From NETNEWS@UICVM.CC.UIC.EDU Mon Jan 24 00:52:38 1994 Received: from phem3 for NETNEWS@UICVM.CC.UIC.EDU by www.ccl.net (8.6.4/930601.1506) id AAA20572; Mon, 24 Jan 1994 00:49:52 -0500 Received: from UICVM.CC.UIC.EDU (MAILER@UICVM) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #3557) id <01H81ITVZZUO95WHI2@phem3.acs.ohio-state.edu>; Mon, 24 Jan 1994 00:49:41 EST Received: from UICVM.UIC.EDU (NJE origin NETNEWS@UICVM) by UICVM.CC.UIC.EDU (LMail V1.1d/1.7f) with BSMTP id 7280; Sun, 23 Jan 1994 23:49:29 -0600 Date: Sun, 23 Jan 1994 22:42:23 -0600 (CST) From: "MARYANNE A.C. CUSTODIO" Subject: Chelation agent needed... Sender: NETNEWS@UICVM.UIC.EDU To: CHEMISTRY@ccl.net Message-id: <94023.224223U34212@uicvm.uic.edu> Organization: University of Illinois at Chicago, ADN Computer Center Content-transfer-encoding: 7BIT Distribution: local Path: uicvm.uic.edu!u34212 Newsgroups: bit.listserv.chemistry Lines: 10 Hello. I don't know if this is the right group to ask this question, but here goes...I am doing some research and I need a chelation agent for soil remediation. I have 350 mg of Cadmium per kg of soil, 100 mg of Silver per kg of soil, and 100 of Copper per kg of soil, and must be removed to the following levels: 15 mg Cadmium, 15 mg Silver, and 15 mg Copper. Is there a chelation agent that can do this? Are there any references that I can turn to? I appreciate any help regarding this matter. Thanks! Maryanne U34212@uicvm.uic.edu From frj@dou.dk Mon Jan 24 03:52:43 1994 Received: from danpost.uni-c.dk for frj@dou.dk by www.ccl.net (8.6.4/930601.1506) id DAA21107; Mon, 24 Jan 1994 03:26:31 -0500 Received: from localhost (ean@localhost) by danpost.uni-c.dk (8.6.4/8.6) id JAA06064 for chemistry@ccl.net; Mon, 24 Jan 1994 09:26:19 +0100 Date: 24 Jan 94 9:26 +0100 From: Frank Jensen To: chemistry@ccl.net Message-ID: <1013*frj@dou.dk> Subject: ORTEP for Mac? A spin-off question from the inquire about a version of ORTEP that runs under DOS: is there a versionof ORTEP that runs on a Macintosh? Frank From orgk2-a.sundin@macpost.lu.se Mon Jan 24 06:03:44 1994 Received: from nomina.lu.se for orgk2-a.sundin@macpost.lu.se by www.ccl.net (8.6.4/930601.1506) id FAA21735; Mon, 24 Jan 1994 05:34:13 -0500 Received: from macpost.lu.se by nomina.lu.se with SMTP (5.65/IDA-1.2.8) id AA08255; Mon, 24 Jan 94 11:35:09 +0100 Subject: Re: MM3 on the Mac To: pbays@saintmarys.edu, chemistry@ccl.net From: Anders.Sundin@orgk2.lth.se Date: Mon, 24 Jan 94 11:34:27 +0100 Message-Id: <940124.113427.26831@macpost.lu.se> Phil Bays wrote: >In response to my inquiry about MM3 on a 486 PC, I have had several >questions raised about the Mac version of MM3 published by InStar. >It is my understanding that MM3 has now been ported as is sold as part >of the MacMimic package. Although I do have a working version of MM3 on my Macintosh Quadra, it is not yet ready for public consumption. I estimate that it will take another two months to test and polish MM3 for the Macintosh. -Anders -- Anders Sundin e-mail: Anders.Sundin@orgk2.lth.se Organic Chemistry 2 ok2aps@selund.bitnet Lund University, P.O. Box 124 voice: +46 46 104130 S-22100 Lund, Sweden fax: +46 46 108209 From chp1aa@surrey.ac.uk Mon Jan 24 06:13:00 1994 Received: from sun2.nsfnet-relay.ac.uk for chp1aa@surrey.ac.uk by www.ccl.net (8.6.4/930601.1506) id FAA21742; Mon, 24 Jan 1994 05:35:32 -0500 Via: uk.ac.surrey; Mon, 24 Jan 1994 10:30:35 +0000 Via: central.surrey.ac.uk; Mon, 24 Jan 94 10:30:29 GMT Received: by central.surrey.ac.uk (1.37.109.8/16.2) id AA18886; Mon, 24 Jan 1994 10:30:27 GMT From: Mr Andrew D Allen Message-Id: <9401241030.AA18886@central.surrey.ac.uk> Subject: Orbital energies in AMPAC To: chemistry@ccl.net Date: Mon, 24 Jan 94 10:30:27 GMT Mailer: Elm [revision: 70.85] Dear All I am trying to calculate accurate orbital energies for a series of molecules using AMPAC2.1 under AMSOL. At the moment I am trying two possible way of obtaining the first excited state orbital, ie the LUMO. a) To use the keyword EXCITED (eqivalent to OPEN(2,2), SINGLET, ROOT=2) and then record the HOMO energy reported, which I think should be equivalent to the HOMO of the ground state. This should allow for any geometry changes that occur during excitation. b) To calculate a very accurate ground state an to take the differences in the eigenvalues reported, for the two middle orbital energies. The problems I have run into are simply that the EXCITED state calculations are difficult to converge, and I have initial gradients in excess of 100Kcal/Ang. The second method is easy to converge, I get some nice Gradients, but the differences in the eigenvalues for the HOMO and LUMO given seem to be much too large. Eg. Benzene Ground State Calculation (Ionisation potential = 9.652 eV) Excited State Calculation (Ionisation potential = 3.275 eV) Eigenvalues for Groundstate (-9.652 and 0.554 eV) method a) gives the UV transition as 194.4 nm, method b) gives the UV transition as 121.5 nm. The experimental is 203.5 nm. Can someone give me pointers to the better method of calculating these orbital energies. I would exclusively use method b) as it it gives results closer to the experimental, but as mentioned, the excited states are difficult to converge, and very time consuming to calculate. Yours in hope Andy. ################################################################################ Andrew David Allen BSc. Hons (SUR) GRSC. chp1aa@surrey.ac.uk - Internet. Structural and Computation Chemistry Group, chp1aa@uk.ac.surrey - JANET. Department of Chemistry, phone +44(483)-300800-2632. University of Surrey, fax +44(483)-300803. Guildford, Surrey, GU2 5XH, UK. fpt 131.227.110.2 ################################################################################ From mrigank@imtech.ernet.in Mon Jan 24 06:52:45 1994 Received: from relay2.UU.NET for mrigank@imtech.ernet.in by www.ccl.net (8.6.4/930601.1506) id GAA22037; Mon, 24 Jan 1994 06:44:09 -0500 Received: from spool.uu.net (via LOCALHOST) by relay2.UU.NET with SMTP (5.61/UUNET-internet-primary) id AAwafm09307; Mon, 24 Jan 94 06:44:07 -0500 Received: from sangam.UUCP by uucp5.uu.net with UUCP/RMAIL (queueing-rmail) id 064259.17795; Mon, 24 Jan 1994 06:42:59 EST Received: by sangam.ncst.ernet.in (4.1/SMI-4.2-ERNET-relay) with UUCP id AA18541; Mon, 24 Jan 94 16:51:11+0530 Received: from imtech.UUCP by ern.doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA24108; Sun, 23 Jan 94 22:41:38+0530 Message-Id: <9401231711.AA24108@ern.doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Sun, 23 Jan 94 14:17:13 +0530 Date: Sun, 23 Jan 94 14:17:13 +0530 From: "Dr. Mrigank" To: chemistry@ccl.net Subject: Proceding of American and Europen peptide sym ? X-Vms-Mail-To: CHEM Hi netters I am looking for the information about the editor, publisher and price of each volume of : 1. Proceedings of American Peptide Symposium From vol I to latest. 2. Proceedings of European Peptide Symposium From vol I to latest. Thanks -- Dr. Mrigank \/Phone +91 172 45004 x216 Institute of Microbial Technology /\Email: mrigank@imtech.ernet.in P O Box 1304, Sector 39A \/UUCP:...!uunet!sangam!vikram!imtech!mrigank Chandigarh 160 014 India. /\Fax +91 172 40985 ==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+ -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From chp1aa@surrey.ac.uk Mon Jan 24 07:00:51 1994 Received: from sun2.nsfnet-relay.ac.uk for chp1aa@surrey.ac.uk by www.ccl.net (8.6.4/930601.1506) id GAA22029; Mon, 24 Jan 1994 06:40:06 -0500 Via: uk.ac.surrey; Mon, 24 Jan 1994 11:33:08 +0000 Via: central.surrey.ac.uk; Mon, 24 Jan 94 11:33:01 GMT Received: by central.surrey.ac.uk (1.37.109.8/16.2) id AA03476; Mon, 24 Jan 1994 11:33:00 GMT From: Mr Andrew D Allen Message-Id: <9401241133.AA03476@central.surrey.ac.uk> Subject: Correction to previous message To: chemistry@ccl.net Date: Mon, 24 Jan 94 11:33:00 GMT Mailer: Elm [revision: 70.85] Whoops method a) as shown below should read ", which I think should be equivalent to the LUMO of the ground state." Sorry for any confusion. I am of course trying to calculate the lamba max (UV transitions) and hence need accurate orbitql energies. > a) To use the keyword EXCITED (eqivalent to OPEN(2,2), SINGLET, ROOT=2) > and then record the HOMO energy reported, which I think should be equivalent to > the HOMO of the ground state. This should allow for any geometry changes that > occur during excitation. -- ################################################################################ Andrew David Allen BSc. Hons (SUR) GRSC. chp1aa@surrey.ac.uk - Internet. Structural and Computation Chemistry Group, chp1aa@uk.ac.surrey - JANET. Department of Chemistry, phone +44(483)-300800-2632. University of Surrey, fax +44(483)-300803. Guildford, Surrey, GU2 5XH, UK. fpt 131.227.110.2 ################################################################################ From GF@chemie.uni-paderborn.de Mon Jan 24 07:52:46 1994 Received: from uni-paderborn.de for GF@chemie.uni-paderborn.de by www.ccl.net (8.6.4/930601.1506) id HAA22393; Mon, 24 Jan 1994 07:35:39 -0500 Received: from physik.uni-paderborn.de by uni-paderborn.de with SMTP id AA10549 (5.65c/IDA-1.5 for ); Mon, 24 Jan 1994 13:35:29 +0100 Received: From FB6/WORKQ1 by physik.uni-paderborn.de via Charon-4.0A-VROOM with IPX id 100.940124133430.352; 24 Jan 94 13:40:48 -0200 Message-Id: From: "Prof. Gregor Fels" To: chemistry@ccl.net Date: Mon, 24 Jan 1994 13:34:56 MESZ Subject: HyperChem and Moby Priority: normal X-Mailer: PMail v3.0 (R1a) Lookink for examples of HypeChem and/or Moby: I am looking for publications that describe the use of HyperChem or Moby for the calculation of organic molecules (organic textbook chemistry) to be used for demonstration in organic chemistry classes. From sfilipek@chem.uw.edu.pl Mon Jan 24 08:01:18 1994 Received: from sunic.sunet.se for sfilipek@chem.uw.edu.pl by www.ccl.net (8.6.4/930601.1506) id GAA22108; Mon, 24 Jan 1994 06:55:29 -0500 Received: from chem.uw.edu.pl by sunic.sunet.se (8.6.4/2.03) id MAA17319; Mon, 24 Jan 1994 12:54:57 +0100 Received: from [148.81.21.71] by chem.uw.edu.pl (4.1/SMI-4.1) id AA07392; Mon, 24 Jan 94 12:46:51 +0100 Organization: Department of Chemistry, University of Warsaw Address: Pasteura 1, 02-093 Warsaw, Poland. From: "Slawomir Filipek" Date: Mon, 24 Jan 94 12:44:08 +0100 Message-Id: <3985.sfilipek@zoolook.chem.uw.edu.pl_POPMail_3.1.8> X-Popmail-Charset: IBM 8-Bit To: CHEMISTRY@ccl.net Subject: MM+ in new HYPERCHEM I know, HyperChem is a very good program, but when I used MM+ in the new version 3.0 of HyperChem I got the following: O compound: R1-N-C-N-R2 R1=R2 (identical topology and charges) H H results (single point of energy for part of molecule): MM+ (bond dipoles) MM+ (atomic charges) AMBER OPLS ------------------------------------------------------------ R1 -1. -5. -37. -40. R2 -3. -437. -39. -46. Results for MM+ (atomic charges) are in obvious way incorrect. Since I have another compounds with atom types that only MM+ can cope with, I will be glad to hear from you how to resolve this problem. HIN file for the molecule is available upon request. _________________________________________________________ |Dr Slawomir Filipek| | | Dept. of Chemistry | e-mail: sfilipek@chem.uw.edu.pl | | | Univ. of Warsaw |__________________________________| | 1 Pasteur St | tel.: (+48 22) 220211 ext. 130 | | 02-093 Warsaw | fax: (+48 22) 225996 | | POLAND | | _________________________________________________________ From raman@bioc01.uthscsa.edu Mon Jan 24 09:52:45 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.4/930601.1506) id JAA23622; Mon, 24 Jan 1994 09:47:33 -0500 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Mon, 24 Jan 1994 8:48:14 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA05387; Mon, 24 Jan 94 08:47:51 CST From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9401241447.AA05387@bioc01.uthscsa.edu> Subject: Re: ORTEP for Mac? To: frj@dou.dk (Frank Jensen) Date: Mon, 24 Jan 1994 08:47:51 -0600 (CST) Cc: chemistry@ccl.net In-Reply-To: <1013*frj@dou.dk> from "Frank Jensen" at Jan 24, 94 09:26:00 am X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1190 Frank: > A spin-off question from the inquire about a version of > ORTEP that runs under DOS: is there a versionof ORTEP that runs > on a Macintosh? During a recent conversation with Norimasa Yamazaki (Tokyo), who ported ORTEP for Unix platforms, I was told that he has a new version which can handle 400 atoms and run on a Macintosh. I didn't gather additional details, but, if you are interested I can find out more. Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From muguet@poly.polytechnique.fr Mon Jan 24 10:52:46 1994 Received: from polytechnique.polytechnique.fr for muguet@poly.polytechnique.fr by www.ccl.net (8.6.4/930601.1506) id KAA23928; Mon, 24 Jan 1994 10:14:57 -0500 Received: from poly.polytechnique.fr (muguet@poly.polytechnique.fr [192.48.98.1]) by polytechnique.polytechnique.fr (8.6.4/8.6.4) with SMTP id QAA08987 for ; Mon, 24 Jan 1994 16:02:06 +0100 Received: by poly.polytechnique.fr (5.57/DEC-Ultrix/4.3) id AA17543; Mon, 24 Jan 94 15:53:33 +0100 Date: Mon, 24 Jan 94 15:53:33 +0100 From: muguet@poly.polytechnique.fr (muguet francis ) Message-Id: <9401241453.AA17543@poly.polytechnique.fr> To: CHEMISTRY@ccl.net Subject: Vectorized MCSCF Subject : Vectorized MCSCF, COLOMBUS Hello, Dear Netters, I would like to know which ab initio MCSCF programs are well vectorized to run on a CRAY. ? ( My experience is that GAMESS is middly vectorized so far, Gaussian92 CASSCF is not very sophisticated, I going to try SIRIUS soon also on a CRAY). I have heard that COLOMBUS is very well vectorized and available by anonymous ftp but where ? What I am looking for is : A very well vectorized direct MCSCF program, with very good convergence properties for the excited states ( if possible, with molecular gradients which should allow geometry optimization ) Thanks in advance Francis F.MUGUET e-mail : muguet@poly.polytechnique.fr From h.rzepa@ic.ac.uk Mon Jan 24 11:56:28 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.4/930601.1506) id LAA25350; Mon, 24 Jan 1994 11:41:03 -0500 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <22603-0@punch.ic.ac.uk>; Mon, 24 Jan 1994 16:37:44 +0000 Received: from macb.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA04736; Mon, 24 Jan 94 16:40:10 GMT Message-Id: <9401241640.AA04736@cscmgb.cc.ic.ac.uk> X-Sender: rzepa@sg1.cc.ic.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 24 Jan 1994 16:40:35 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: C6H5O2: Geom Opt with "difficult systems" Benzoic radical has been causing some problems, due to pathological coupling between doublet states and geometry causing optimisation of the latter to go haywire. I have often found that if a geometry is adjusted in a "chemical sense", the problem can often be solved. In this case, starting with an orthogonal (C2v) geometry for the radical and then doing a reaction path to twist it to planarity presumably removes the sigma/pi degeneracies that were causing the problem. The final energy by the way is -10.8 kcal/mol, about 10 lower then previously obtained, and a gradient norm of <0.8 can be obtained using MOPAC-93. The EF option in this event does not appear to work, but BFGS is just fine (gradient problems?) Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.01, Tel:+44 71 225 8339, Fax:+44 71 589 3869. >From June '94: (44) 171 584 5774, Fax: (44) 171 584 5804 http://www.ch.ic.ac.uk/rzepa.html From wolpert@neon.chem.utk.edu Mon Jan 24 12:52:47 1994 Received: from neon.chem.utk.edu for wolpert@neon.chem.utk.edu by www.ccl.net (8.6.4/930601.1506) id MAA25882; Mon, 24 Jan 1994 12:47:12 -0500 Received: by neon.chem.utk.edu (4.0/1.34) id AA14552; Mon, 24 Jan 94 12:52:05 EST Date: Mon, 24 Jan 94 12:52:05 EST From: wolpert@neon.chem.utk.edu (Edward Wolpert) Message-Id: <9401241752.AA14552@neon.chem.utk.edu> To: CHEMISTRY@ccl.net Subject: Request: Prog or code to convert xyz f. const to int. Netters- I'm trying to write a little program to convert force constants from xyz co-ordinates to internal co-ordinates without having to worry about redundencies. This code would assume the force constants in xyz and b-matrix already exist. (They come from hondo 8.2) I'm also interested in programs that are freely available that do this already. Due to my limited funding, I'm not currently able to get the proper programs from QCPE that do this. I do not need to generate the vibrational frequencies, just convert force constants from one format to another. I know that the following should work: F(int) = B x F(xyz) x B-1 where B is the b-matrix, and B-1 is the transposed b-matrix. However, I noticed that in hondo, they seem to use the inverse B matrix instead. I would like to use the 'normal' b-matrix for such work. Also, to be able to convert the units within the program. If such a program exists in the public domain, please send me information on it. If not, I would like suggestions on how I can write such a program. Once written, I will be more than happy to put the source code in the public domain, giving credit to those who help. My current work is in C, but current fortran code is also useful. Virtually, Edward Wolpert -------------------------------- wolpert@neon.chem.utk.edu | Graduate Chemistry Student wolpert@lead.chem.utk.edu | wolpert@osti.slip.utk.edu | System Administrator wolpert@utkux.utk.edu | wolpert@novel.chem.utk.edu | Systems Programmer wolpert@utkvx.utk.edu | pa153568@utkvm1.utk.edu | Still waiting for Godot... -------------------------------- From SAVARY@sc2a.unige.ch Mon Jan 24 13:54:03 1994 Received: from chx400.switch.ch for SAVARY@sc2a.unige.ch by www.ccl.net (8.6.4/930601.1506) id MAA26038; Mon, 24 Jan 1994 12:57:02 -0500 From: X400-Received: by mta chx400.switch.ch in /PRMD=switch/ADMD=arcom/C=CH/; Relayed; Mon, 24 Jan 1994 18:55:42 +0100 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Mon, 24 Jan 1994 18:55:12 +0100 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Mon, 24 Jan 1994 15:56:12 +0100 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Mon, 24 Jan 1994 15:55:41 +0100 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Mon, 24 Jan 1994 15:55:41 +0100 Date: Mon, 24 Jan 1994 15:55:41 +0100 X400-Originator: SAVARY@sc2a.unige.ch X400-Recipients: chemistry@ccl.net X400-MTS-Identifier: [/PRMD=SWITCH/ADMD=ARCOM/C=CH/;<01H82CC2PCDU002F9G@sc2a.unige.c] X400-Content-Type: P2-1984 (2) Content-Identifier: Re : MM+ in n... Message-ID: <01H82CC2PCDU002F9G@sc2a.unige.ch> To: chemistry@ccl.net Subject: Re : MM+ in new HYPERCHEM X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hi, I have the mail about the problem with charges in MM+. I was wondering how do you get charges at all ? -------------------------------------------------------------- Francois Savary Department of Physical Chemistry University of Geneva 30, quai Ernest-Ansermet CH-1211 Geneva 4 phone : +4122 702 65 32 fax : +4122 702 65 18 e-mail : savary@sc2a.unige.ch -------------------------------------------------------------- From d3e129@cagle.pnl.gov Mon Jan 24 13:58:28 1994 Received: from pnlg.pnl.gov for d3e129@cagle.pnl.gov by www.ccl.net (8.6.4/930601.1506) id NAA26113; Mon, 24 Jan 1994 13:04:47 -0500 From: Received: from carbon.pnl.gov (130.20.188.38) by pnlg.pnl.gov; Mon, 24 Jan 94 10:02 PST Received: from cagle.pnl.gov by carbon.pnl.gov (4.1/SMI-4.1) id AA05010; Mon, 24 Jan 94 10:02:45 PST Received: by cagle.pnl.gov (4.1/SMI-4.1) id AA00394; Mon, 24 Jan 94 10:02:44 PST Date: Mon, 24 Jan 94 10:02:44 PST Subject: Vectorized MCSCF To: muguet@poly.polytechnique.fr Cc: CHEMISTRY@ccl.net Message-id: <9401241802.AA00394@cagle.pnl.gov> In-Reply-To: muguet@poly.polytechnique.fr's message of Mon, 24 Jan 94 15:53:33 +0100 <9401241453.AA17543@poly.polytechnique.fr> X-Envelope-to: CHEMISTRY@ccl.net |> Resent-From: chemistry-request@ccl.net |> Resent-Date: Mon, 24 Jan 94 09:31 PST |> Date: Mon, 24 Jan 94 15:53:33 +0100 |> From: muguet@poly.polytechnique.fr |> Sender: chemistry-request@ccl.net |> Resent-To: D3E129@CAGLE.PNL.GOV |> Precedence: bulk |> X-Envelope-To: D3E129@CAGLE.PNL.GOV |> X-Vms-To: CHEMISTRY@ccl.net |> |> |> |> Subject : Vectorized MCSCF, COLOMBUS |> |> Hello, |> Dear Netters, |> |> I would like to know which ab initio MCSCF programs are well vectorized |> to run on a CRAY. ? |> ( My experience is that GAMESS is middly vectorized so far, |> Gaussian92 CASSCF is not very sophisticated, |> I going to try SIRIUS soon also on a CRAY). |> I have heard that COLOMBUS is very well |> vectorized and available by anonymous ftp but where ? |> Columbus is available from ftp.tcg.anl.gov in /pub/columbus. The last version of SIRIUS I played with was reasonably vectorized. That was 5+ years ago so they have probably done a great deal of optimization on it by now. |> What I am looking for is : |> A very well vectorized direct MCSCF program, with very good |> convergence properties for the excited states ( if possible, |> with molecular gradients which should allow geometry optimization ) The Columbus MCSCF is not direct but will meet most of your other requirements. |> |> |> Thanks in advance |> |> Francis F.MUGUET |> e-mail : muguet@poly.polytechnique.fr |> |> ---Administrivia: This message is automatically appended by the mail exploder: |> CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator |> MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net (port 70 or 73) |> Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search |> |> Regards, Rick ============================================================================= === Ricky A. Kendall === === Mail Stop K1-90 === === Molecular Science Software Group === === Theory, Modeling, and Simulation Program === === Molecular Science Research Center === === Pacific Northwest Laboratory === === Richland, WA 99352 === === Phone: (509) 375-2602 === === Fax: (509) 375-6631 === ============================================================================= ============================================================================= === All opinions are my own and not those of any other life form, === === living, dead or unknown === ============================================================================= ============================================================================= === Parallel computing is the way of the future === === Always was ........ always will be!!!!! === ============================================================================= ============================================================================= === One must be careful to not end up as === === ROADKILL on the Information Highway === ============================================================================= ============================================================================= === === === Support the American Diabetes Association === === === ============================================================================= From GDURST@ELINET1.DOWELANCO.COM Mon Jan 24 15:52:48 1994 Received: from ELINET1.DOWELANCO.COM for GDURST@ELINET1.DOWELANCO.COM by www.ccl.net (8.6.4/930601.1506) id PAA27409; Mon, 24 Jan 1994 15:07:02 -0500 Date: Mon, 24 Jan 1994 15:04:20 -0500 (EST) From: "Gregory L. Durst - DowElanco Discovery Research" To: chemistry@ccl.net CC: GDURST@ELINET1.DOWELANCO.COM Message-Id: <940124150420.4be@ELINET1.DOWELANCO.COM> Subject: Rank Data in QSAR Summary I've summarized responses and further "diggings" of my own concerning the request I posted earlier about using ranked bio-data in QSAR... >Dear Netters, >Do any of you QSAR practitioners out there know of any literature references >(or personal experiences) using ranked bio data in QSAR studies? I am >especially interested in regression or discriminant analyses using ranked >biological data. Since many of you are involved in bio-active design groups, >I'd like to hear of your adventures using this type of data. I'll summarize >responses for the net. >Greg Durst =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= It turns out that after a *serious* scouring of the literature I was able to find several references on the use of the Rank Transform in QSAR... A paper covering the "fundamentals" of the Rank Transform for use in regression is: * R.L. Inman and W.J. Conover, Technometrics, 21, 499, 1979. >From this article a "bottom-line" finding is that ALL parameters, both dependent and independent variables are ranked to do regression. (This can easily be accomplished using a program like SAS.) Applications of the Rank Transform to QSAR problems were refered to in an article by P. Magee for the QSAR Newsletter (written for the International QSAR Society, Winter 1993). This article was abstracted by the author, (P. Magee) from "Rational Approaches to Structure, Activity, and Ecotoxicology of Agrochemicals", W. Draber and T. Fujita eds., CRC Press, Boca Raton, FL, Chapter 3, (1992). Other public literature cited in P. Magee's article included: * A.R. Bell, R.A. Covey, D.I. Relyea and P.S. Magee, "Proc. Br. Crop Prot. Conf.-Weeds", (1), 249, (1987). * M.A.Pleiss in "QSAR in Design of Bioactive Compounds", M. Kuchar ed., J.M. Prous International Publishers, Barcelona, Spain, 403, (1984). =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Info from other netters on using ranked data in QSAR included email from Dora Schnurr and Terry Stouch, summarized below... =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Date: Wed, 5 Jan 94 10:52:17 -0600 From: dmschn@bb1t.monsanto.com To: " gdurst@dowelanco.com"@tin.monsanto.com Subject: rank sums Greg, Robert D. Clark and Dave Duewer (now at NIST) from Monsanto Ag have published in this area ... * D.L. Duewer and R.D. Clark, J. of Chemometrics, Vol 5, 503, (1991). Dora =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Date: Mon, 10 Jan 1994 14:33 EDT From: "TERRY R. STOUCH (609)252-5442" Subject: using ranked bio data in QSAR studies To: gdurst@dowelanco.com Hi - you might want to check the following references. We used two class bio data in the following, but similar work could be done with multiple ranks. Edward P. Jaeger, Peter C. Jurs, Terry R. Stouch, "Structure-Activity Relationship Studies of Retinoid Cancer Inhibition," European Journal of Medicinal Chemistry 1993, 28, 275-290. Terry R. Stouch, "Structure-Activity Relationships Using Multivariate Analysis Techniques: Application to Topical Corticosteroids," Topical Corticosteroids, H.I.Maibach, Ch. Surber, Eds., S. Karger: Basel, 1991, 93-127. Terry R. Stouch and Peter C. Jurs, "Pattern Recognition Studies of the Structure-Activity Relationships of Antiinflammatory Steroids," Journal of Medicinal Chemistry 1986, 29, (11), 2125-2136. Terry R. Stouch, Ph.D. Room H3812, Department of Macromolecular Modeling Bristol-Myers Squibb Pharmaceutical Research Institute P.O. Box 4000, Princeton, NJ 08543-4000 PH: (609)252-5442 - FAX: (609)252-6030 - EMAIL: Stouch@bms.com =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Thanks to those who responded and I hope this is useful to others, It was for me! +-----------------------------------------------------------------------+ | Gregory L. Durst Computational Chemistry | | phone: 317/337-3413 DowElanco Discovery Research | | email: gdurst@dowelanco.com 9410 Zionsville Rd. Bldg 306/D2 | | Indianapolis, IN 46268 USA | +-----------------------------------------------------------------------+ From palres.dnet.sandoz.com!bowlus@sandoz.com Mon Jan 24 10:52:45 1994 Received: from tigger.jvnc.net for palres.dnet.sandoz.com!bowlus@sandoz.com by www.ccl.net (8.6.4/930601.1506) id KAA23873; Mon, 24 Jan 1994 10:08:58 -0500 Received: from sndzeh.UUCP by tigger.jvnc.net with UUCP id AA21558 (5.65c/IDA-1.4.4); Mon, 24 Jan 1994 09:51:29 -0500 Message-Id: <199401241451.AA21558@tigger.jvnc.net> Date: Mon, 24 Jan 94 09:47:26 -0500 From: bowlus@palres.dnet.sandoz.com (Steve Bowlus) To: "chemistry@ccl.net"@SNDZEH.dnet.sandoz.com Cc: BOWLUS@sandoz.com HyperChem for Windows was recently reviewed: J. Chem. Inf. Comput. Sci., 33, 931 (1993). From vis@genny.gensia.com Mon Jan 24 18:52:51 1994 Received: from genny.gensia.com for vis@genny.gensia.com by www.ccl.net (8.6.4/930601.1506) id SAA29520; Mon, 24 Jan 1994 18:09:12 -0500 From: Received: by genny.gensia.com (930416.SGI/920502.SGI) for chemistry@ccl.net id AA05278; Mon, 24 Jan 94 14:10:50 -0800 Date: Mon, 24 Jan 1994 14:07:08 -0800 (PST) Subject: Workshop on Quantum Chemical Methods in Florida To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Does anyone know about the workshop on Quantum Chemical Methods held once a year (probably in Gainesville, but I am not sure). I need the dates and the address. I will let everybody know about this, once I have the answer. vis@gensia.com From friedman@tammy.harvard.edu Mon Jan 24 18:54:10 1994 Received: from tammy.harvard.edu for friedman@tammy.harvard.edu by www.ccl.net (8.6.4/930601.1506) id SAA29577; Mon, 24 Jan 1994 18:31:26 -0500 Received: by tammy.harvard.edu (5.64/10.0) id AA01554; Mon, 24 Jan 94 18:19:39 -0500 Date: Mon, 24 Jan 94 18:19:39 -0500 From: friedman@tammy.harvard.edu (Dawn Friedman) Message-Id: <9401242319.AA01554@tammy.harvard.edu> To: chemistry@ccl.net Subject: ACS abstract form Cc: friedman@tammy.harvard.edu Is there an online submission process for abstracts for posters at upcoming ACS conferences? Is there an online source for abstract forms? Is there an online source for abstract instructions? Is there a FAST real-world source for abstract forms? They're like hens' teeth around here, and the only one I could find was from 1984 and looks like an income tax sheet. Thanks, Dawn