From chemistry-request@server.ccl.net Tue Feb 29 08:55:55 2000 Date: Tue, 29 Feb 2000 10:52:23 -0700 To: CHEMISTRY@ccl.net Message-Id: From: jkl@ccl.net Subject: Re: Text file transfer between linux and dos Sorry for this terrible interferrence, but I combined some of the messages about DOS -> UNIX text file translation from different authors into one file. Actually, they are all kind of different, and I learned some UNIX from this. Individual messages are separated by the line starting with > From Jan jkl@ccl.net P.S. Sorry again for the intervention... =============================================================== > From chemistry-request@server.ccl.net Tue Feb 29 08:55:55 2000 Date: Tue, 29 Feb 2000 06:52:23 -0700 To: CHEMISTRY@ccl.net From: "James J. P. Stewart" Subject: Re: Text file transfer between linux and dos The easiest way I've found to handle WINDOWS files in a UNIX environment has been to convert them using the UNIX utility "sed". To convert file A.B to remove the "^M"s, run sed "s+^M+++" < A.B > temp$$ rm A.B mv temp$$ A.B In this script, "^M" is typed as (cntl)-v (cntl)-m not as (cap)-6 (cap)-m Of course, to make this useful, I have it as the heart of a utility, 2u, and A.B is replaced by $1. To use the utility: %: 2u A.B If the utility is then buried in the UNIX copy command, it will then do its job invisibly. Jimmy Stewart ( @ @ ) .-------------oOOo----(_)----oOOo-------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry | E-mail: jstewart@fujitsu.com | | 15210 Paddington Circle | WWW: http://home.att.net/~MrMOPAC | | Colorado Springs CO 80921-2512 | | | USA .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo. | | .--------------------\ (----( )-------------------------------------. \_) ) / (_/ ================================= > From chemistry-request@server.ccl.net Tue Feb 29 09:33:06 2000 From: Jijun Xu To: Yubo Fan Subject: Re: CCL:Text file transfer between linux and dos Date: Tue, 29 Feb 2000 14:39:06 +0000 I think it is a common phenomenon when you copy files from DOS to Unix. Perhaps there are two methods to solve this problem: 1. open this file using "vi", input: %s/^V^M//g in the command mode 2.sed 's/^V^M//g' foo > foo.new (suppose foo is your file) Dr. J.J.Xu pcxjx@unix.ccc.nottingham.ac.uk School of Chemistry University of Nottingham University Park Nottingham NG7 2RD U.K. ============================================ > From chemistry-request@server.ccl.net Tue Feb 29 09:43:08 2000 Date: Tue, 29 Feb 2000 06:51:42 -0800 (PST) From: "Michael D. Bartberger" To: Yubo Fan Subject: Re: CCL:Text file transfer between linux and dos Dear Yubo: You could obtain the 'dos2unix' program which will strip out the characters at the end of the line. This is available in RPM format for Red Hat. (Check altavista.com or another search engine for dos2unix; I'm afraid I don't have the site handy). Alternatively, you could do this just as easily in Perl, with something like perl -p -i.backup -e 's/\r\n$/\n/' (no brackets around the file names) This will save your original files with the ".backup" extension. I hope this helps. -Michael +-----------------------------------------------------------------+ | Michael D. Bartberger, Ph.D. | | NIH Postdoctoral Fellow TEL: 310.206.0553 | | Department of Chemistry and Biochemistry FAX: 310.206.1843 | | University of California, Los Angeles | | Los Angeles, California 90095-1569 mdb@chem.ucla.edu | +-----------------------------------------------------------------+ =================================================================== > From chemistry-request@server.ccl.net Tue Feb 29 10:00:57 2000 Date: Tue, 29 Feb 2000 15:57:13 +0100 From: Volford Andras To: Yubo Fan cc: CHEMISTRY@ccl.net Subject: Re: CCL:Text file transfer between linux and dos Try this script. I hope it helps. Or man mcopy t Text file transfer. Mcopy translates incoming car- riage return/line feeds to line feeds. #! /bin/sh -e # convert a DOS ASCII file to a UNIX ASCII file by removing trailing ^M at # the end of each line and ^Z at the end of the file TMPFILE=/tmp/to_unix$$ if [ $# -gt 2 ] then echo "usage: to_unix [ []]" exit 1 fi # First strip out all carriage-return and ctrl-Z's if [$# -gt 0 ] then tr -d '\015\032' < "$1" > $TMPFILE else tr -d '\015\032' > $TMPFILE fi if [ $# -eq 2 ] then mv -f $TMPFILE "$2" else cat $TMPFILE rm $TMPFILE fi All the best Volford Andras =============================================== > From chemistry-request@server.ccl.net Tue Feb 29 11:08:53 2000 From: "Jochen Küpper" Date: Tue, 29 Feb 2000 17:09:02 +0100 (CET) To: CHEMISTRY@ccl.net Subject: CCL:Text file transfer between linux and dos Use dos2unix or recode or other little Unix-tools to convert the ASCII files to simple line-endings. dos2unix might be the simplest to use - no flags needed :-) Jochen -- Heinrich-Heine-Universität Institut für Physikalische Chemie I Jochen Küpper Universitätsstr. 1, Geb. 26.43 Raum 02.29 40225 Düsseldorf, Germany phone ++49-211-8113681, fax ++49-211-8115195 http://www.Jochen-Kuepper.de ====================================================== > From chemistry-request@server.ccl.net Tue Feb 29 11:40:26 2000 Date: Tue, 29 Feb 2000 11:38:31 -0500 (EST) From: "Xianofeng . Duan MLBP CON" To: Yubo Fan cc: CHEMISTRY@ccl.net Subject: Re: CCL:Text file transfer between linux and dos When we copied an input file from a dos floppy/zip disk, which was mounted simply by "mount -t msdos ....." comand on the linux machine, we had the same problem. However when we mounted the disks by "mount -t msdos -o conv=text, umask=022, uid=100, gid=100 ....", the problem was solved! Hope this will help. **************************************** Xiaofeng Duan, Ph.D. AFRL/MLBP, Bldg. 654 2941 P St. Ste. 1 Wright-Patterson AFB, OH 45433 **************************************** =============================================================== > From chemistry-request@server.ccl.net Tue Feb 29 12:01:40 2000 Date: Tue, 29 Feb 2000 12:01:05 -0500 (EST) From: Ruth Marie Tanner To: chemistry@ccl.net Subject: Re: CCL:Text file transfer between linux and dos At the unix prompt, you can use the tr command to remove ^M characters: 1.) Make a copy of your file cp filename.txt temp.txt 2.) Use tr to remove the ^M character (015) tr -d '\015' < temp.txt > filename.txt This will filter the copy and produce a file with no ^M characters in it. You can also use vi to get rid of the ^M characters 1.) Open file in vi 2.) Type :1,$s/ctrl-V ctrl-M//g (there are no spaces, the ctrl-V makes ^) What should show up at the bottom of the screen is: :1,$s/^M//g Then press enter This will get rid of all ^M characters and then you save the file. Good Luck, Ruth ----------------------------------------------------------------------------- Ruth Tanner rtanner@uoguelph.ca M.Sc. Candidate in Physical Chemistry University of Guelph ----------------------------------------------------------------------------- =========================================== From chemistry-request@server.ccl.net Tue Feb 29 21:14:07 2000 Received: from sahara.dupontpharma.com (firewall-user@sahara.dupontpharma.com [204.249.5.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA31753 for ; Tue, 29 Feb 2000 21:14:06 -0500 Received: by sahara.dupontpharma.com; id VAA12959; Tue, 29 Feb 2000 21:13:26 -0500 (EST) Received: from unknown(158.117.31.71) by sahara.dupontpharma.com via smap (4.1) id xma012929; Tue, 29 Feb 00 21:13:21 -0500 Received: from hermes.combichem.com (hermes.dmpc.com) by DMPHUB.dmpc.com (PMDF V5.1-10 #24771) with ESMTP id <01JMHSK563RK005ELW@DMPHUB.dmpc.com> for chemistry@ccl.net; Tue, 29 Feb 2000 21:13:21 EST Received: from combichem.com ([158.117.188.76]) by hermes.combichem.com (Post.Office MTA v3.1.2 release (PO205-101c) ID# 0-49457U200L100S0) with ESMTP id AAA247 for ; Tue, 29 Feb 2000 18:11:47 -0800 Date: Tue, 29 Feb 2000 18:11:32 -0800 From: pgrootenhuis@combichem.com (Peter Grootenhuis) Subject: Combinatorial libraries To: chemistry@ccl.net Reply-to: pgrootenhuis@combichem.com Message-id: <38BC7C54.834EFCE6@combichem.com> Organization: CombiChem, Inc. MIME-version: 1.0 X-Mailer: Mozilla 4.51 [en] (WinNT; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en I am looking for published combinatorial libraries (single compounds NOT mixtures) that have been screened against one or more biological targets. Since I want to generate the corresponding virtual libraries all information on the templates and reagents should be given in the publication as well as the activity data. Any suggestions ? Thanks a lot. Peter Grootenhuis -- Dr. Peter D.J. Grootenhuis - Senior Director, Molecular Design group DuPont Pharmaceuticals Research Laboratories 4570 Executive Drive, Suite 400 - San Diego CA 92121 Tel: +1(858)625-6401, Fax:+1(858)625-6487, pgrootenhuis@combichem.com From chemistry-request@server.ccl.net Wed Mar 1 01:15:03 2000 Received: from dns.campus.mlsultan.ac.za ([196.13.103.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA32671; Wed, 1 Mar 2000 01:14:53 -0500 Received: from wpogate.mlsultan.ac.za (wpogate.campus.mlsultan.ac.za [196.13.102.11]) by dns.campus.mlsultan.ac.za (AIX4.2/UCB 8.7/8.7) with SMTP id HAA09784; Wed, 1 Mar 2000 07:36:59 +0200 (USAST) Received: from MLSTGW-Message_Server by wpogate.mlsultan.ac.za with Novell_GroupWise; Wed, 01 Mar 2000 08:15:41 +0200 Message-Id: X-Mailer: Novell GroupWise 5.5.2 Date: Wed, 01 Mar 2000 08:15:04 +0200 From: "Thishana Singh" To: , Subject: Summary : Bond length of HCl gas Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id BAA32680 Dear CClLers There was a request for a summary, so here goes.... Thank you again. Best wishes Thishana 1.Please read the article in J. Chemical Physics, 109, 973-977(1998). >From Masao Masamura 2.Any textbook in physical chemistry would do. Here it is: 1.2745 A, from Atkins, 6th edition. >From Jan Dillen 3.r(e) = 1.2746 Å Herzberg, G. "Molecular Spectra and Molecular Structure", 2nd. Ed., van Nostrand, Princeton (1950) >From Ole Swang 4.There is a nice demo about the Morse potential to be found at http://www.monmouth.edu/~tzielins/mathcad/tjz/doc009.htm where HCl is taken as an example. The bond length is reported there with 1.275 * 10^-8 cm referring to some text book Physical Chemistry 3rd edition by J.Noggle p.768 >From Siegfried Hoefinger 5.You could try: http://webbook.nist.gov/chemistry The value from there is 1.27455 A for the electronic ground state. You can get the reference for this number from the web page. >From Gert von Helden 6.Handbook of Chemistry and Physics RH-Cl=1.27246 A >From olivier Maresca 7.The value of 1.27455 Angstrom can be found for the ground state in: Huber, Herzberg, 'Molecular Spectra and Molecular Structure 4, Constants of Diatomic Molecules', Van Nostrand N.Y. (1979) (i.e. spectroscopic data) >From Harald Svedung 8.Bond length of HCl in the gas phase T. van Mourik and T.H. Dunning, Jr., Int. J. Quantum Chem. 76, 205 (2000). In this paper, we report spectroscopic constants (including equilibrium bond lengths, harmonic frequencies, and anharmonicity constants) of a few diatomic molecules, among them HCl. These have been calculated with several theoretical methods and the correlation consistent basis sets up to aug-cc-pV6Z. >From Tanja van Mourik End of Summary **************************************************************************************** Thishana Singh Lab Assistant Dept.Of Chemistry ML Sultan Technikon Durban South Africa email : singht@wpo.mlsultan.ac.za From chemistry-request@server.ccl.net Wed Mar 1 03:04:15 2000 Received: from batch13.uni-muenster.de (BATCH13.UNI-MUENSTER.DE [128.176.188.111]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA00472 for ; Wed, 1 Mar 2000 03:04:15 -0500 Received: from asterix.uni-muenster.de (ASTERIX.UNI-MUENSTER.DE [128.176.188.90]) by batch13.uni-muenster.de (Postfix) with ESMTP id B613B1041; Wed, 1 Mar 2000 09:03:32 +0100 (MEZ) Received: by asterix.uni-muenster.de (Postfix, from userid 40127) id 70797B80A; Wed, 1 Mar 2000 09:03:31 +0100 (MEZ) Subject: Re: CCL:mount zip/cdrom on linux? In-Reply-To: from "Xianofeng . Duan MLBP CON" at "Feb 29, 2000 01:31:04 pm" To: "Xianofeng . Duan MLBP CON" Date: Wed, 1 Mar 2000 09:03:31 +0100 (MEZ) Cc: chemistry@ccl.net X-Mailer: ELM [version 2.4ME+ PL60 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Message-Id: <20000301080331.70797B80A@asterix.uni-muenster.de> From: cml@uni-muenster.de (Christian Mück-Lichtenfeld) Dear Xianofeng, don't be surprised if the entry in the /etc/fstab does not work. There are two kinds of zip disks on the market which differ in their low level format (I suppose). You have to try to mount it as either /dev/sdb1 OR /dev/sdb4, depending on the actual disk in your drive. I have two entries in my fstab, like: /dev/sdb1 /zip1 ext2 noauto,user 0 0 /dev/sdb4 /zip4 ext2 noauto,user 0 0 If the first line ("mount /zip1") does not work, I use the second ("mount /zip4"). This will probably hold on your system as well. Best wishes, Christian ---------------------------------------------- Dr. Christian Mueck-Lichtenfeld Westfaelische Wilhelms-Universitaet Organisch-Chemisches Institut Corrensstrasse 40 D-48149 Muenster, Germany cml@uni-muenster.de | +49 251 83 33239 ---------------------------------------------- > Hi Xianofeng, > In your /etc/fstab include a line like this: > /dev/sdb1 /zip ext2 noauto,user 0 0 > The user option allows the user to mount the disk. > See the mount man page as well. > -Matt > +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > + Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ + > + Los Alamos National Laboratory email: mchalla@t12.lanl.gov + > + Theoretical Division vmail: (505) 698-4112 + > + Group T-12, Mail Stop B268 phone: (505) 665-5905 + > + Los Alamos, New Mexico 87545 fax: (505) 665-3909 + > + + > + "The secret to mountain biking is pretty simple. The slower you go + > + the more likely it is you'll crash." -- Julie Furtado + > +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > On Tue, 29 Feb 2000, Xianofeng . Duan MLBP CON wrote: > > Dear CCLers: > > We set up a linux to run G98. Frequently we need to trasfer input and > > output files to zip disks. Since only root user has privilege to > > mount/unmount zip/cdrom, now the question is: Are there are any ways for > > a general user to do so without login to the root account? > > I asked the same question on a linux forum, but so far there are no answers. > > > > Thanks! > > > > **************************************** > > Xiaofeng Duan, Ph.D. > > AFRL/MLBP, Bldg. 654 > > 2941 P St. Ste. 1 > > Wright-Patterson AFB, OH 45433 > > **************************************** > > > > From chemistry-request@server.ccl.net Wed Mar 1 03:39:46 2000 Received: from kasei.materials.ox.ac.uk (kasei.materials.ox.ac.uk [163.1.64.46]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA00903 for ; Wed, 1 Mar 2000 03:39:45 -0500 Received: from localhost (hfield@localhost) by kasei.materials.ox.ac.uk (8.9.3/8.9.3) with ESMTP id IAA04548 for ; Wed, 1 Mar 2000 08:38:40 GMT X-Authentication-Warning: kasei.materials.ox.ac.uk: hfield owned process doing -bs Date: Wed, 1 Mar 2000 08:38:40 +0000 (GMT) From: Andrew Horsfield X-Sender: hfield@kasei.materials.ox.ac.uk Reply-To: Andrew Horsfield To: Computational Chemistry List Subject: Lebedev integral meshes Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Many thanks to all those who replied to my request for the tables of Lebedev integrals. Since several people asked for the tables should I receive them, I am forwarding the following reply from Motohiro Nakano >from the Department of Applied Chemistry, Osaka University: You can find it in: Mattias Eden and Malcolm H. Levitt, Journal of Magnetic Resonance 132, 220 (1998) and download their mesh data from http://www.fos.su.se/~mhl/science/software.html Cheers, Andrew +----------------------------------------------------+ Andrew Horsfield e-mail: horsfield@fecit.co.uk FECIT, 2 Longwalk Road, Stockley Park, Uxbridge, Middlesex UB11 1AB, United Kingdom. phone: +44-(0)181-606-4653 FAX: +44-(0)181-606-4422 +----------------------------------------------------+ From chemistry-request@server.ccl.net Wed Mar 1 05:20:47 2000 Received: from ns.abpiotech.com (ns.apbiotech.com [192.36.117.130]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA01685 for ; Wed, 1 Mar 2000 05:20:46 -0500 From: enrique.carredano@eu.apbiotech.com Received: from eunotes.apbiotech.com (unverified [193.180.20.124]) by ns.abpiotech.com (Rockliffe SMTPRA 3.4.2) with SMTP id for ; Wed, 1 Mar 2000 11:19:32 +0100 Received: by eunotes.apbiotech.com(Lotus SMTP MTA v4.6.3 (778.2 1-4-1999)) id 41256895.00388621 ; Wed, 1 Mar 2000 11:17:23 +0100 X-Lotus-FromDomain: XYNET To: Chemistry@ccl.net Message-ID: <41256895.003883FE.00@eunotes.apbiotech.com> Date: Wed, 1 Mar 2000 11:18:36 +0100 Subject: CCL:programs for protein charge and lipophilicity calculations Mime-Version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id FAA01686 Dear CCL'ers Given a protein structure: 1) We would like to obtain a program (freeware or commercial) to calculate the charge and the total dipole of a protein at different pH?s. 2) We would like to obtain a program (freeware or commercial) to calculate one number, which could be related to the surface lipophilicity of the protein (something like ClogP but related only to the atoms at the surface). Does anyone know of any program (programs) which can accomplish tasks 1) and/or 2) in a fairly reliable way? Answers will be appreciated and summarized. Enrique Carredano, MSc, PhD +46 (0)18 612 00 00 tel Polymer and Surface Chemistry +46 (0)18 612 01 65 direct Amersham Pharmacia Biotech +46 (0)18 612 18 44 fax Björkg 30, 751 84 Uppsala Sweden enrique.carredano@eu.apbiotech.com From chemistry-request@server.ccl.net Wed Mar 1 07:13:17 2000 Received: from guppy.vub.ac.be (guppy.vub.ac.be [134.184.129.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA03300 for ; Wed, 1 Mar 2000 07:13:16 -0500 Received: from mach.vub.ac.be (mach.vub.ac.be [134.184.129.3]) by guppy.vub.ac.be (8.9.1b+Sun/3.17.0.ap (guppy)) id NAA13478; Wed, 1 Mar 2000 13:11:05 +0100 (MET) for Received: from algc (algcpc1.vub.ac.be [134.184.24.91]) by mach.vub.ac.be (8.9.3/%I%.1.ap (mach.test)) id NAA01441; Wed, 1 Mar 2000 13:12:15 +0100 (MET) for Message-Id: <3.0.5.32.20000301132140.00920c50@pop.vub.ac.be> X-Sender: pgeerlin@pop.vub.ac.be X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Wed, 01 Mar 2000 13:21:40 +0100 To: chemistry@ccl.net From: "P. GEERLINGS" Subject: DFT : A bridge between chemistry and physics - Proceedings Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear Colleague, I hereby inform you that the book "Density Functional Theory : a Bridge Between Chemistry and Physics" is now available. The book contains the Proceedings of a two day International Symposium at the Free University of Brussels in May 1998. All information can be found at the following website : http://homepages.vub.ac.be/~fdeprof/dftvub.html Yours sincerely, Prof. P. Geerlings Prof. P. GEERLINGS Faculty of Sciences Department of General Chemistry Vrije Universiteit Brussel Pleinlaan 2 1050 Brussels Belgium Tel. : 32.2.629.33.14 Fax. : 32.2.629.33.17 e-mail : pgeerlin@vub.ac.be From chemistry-request@server.ccl.net Wed Mar 1 07:22:32 2000 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA03392 for ; Wed, 1 Mar 2000 07:22:32 -0500 Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (XT-PP); Wed, 1 Mar 2000 12:20:01 +0000 From: uccatvm Message-Id: <24095.200003011220@socrates-a.ucl.ac.uk> Subject: Re: CCL:NT parallel cluster To: chemistry@ccl.net Date: Wed, 1 Mar 2000 12:20:20 +0000 (GMT) In-Reply-To: <38BBEBBD.93CEBE07@engr.uconn.edu> from "Bhupendra Wakankar" at Mar 01, 2000 12:19:01 PM X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Bhupendra, > > Almost all network of PC clusters that I read about on the web run under > Linux. Is there any particular reason for not choosing NT (lack of > parallel programs perhaps ?). You may also have a look at these sites: http://www.ncsa.uiuc.edu/General/CC/ntcluster/ http://www.windowsclusters.org/ Tanja -- ==================================================================== Tanja van Mourik phone University College London work: +44 (0)207-679-4665 Christopher Ingold Laboratories home: +44 (0)1895-259-312 20 Gordon Street e-mail London WC1H 0AJ work: T.vanMourik@ucl.ac.uk United Kingdom home: tanja@netcomuk.co.uk ==================================================================== From chemistry-request@server.ccl.net Wed Mar 1 06:04:51 2000 Received: from kasei.materials.ox.ac.uk (kasei.materials.ox.ac.uk [163.1.64.46]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA02059 for ; Wed, 1 Mar 2000 06:04:50 -0500 Received: from localhost (hfield@localhost) by kasei.materials.ox.ac.uk (8.9.3/8.9.3) with ESMTP id LAA07365 for ; Wed, 1 Mar 2000 11:03:43 GMT X-Authentication-Warning: kasei.materials.ox.ac.uk: hfield owned process doing -bs Date: Wed, 1 Mar 2000 11:03:43 +0000 (GMT) From: Andrew Horsfield X-Sender: hfield@kasei.materials.ox.ac.uk Reply-To: Andrew Horsfield To: Computational Chemistry List Subject: Software Meeting: 2nd announcement Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, This is the second announcement of the meeting on "Modern Software Design for Scientific Applications". For details, see http://joule.physics.salford.ac.uk/iopcpg/Events.html Cheers, Andrew +----------------------------------------------------+ Andrew Horsfield e-mail: horsfield@fecit.co.uk FECIT, 2 Longwalk Road, Stockley Park, Uxbridge, Middlesex UB11 1AB, United Kingdom. phone: +44-(0)181-606-4653 FAX: +44-(0)181-606-4422 +----------------------------------------------------+ From chemistry-request@server.ccl.net Wed Mar 1 08:39:00 2000 Received: from ns.mnc.md (root@ns.mnc.md [212.0.192.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA03797 for ; Wed, 1 Mar 2000 08:38:50 -0500 Received: from ppp-166.mnc.md (ppp-166.mnc.md [212.0.193.166]) by ns.mnc.md (8.8.7/8.8.7) with ESMTP id PAA09142 for ; Wed, 1 Mar 2000 15:37:53 +0200 Date: Wed, 1 Mar 2000 15:41:09 +0200 From: Mike Peleah X-Mailer: The Bat! (v1.39) Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <6653.000301@mnc.md> To: chemistry@ccl.net Subject: Summary: add H to XRay data Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit +======================---------------- --- -- - - - - . | Dear chemistry, : . A couple of days ago I've asked question how could one add H atoms to XRay data. Here are the summery of answers I received. I would like to note that I use Babel 1.6 and didn't try other programs mentioned. XHYDEX could be found here: http://xray.chm.bris.ac.uk:8000/software/xhydex/index.html. I have no URL for Babel, only authors e-mail: babel@mercury.aichem.arizona.edu >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=< Date: Mon, 28 Feb 2000 17:48:26 From: "Nikos" >-------------------------------------------------------------------< Hi.. You may use the babel program which adds the hydrogen data automatically... After converting your file to a format you can handle, change back to a crystallographic format... For a windows front-end for babel which simplifies the procedure of conversion pay a visit to my homepage http://www.geocities.com/CapeCanaveral/Lab/9248/ under the programs section... Hope this helps Best regards, Nikos Kourkoumelis >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=< Date: Tue, 29 Feb 2000 10:13:12 From: "Tamas E. Gunda" >-------------------------------------------------------------------< Dear Mike, Mol2mol can do it. See http://www.compuchem.com/mol2mol.htm Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. L. Kossuth University, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 316666/2472 fax: (+36-52) 512914 >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=< Date: Tue, 29 Feb 2000 16:00:48 From: Ricardo Grau Crespo >-------------------------------------------------------------------< Mike, there is a program called Xp that can do it, but I don't have the reference now. Please summarize answers. Regards, Ricardo ************************************************************** * Ricardo Grau Crespo * * Catalysis Department, Center for Petroleum Research. * * Washington # 169. Cerro, Havana, CUBA * ************************************************************** >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=< Date: Mon, 28 Feb 2000 17:31:30 From: "Fred P. Arnold" >-------------------------------------------------------------------< Hello, Molden (www.cmbi.kun.nl/~schaft/molden.html) seems to be able to, as is MSI's WebLab Viewer (www.msi.com), and any number of other commercial packages. If you truly don't know where they are (i.e. you know you have one, but it's not in a standard position) there used to be an old program called XHYDEX that could search for them. I don't have a copy, and all I remember is that it was page after page of Block GOTO, but someone may have finally updated it for the modern world. -fred "No science has ever made Frederick P. Arnold, Jr. more rapid progress in a A&HPRC, U. of Chicago shorter time than Chemistry." 5640 S. Ellis Ave -Martin Heinrich Kloproth, 1791 Chicago, IL 60637 Best regards, Mike mailto:mike@mnc.md . : | . - - - - -- --- ----------------======================+ From chemistry-request@server.ccl.net Wed Mar 1 09:57:17 2000 Received: from comm1.umaryland.edu (comm1.umaryland.edu [134.192.1.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA04248 for ; Wed, 1 Mar 2000 09:57:17 -0500 Received: from winslow.umaryland.edu (winslow.umaryland.edu [134.192.72.40]) by comm1.umaryland.edu (8.9.3/8.9.3) with ESMTP id JAA18311; Wed, 1 Mar 2000 09:56:08 -0500 (EST) Received: (from strahan@localhost) by winslow.umaryland.edu (8.9.3/8.9.3) id JAA02364; Wed, 1 Mar 2000 09:55:03 -0500 (EST) From: "Gary Strahan" Message-Id: <10003010955.ZM2362@winslow.umaryland.edu> Date: Wed, 1 Mar 2000 09:55:02 -0500 In-Reply-To: Bhupendra Wakankar "CCL:NT parallel cluster" (Jun 8, 3:55pm) References: <38BBEBBD.93CEBE07@engr.uconn.edu> X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: Bhupendra Wakankar , CCL_posting Subject: Re: CCL:NT parallel cluster Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Another option: You should be able to reboot your NT machines using a Linux boot-floppy, and then run calculations on them as part of a Linux cluster. Bhupendra Wakankar wrote: > Subject: CCL:NT parallel cluster > Dear CCLers, > Hi. > > We have 6 computers in our lab (4 running on WINNT and 2 on RedHat 6.0). > I use the Linux PC's for my computations while the 4 NT PC's stay > relatively idle. All these PC's are fairly powerful (> 400MHz > multiprocessor Pentiums) and thus have untapped number crunching power. > I am wondering if it is possible to build a parallel cluster using these > 4 NT PC's (and better still, using all 6 PC's). > > Almost all network of PC clusters that I read about on the web run under > Linux. Is there any particular reason for not choosing NT (lack of > parallel programs perhaps ?). > > I would also like to know if there are any DFT programs (parallel/single > processor, free/commercial) running on Windows NT? > > Thanks in advance, > > Regards, > Bhupendra > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > >-- End of excerpt from Bhupendra Wakankar From chemistry-request@server.ccl.net Wed Mar 1 10:02:55 2000 Received: from smtpsrv1.isis.unc.edu (smtpsrv1.isis.unc.edu [152.2.1.138]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA04319 for ; Wed, 1 Mar 2000 10:02:54 -0500 Received: from login6.isis.unc.edu (login6.isis.unc.edu [152.2.1.103]) by smtpsrv1.isis.unc.edu (8.9.3/8.9.1) with ESMTP id KAA19307 for ; Wed, 1 Mar 2000 10:02:06 -0500 (EST) Received: (from viggan@localhost) by login6.isis.unc.edu (8.9.3/8.9.3) id KAA84242; Wed, 1 Mar 2000 10:02:06 -0500 Date: Wed, 1 Mar 2000 10:02:05 -0500 (EST) From: Ganesh Ethiraj X-Sender: viggan@login6.isis.unc.edu To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Everybody, I have two questions 1) Are there methods to find active sites/binding sites in a protein 2) I am aware of a recent work were the authors conclude that the residue in the active site can be classified as core and non-core residues for the DHFR receptor, my question is this true for all proteins which exhibit enzymatic or receptor function. I would summarize the responses. Regards Ganesh Department of Biochemistry Howard University Washington, D.C. From chemistry-request@server.ccl.net Wed Mar 1 10:40:32 2000 Received: from wirehead.arqule.com (email.arqule.com [12.27.160.89]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA04518 for ; Wed, 1 Mar 2000 10:40:32 -0500 Received: by WIREHEAD with Internet Mail Service (5.5.2650.21) id ; Wed, 1 Mar 2000 10:35:37 -0500 Message-ID: <6B00FB949906D211A88800104B8AE5200183D473@WIREHEAD> From: "Czerminski, Ryszard" To: "'Gary Strahan'" , Bhupendra Wakankar , CCL_posting Subject: RE: NT parallel cluster Date: Wed, 1 Mar 2000 10:35:36 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" And if you need to use NT functionality you might want to install VMWARE on top of linux (http://www.vmware.com) and NT on top of vmware. Then you can: (1) use all 6 PC as a linux cluster (2) use NT functionality without rebooting while all your heavy-duty-parallel-number-crunching is running happily in the background. (3) kill virtual machine when you are done with your NT task in order to have more CPU for number crunching R Ryszard Czerminski phone: (781)994-0479 ArQule, Inc. email:ryszard@arqule.com 19 Presidential Way http://www.arqule.com Woburn, MA 01801 fax: (781)994-0679 -----Original Message----- From: Gary Strahan [mailto:strahan@outerbanks.umaryland.edu] Sent: Wednesday, March 01, 2000 9:55 AM To: Bhupendra Wakankar; CCL_posting Subject: CCL:NT parallel cluster Another option: You should be able to reboot your NT machines using a Linux boot-floppy, and then run calculations on them as part of a Linux cluster. Bhupendra Wakankar wrote: > Subject: CCL:NT parallel cluster > Dear CCLers, > Hi. > > We have 6 computers in our lab (4 running on WINNT and 2 on RedHat 6.0). > I use the Linux PC's for my computations while the 4 NT PC's stay > relatively idle. All these PC's are fairly powerful (> 400MHz > multiprocessor Pentiums) and thus have untapped number crunching power. > I am wondering if it is possible to build a parallel cluster using these > 4 NT PC's (and better still, using all 6 PC's). > > Almost all network of PC clusters that I read about on the web run under > Linux. Is there any particular reason for not choosing NT (lack of > parallel programs perhaps ?). > > I would also like to know if there are any DFT programs (parallel/single > processor, free/commercial) running on Windows NT? > > Thanks in advance, > > Regards, > Bhupendra > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > >-- End of excerpt from Bhupendra Wakankar -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Mar 1 10:49:28 2000 Received: from lilith.dpo.uab.edu (root@lilith.dpo.uab.edu [138.26.1.128]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA04571 for ; Wed, 1 Mar 2000 10:49:27 -0500 Received: from asc.edu (ZeeMan.tucc.uab.edu [138.26.15.137]) by lilith.dpo.uab.edu (8.9.3/8.9.3) with ESMTP id JAA10202 for ; Wed, 1 Mar 2000 09:48:39 -0600 Message-ID: <38BD3B92.80A9554C@asc.edu> Date: Wed, 01 Mar 2000 09:47:30 -0600 From: "Mark A. Zottola" X-Mailer: Mozilla 4.61 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Re: CCL:NT parallel cluster References: <24095.200003011220@socrates-a.ucl.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > > > > Almost all network of PC clusters that I read about on the web run under > > Linux. Is there any particular reason for not choosing NT (lack of > > parallel programs perhaps ?). > Dear Bupendra, There are several reasons why NT is not widely used as a cluster OS. The first is scalability. While Microsoft would like you to believe that NT scales to any number, the fact is that it does not. Research funded by Microsoft is ongoing at NCSA to build NT clusters and solve the scalability problem. The second problem is that of cost. NT licenses are not cheap. Nor are multiple licenses for the same. Linux clusters are cheap simply because the OS is free. A third problem is robustness. The expression "blue screen of death" is an occurrence which happens many times to NT users. Depending on how hard one is pressing a system will determine how often the machine goes down. Those problems can be eradicated to a small degree. However, basic kernel changes can never be made to NT since you have no access to the source. Linux on the other hand allows you full access to the source, you can make major kernel modifications readily. Witness dipc which requires a kernel recompile to run on most linux clusters - an unthinkable option for NT. While I do not want to turn this into an anti-Microsoft rant, the technology for building robust, effective and cheap computational clusters is NOT Microsoft but Linux. To the best of my knowledge active development of tools for cluster development/computing is within the Linux/Beowulf community. it is my opinion that this is where the cutting edge of development will always be. Best Regards, Mark -- Mark A. Zottola Alabama Research and Education Network 119 Rust Research Center Computer Sciences Corporation 1801 University Boulevard VOICE: (205) 934 - 3893 Birmingham AL 35294 E-MAIL: asnmaz01@asc.edu From chemistry-request@server.ccl.net Wed Mar 1 12:09:53 2000 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA04912 for ; Wed, 1 Mar 2000 12:09:53 -0500 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with ESMTP id <01JMINTE70OS001ULZ@trentu.ca> for chemistry@ccl.net; Wed, 1 Mar 2000 12:08:49 EST Date: Wed, 01 Mar 2000 12:12:34 -0500 From: elewars Subject: SEMIEMPIRICAL REVIEWS SUMMARY To: chemistry@ccl.net Message-id: <38BD4F82.4CAD4C@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 8BIT X-Accept-Language: en Wed, 2000 March 1 Here is the summary of the answers I received to my question about recent reviews of semiempirical methods. Thanks very much to all who responded. EL ===== The Question Friday Feb 25 Hello, If anyone knows of a *recent* (1995 or later) review of semiempirical methods, including or devoted to AM1 and PM3, I would appreciate receiving the reference. (I looked in the CCL archives first; no luck). Thanks very much, EL ====== The Responses (#1--#8) #1 One of the books which accompanies Spartan has a discussion of semi-empirical methods and a significant amount of data comparing them to other methods. Unfortunately, I do not think this book is readily available. Here is the reference anyway: @Book{Hehre1998, author = {Hehre, Warren J. and Yu, Jianguo and Klunzinger, Philip E. and Lou, Liang}, title = {A Brief Guide to Molecular Mechanics and Quantum Chemical Calculations}, publisher = {Wavefunction Inc.}, year = 1998, annote = {accompanied Spartan program - good overview, ISBN 1-890661-05-8} Good luck - ned Ned C. Haubein Graduate Student Dept. of Chemical Engineering Northwestern University 2145 Sheridan Rd / Rm E136 Evanston, IL 60208-3120 Phone: 847-467-1402 Fax: 847-491-3728 Email: n-haubein@nwu.edu = #2 Did you consult the "Encyclopedia of Computational Chemistry"? There are several articles about semiempirical topics including one devoted to PM3 and one about AM1. Good luck, Matthias --------------------------------------------------------------------------- Dr. Matthias Hofmann Anorganisch-Chemisches Institut Ruprecht-Karls Universität Heidelberg Tel.: (INT+) 6221 54-8451 In Neuenheimer Feld 270 Fax.: (INT+) 6221 54-8439 D-69120 Heidelberg Germany e-mail: matthias.hofmann@urz.uni-heidelberg.de ------------------------------------------------------------------------- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ =========== #3 Damien Laage To: elewars Hello, Could you please send me a copy of the answers you get? Thank you very much, D. Laage ========= #4 Hi, try: M.C. Zerner, Semiempirical molecular orbital methods, i.e. chapter 8 in K.B. Lipkowitz, D.B. Boyd, Reviews in computational chemistry II (VCH, NY, 1994, p. 313) Serge _________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 011/268315 fax : 011/268301 email : sergiusz.kwasniewski@luc.ac.be _________________________________________________ ========== #5 Could you, please, summarize answers? Best regards, Mike mailto:mike@mnc.md =========== #6 From: David Young To: elewars Try the Encylopedia of Computational Chemistry, John Wiley & Sons (1998). Dave Young youngd2@mail.auburn.edu ------------------------------------------------------------------------ Live long and maintain marketable job skills. ------------------------------------------------------------------------ ============= #7 Dear E. Lewars, I am sorry that I don't have a suggested reference at the moment, but I would be very interested in knowning about these references as well. Would you please forward suggestions to me? I have been using MOPAC/PM3 and at a recent meeting someone blasted me telling me how bad PM3 was for hydrogen bonding and asked my why I was bothering to use it. I am planning on looking into this myself to get an idea on how bad/good it is - from other reading I have had the impression that PM3 was one of the best semi-empirical parameters sets to use for energy values. I will email you any reviews that I find related to this as well. Thanks very much, Bob Latour Robert A. Latour Jr., Ph.D. Associate Professor of Bioengineering and Materials Science & Engineering 501 Rhodes Research Center Clemson University, Clemson, SC 29634 robert.latour@ces.clemson.edu tel: (864) 656 -5552 / fax: (864) 656-4466 ============ #8 Hello E. Lewars, Here is an article of your interest, ''Some difficulties encountered with AM1 and PM3 calculations.'' Tetrahedron, 54 (1998) 12841-12852 Gloria Dr. Gloria Ines Cardenas-Jiron ============================== Departamento de Quimica de los Materiales, Facultad de Quimica y Biologia, Universidad de Santiago de Chile, Casilla 40 Correo 33, Santiago, CHILE. Fax: (56-2) 681.2108 Phone: (56-2) 681.2575 ============== From chemistry-request@server.ccl.net Wed Mar 1 12:34:54 2000 Received: from ivory.trentu.ca (trentu.ca [192.75.12.103]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA05010 for ; Wed, 1 Mar 2000 12:34:53 -0500 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with ESMTP id <01JMIOP5EYFM001XGA@trentu.ca> for chemistry@ccl.net; Wed, 1 Mar 2000 12:33:38 EST Date: Wed, 01 Mar 2000 12:37:24 -0500 From: elewars Subject: SAM1 SUMMARY To: chemistry@ccl.net Message-id: <38BD5553.A87FB87F@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Wed 2000 March 1 Here is the summary to my question about SAM1. I thank everyone who responded. EL --- The Question Wed, 2000 Feb 23 Hello, In 1993 the Dewar group announced the development of the SAM1 ("semi ab initio #1") method. I know the basic principles behind it, but would like to know: 1) What became of it? It does not seem to appear much in the literature. 2) Did computational chemists conclude it is not much better than AM1, and so let it fall into disuse? 3) I think it is offered in AMPAC; does any other package have it? Thanks EL ==== The Responses (#1--#5) #1 Subject: Re: CCL:SAM1 semiempirical method Date: Wed, 23 Feb 2000 19:23:18 -0500 (EST) From: Joe M Leonard To: elewars Semichem's AMPAC contains SAM/1 along with various other semi-empirical methods, and it's still a going concern. Tripos sells it commercially, but the development's done in KC, not StL. We've integrated it with our small/large molecule visualization software, FYI. Joe === #2 From: Thomas Heine To: elewars References: Hello, You could ask Slanina who published 1998 SAM1 results of fullerenes. Though they were not really good :) Z. Slanina et al., CPL 290:311, 1998. I don't know his exact address but he lives in Japan (Osaka I think) and has a webpage. Cheers, Thomas ============ #3 Re: CCL:SAM1 semiempirical method Date: Thu, 24 Feb 2000 10:10:01 -0500 From: Andrew T Pudzianowski Organization: Bristol-Myers Squibb To: elewars Dr. Lewars - I've been using SAM1 extensively for a few years now. It offers significant improvements over previous Dewar-style methodologies, especially in its performance with H-bonded systems. I've also had a chance to compare SAM1 results for isomer and conformer structures and energies directly with various ab initio and DFT results, the latter usually at levels like B3-LYP/6-31+G(d,p) or another augmented double-zeta basis with polarization functions, and have found near-quantitative agreement in most cases. On the other hand, SAM1 continues to share some notable failures with its MNDO and AM1 predecessors, and it has a fluke or two of its own. On the whole I'd say SAM1 represents some real progress in semiempirical methodology, but it isn't more widely used because it's currently available only in the commercial AMPAC software from Andy Holder's company, Semichem. Also, the rationale for not fully disclosing the parametrization of SAM1 in the open literature is that SAM1 is a unique feature of AMPAC, the sale of which is a source of funding for the continuing development of semiempirical methodologies in Holder's group. Because many chemists are reluctant to work with a methodology that has a significant unpublished component, I think this has also tended to limit both the use of SAM1 and dissemination of results. The latter aspect may be compounded by the possibility that, like yours truly, a lot of AMPAC users are employed in industry and can't publish the relevant results until patents and other competitive issues have been resolved. I think these factors have conspired to limit the exposure of SAM1 to the computational community, ultimately to the detriment of continued improvement of semiempirical methodologies, I'm afraid. Regards, Andrew Pudzianowski =============== #4 Hi EL, You asked about the SAM1 method: >I know the basic principles behind it, but would like to know: >1) What became of it? It does not seem to appear much in the literature. > >2) Did computational chemists conclude it is not much better than AM1, >and so let it fall into disuse? >3) I think it is offered in AMPAC; does any other package have it? Yes, it is offered in Ampac, and is continuing to be developed by Andy Holder's group (with Dewar's blessing, when he "passed the torch" to Andy). You can contact them at Semichem: http://www.semichem.com/ I believe you can also get AMPAC through Serena Software: http://www.serenasoft.com/ although I think they only provide an alternative interface. So far as SAM1, it does seem to be much better than AM1 in at least 2 respects; it includes d orbitals, so it has been parameterized to model some transition metal compounds, and it also provides more accurate vibrational frequencies than AM1 calculations. (Scaling is still required, but SAM1 frequencies are more accurate and much more consistent.) Parameterization of the metals has been a slow process, so only a few are available, and in fact the final "certified" SAM1 parameters for Fe were only released last year, hence not many publications yet. (In my own experience, SAM1 works much better for organometallic Fe complexes than it does for simple hydrates.) The improvement in frequency calculations has been published, see: A. J. Holder & R. D Dennington II, J. Mol. Struct. (THEOCHEM), 401(3), 207-18 (1997). I expect to see more published with SAM1 in the future, particularly as more transition metals are parameterized. EC --- Ernest Chamot Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 (630)637-1559 echamot@chamotlabs.com http://www.chamotlabs.com/cl ============== #5 Colleagues, Several days ago the following questions were posed. Sorry it took me some time to respond. > In 1993 the Dewar group announced the development of the SAM1 ("semi ab > initio #1") method. > I know the basic principles behind it, but would like to know: > 1) What became of it? It does not seem to appear much in the literature. The SAM1 method is still under development in my Group at the University of Missouri-Kansas City. We are working on refining some additional parameters and have added some new computational algorithms (an improved CI (1) and a quadratically (to be published) convergent SCF procedure) to make the method tractable for open-shell transition metals. The references to the method currently extant in the literature are listed below. A major paper describing the full implementation and listing parameter values is in preparation. > 2) Did computational chemists conclude it is not much better than AM1, > and so let it fall into disuse? Actually, SAM1 performs better than AM1 in most cases for CHON and the halogens. We have parameters for Si, S, P that are better than AM1 as well, especially for hypervalent species. The TM parameters for Fe, Cu, and Zn are basically completed and others are underway. > 3) I think it is offered in AMPAC; does any other package have it? Currently Semichem's AMPAC is the only program in which it has been implemented, but we expect other vendors to put it in when the theoretical paper and parameters are published. References: ----------- (1) [CI paper] Liotard, D.L.; Holder, A.J. J. Chem. Inf. Comput. Sci. 1999, 39, 587. (2) [SAM1] Dewar, M. J. S.; Jie, C.; Yu, G. Tetrahedron 1993, 23, 5003. (3) [SAM1] Holder, A. J.; Dennington, R. D.; Jie, C. Tetrahedron 1994, 50, 627. (4) [SAM1] Holder, A. J.; Evleth, E. M. in Modeling the Hydrogen Bond; Smith, D. A.; American Chemical Society, Washington, DC, 1994; p 113. Regards, Andy Holder -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- UUUU UUU MMM MMKK KKKK CCCC | ANDREW J. HOLDER UU U MM MMK K CC CC | Assoc. Prof. of Comp./Org. Chemistry UU U MMM M MK KK CCC | Dept. of Chemistry UU U M MM MK KK CC CC | University of Missouri-Kansas City UUUUU MMM M MMKK KK CCCC | Kansas City, MO 64110 KK | holdera@umkc.edu K | (816) 235-2293, FAX (816) 235-6543 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- ============= From chemistry-request@server.ccl.net Wed Mar 1 23:16:55 2000 Received: from amon.reed.edu (amon.reed.edu [134.10.2.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA09322 for ; Wed, 1 Mar 2000 23:16:54 -0500 Received: from isis.reed.edu (isis.reed.edu [134.10.2.1]) by amon.reed.edu (8.8.8/8.8.8) with ESMTP id PAA24172 for ; Wed, 1 Mar 2000 15:18:14 -0800 (PST) Message-id: <11242076@isis.reed.edu> Date: 01 Mar 2000 15:00:12 PST From: Alan.Shusterman@directory.reed.edu (Alan Shusterman) Subject: Summary: diatomic MOs To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id XAA09323 Thanks to all who responded. My original question concerned a claim in my inorganic chemistry textbook (and the many other books that people referred me to) that said that the pz-pz sigma bonding level lies above the degenerate pi bonding levels in B2, C2 and N2, and below in O2 and F2. If the textbook had simply said that this analysis was based on experimental data my question would have been moot because my interest was not in experimental results at this point in the course. Indeed, many people directed me to various sources of "experimental orbital energies" of which the most convenient turned out to be the NIST webbook. (webbook.nist.gov/chemistry/) Since my textbook's claim is widely repeated in many books (and since many people wrote fervently to me on this topic), I think a few more comments are in order. 1. There is no such thing as an 'experimental orbital energy'. 'Orbital' shapes and energies are not experimentally measurable. So if the NIST data are not 'experimental orbital energies', what are they? The NIST data turn out to be the energies of different electronic states of the cation produced by ionized of the diatomic molecule. If you look at the NIST table of X2 CATION energies you will see many states listed for each diatomic ion, their relative energies, their term symbols ("2_Pi_U"), and other properties besides. If one assumes that the neutral diatomic and all of its ions have the same orbitals at the same energies (i.e., Koopman's theorem) one can use the term symbols and state energies to guess the sequence of orbital energies in the neutral. These assumptions may be useful for practicing chemists, but it is important to realize what a tremendous leap of faith they represent. Orbital energies and molecular geometries change upon ionization; why can't the sequence of orbitals change as well? (This would explain the behavior of F2, see below.) Which brings me to my next comment: 2. Many people advised me NOT to use HF calculations to get the correct sequence of orbital energies. Specific advice included, "don't use Koopman's theorem", "HF calculations are too crude to give the correct orbital energies" and other statements to the same effect. The advice was well intended, but it was based on the mistaken assumption that I was trying to fit the ionization measurements, something that I was NOT trying to do (see below). The advice is also fascinating in another way. Consider: "don't use Koopman's theorem" - The fact that HF orbital energies do not reproduce ionization potentials is well-known. I have nothing to add. But, I do wonder, how does one get from the term symbols in the NIST table to the orbital energies without using Koopman's theorem? There seems to be a double standard at work - computational chemists should not use Koopman's theorem, but experimentalists should use poor Koopman. Isn't it equally flawed for both? "HF calculations are too crude to give the correct orbital energies" - What other method would people advise? Orbital energies are not physical observables. Orbitals do not exist in correlated treatments. What method is there that is less crude than HF, but still has orbital energies and generates results that can be anticipated using qualitative MO theory? (DFT orbital energies may be numerically interesting, but there is no reason to expect that the qualitative MO theory in my textbook was designed to anticipate DFT orbital energies). 3. Teachers and students beware. The textbook that I am using introduces the subject of diatomic MO energies in the context of "here is how to mix AO's and guess MO shapes and energies". I assumed that the book was trying to teach qualitative mixing techniques that mimic what happens in a more sophisticated Hartree-Fock calculation. Unfortunately, either I am wrong or the authors simply did not realize that they were changing the rules of the game in mid-chapter. Given the willingness of textbook authors to use expt'l data to say how orbitals "mix" I think a different point-of-view must be adopted by students and teachers. They must view the "MO theory" in the textbook as merely a conceptual framework in which one mixes AOs and MOs to arrive at an experimental result. Yes, we mix AOs just like the computer does during an HF calculation, but we adjust our mixing empirically to fit experimental data (forget all that perturbation theory and secular determinant stuff). The situation is entirely analogous to the way organic chemists use "resonance theory". One starts with a solid foundation (VB-CI theory), simplifies it so almost anyone can use it, and then drops all theoretical pretensions and fits the remaining parameters ("major/minor resonance contributors") to get a desired result. Good-bye theoretical foundation. Now I will know better than to believe my book when it tells me about orbital energies, overlaps, and mixings - it is probably talking about empirically derived quantities, and not calculated ones. 4. I took another look at the calculation of HF orbital energies. Instead of using UHF for open-shell molecules, I used ROHF (Jaguar) and a large basis set: cc-pvtz(-f)++ (32 functions per atom). The orbital sequences are: triplet B2: s-s < s-s* < pi_x (1 electron) = pi_y (1 electron) < pz-pz [LUMO] singlet C2: same as triplet B2 except pi_x and pi_y are filled. triplet C2: s-s < s-s* < pi_x (1 electron) = pi_y (1 electron) < pz-pz (filled) < pz-pz* [LUMO] >>triplet C2 (ROHF) was given a lower energy than single C2 (RHF). Notice that the pi levels in triplet C2 are half-filled but lower in energy than the filled pz-pz level. N2 : s-s < s-s* < pz-pz < pi_x = pi_y < pz-pz* [LUMO] triplet O2: s-s < s-s* < pz-pz < pi_x = pi_y < pi*_x (1 electron) = pi*_y (1 electron) < pz-pz* [LUMO] F2: s-s < s-s* < pi_x = pi_y < pz-pz < pi_x* = pi_y* < pz-pz* [LUMO] F2 is the most interesting molecule of all(?). Koopman's theorem predicts that ionization should happen more easily from the sigma z-z level than from the pi bonding levels, but the experimental ordering of cation states says the opposite. Because of the high electron density around two F atoms, this is exactly the kind of case where electron correlation effects are likely to be substantial. I have no results to support this, but it seems entirely conceivable that different electronic states of the CATION represent different orbital sequences, and these sequences may be quite different from those of the neutral (differential orbital relaxation, geometry changes, and electron correlation all seem likely here). I will tell my class that calculations correctly give the order of orbitals in the neutral F2 molecule, and this order is different from the one in the book (so don't trust what the book says about when to mix/not mix orbitals!), mainly because I think calculations tell us about orbitals and experiments don't. I'll also point out to them that the orbital sequence in F2 is not a good guide to the sequence of electronic states in F2+. But F2 and various states of F2+ are all very different molecules, so why should an orbital sequence in one tell me about the energy of the other? -Alan ------------------------ Alan Shusterman Department of Chemistry Reed College Portland, OR www.reed.edu/~alan