Server v1.1) with SMTP id AAA128 for ; Thu, 14 Mar 1996 04:44:06 +0000 X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: dsmith@debye.dasgroup.com (Doug Smith) Subject: ZINDO/S paramter for Ru? Date: Thu, 14 Mar 1996 04:44:06 +0000 Message-ID: <19960314044405509.AAA128@mailer> Is anyone aware of ZINDO/S parameters for ruthenium (Ru)? I am running an organometallic species using Hyperchem 4.5 and the only available semiempirical method is ZINDO/1. Doug -- Douglas A. Smith, Ph.D. President and CEO | voice: (814) 262-9091 The DASGroup, Inc. | fax: (814) 262-9337 325 Beaver Court | email: dsmith@dasgroup.com Johnstown, PA 15905-1801 | or: dsmith@debye.dasgroup.com Contract R&D specialists in computational chemistry, process modeling, synthesis and design of new compounds for organic, bioorganic, polymer and biotechnology. From owner-chemistry@ccl.net Thu Mar 14 17:23:13 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id QAA12179; Thu, 14 Mar 1996 16:28:34 -0500 (EST) Received: from tribeca.ios.com for janetc@cache.com by bedrock.ccl.net (8.7.1/950822.1) id QAA00925; Thu, 14 Mar 1996 16:28:04 -0500 (EST) Received: from [206.20.33.48] (ppp-48.ts-1.hp.idt.net [206.20.33.48]) by tribeca.ios.com (8.6.11/8.6.9) with SMTP id QAA03581 for ; Thu, 14 Mar 1996 16:25:31 -0500 X-Sender: janetc@tribeca.ios.com Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 14 Mar 1996 16:27:50 -0400 To: chemistry@ccl.net From: janetc@cache.com (Janet Cicariello-Cook) Subject: VersaTerm Pro VersaTerm Pro is from Synergy Software Their URL is http://www.synergy.com/ Janet ********************************************************************** * * * Janet Cicariello-Cook, Ph.D. * * Applications Scientist ############### * * CAChe Scientific - Oxford Molecular Group ## ##### ##### * * 1200 Route 22 East ## ##### ##### * * Suite 2000 ## ##### ##### * * Bridgewater, NJ 08807 ## #### #### * * ph: (908) 253-3610 ## ### ### * * fax: (908) 725-0296 ## ## ## * * e-mail: janetc@cache.com ############### * * http://www.oxmol.com/ * * * **********************************************************************