From chemistry-request@server.ccl.net Mon Oct 23 07:54:40 2000 Received: from fyserv1.fy.chalmers.se (fyserv1.fy.chalmers.se [129.16.110.66]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA28531 for ; Mon, 23 Oct 2000 07:54:40 -0400 Received: from fy.chalmers.se (ftf-pc32.fy.chalmers.se [129.16.112.162]) by fyserv1.fy.chalmers.se (8.8.8/8.8.8) with ESMTP id NAA11432 for ; Mon, 23 Oct 2000 13:54:34 +0200 (MET DST) Message-ID: <39F426FA.A57EC8C1@fy.chalmers.se> Date: Mon, 23 Oct 2000 13:54:34 +0200 From: Patrik Johansson Organization: CTH X-Mailer: Mozilla 4.51 [sv] (Win98; I) X-Accept-Language: sv MIME-Version: 1.0 To: chemistry@ccl.net Subject: Efield and Raman spectra? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers I would like to use an external electric field while optimising molecular geometry and then calculate the Raman spectra under the influence of this external field. Since the evaluation of Raman spectra itself uses electric fields is this approach valid?? Replies will be summarised. Sincerely Patrik Johansson Scientist Materials Physics Chalmers University of Technology patrikj@fy.chalmers.se From chemistry-request@server.ccl.net Mon Oct 23 09:20:29 2000 Received: from bbhm.na.pg.com (bbhm.na.pg.com [192.44.184.159]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA29051 for ; Mon, 23 Oct 2000 09:20:29 -0400 X-ExtMailInfo: laidig@pandora.na.pg.com pandora.na.pg.com [155.118.176.101] Received: from pandora.na.pg.com (pandora.na.pg.com [155.118.176.101]) by bbhm.na.pg.com (8.8.8/8.10.1/D3r7) with ESMTP id e9NDCTZ22935; Mon, 23 Oct 2000 09:12:29 -0400 (EDT) Received: from morpheus.na.pg.com (morpheus.na.pg.com [143.5.24.124]) by pandora.na.pg.com (8.8.8/8.8.8) with ESMTP id JAA49241669 for <@pandora.na.pg.com:chemistry@ccl.net>; Mon, 23 Oct 2000 09:17:23 -0400 (EDT) Received: from pg.com (localhost [127.0.0.1]) by morpheus.na.pg.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id JAA25530 for ; Mon, 23 Oct 2000 09:18:20 -0400 (EDT) Sender: laidig@pg.com Message-ID: <39F43A9B.8310CE9E@pg.com> Date: Mon, 23 Oct 2000 09:18:19 -0400 From: Bill Laidig X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Synthesis and retrosynthesis prediction programs Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit All, I am trying to find out about the current status of programs for synthesis/retrosynthesis. It has been at least 5 years since I have looked at this area and need to find out about the players, state-of-the-art, etc. I will summarize what I learn back to the list. Thanks, Bill Laidig -- ************************************************************************ * "Like jewels in a crown, the precious stones glittered in the * * queen's round metal hat." - Jack Handey * * * * Bill Laidig * * The Procter & Gamble Co. tel 513-627-2857 fax - 1233 * * Miami Valley Laboratories laidig@pg.com (preferred) * * P.O. Box 538707 laidig.wd@pg.com * * Cincinnati, OH 45253-8707 * ************************************************************************ From chemistry-request@server.ccl.net Mon Oct 23 09:39:32 2000 Received: from asp.biogeo.uw.edu.pl (root@asp.biogeo.uw.edu.pl [212.87.8.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA29226 for ; Mon, 23 Oct 2000 09:39:30 -0400 Received: (from grzesb@localhost) by asp.biogeo.uw.edu.pl (8.9.3/8.9.3) id PAA04027; Mon, 23 Oct 2000 15:38:14 +0200 Date: Mon, 23 Oct 2000 15:38:14 +0200 From: Grzegorz Bakalarski To: CHEMISTRY@ccl.net Cc: Grzegorz Bakalarski Subject: program for viewing MD Message-ID: <20001023153814.A27922@asp.biogeo.uw.edu.pl> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2i Hello, I look for a graphical program to visualize MD. The program should be as simple as possible. It is for my students that write their first MD code. The input should be as simple as possible ,eg. atom_type, x,y,z for some 1000 steps, system consists of max 1000 atoms. It would be nice if it could color atoms using kinetic energy, but this is not very important. It does not have to have advanced graphics - spheres or crosses would be OK. It has to run on SGI Indy IRIX 6.2 R4400 old machine. It should also be for free ... I tested VMD and MOIL-VIEW, however they are to complex (and I don't know AMBER trajectory format). It just should show my student the behavior of system. Any suggestions ? (|:-) gb From chemistry-request@server.ccl.net Mon Oct 23 10:45:41 2000 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA29702 for ; Mon, 23 Oct 2000 10:45:40 -0400 Received: (from ib@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) id RAA20403; Mon, 23 Oct 2000 17:11:41 +0200 (CEST) Date: Mon, 23 Oct 2000 17:11:41 +0200 (CEST) Message-Id: <200010231511.RAA20403@oc30.uni-paderborn.de> X-Authentication-Warning: oc30.uni-paderborn.de: ib set sender to ib@oc30.uni-paderborn.de using -f From: Ingo Brunberg To: grzesb@asp.biogeo.uw.edu.pl CC: CHEMISTRY@ccl.net In-reply-to: <20001023153814.A27922@asp.biogeo.uw.edu.pl> (message from Grzegorz Bakalarski on Mon, 23 Oct 2000 15:38:14 +0200) Subject: Re: CCL:program for viewing MD References: <20001023153814.A27922@asp.biogeo.uw.edu.pl> Try XMakemol, it is the simple program you search for. Its homepage location is http://vegemite.chem.nott.ac.uk/~xmakemol/ Good luck, Ingo Brunberg > Hello, > > I look for a graphical program to visualize MD. The program should be as simple > as possible. It is for my students that write their first MD code. The input > should be as simple as possible ,eg. > atom_type, x,y,z > > for some 1000 steps, system consists of max 1000 atoms. It would be nice if it could color > atoms using kinetic energy, but this is not very important. It does not have to have advanced graphics - > spheres or crosses would be OK. It has to run on SGI Indy IRIX 6.2 R4400 old machine. > It should also be for free ... > I tested VMD and MOIL-VIEW, however they are to complex (and I don't know AMBER > trajectory format). It just should show my student the behavior of system. > > Any suggestions ? (|:-) > > gb From chemistry-request@server.ccl.net Mon Oct 23 10:02:49 2000 Received: from dsmtp5.dion.ne.jp (dsmtp5.dion.ne.jp [210.196.3.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA29403 for ; Mon, 23 Oct 2000 10:02:48 -0400 Received: from b159504364 by dsmtp5.dion.ne.jp (8.9.3/3.7W-00031710) id XAA24113; Mon, 23 Oct 2000 23:02:33 +0900 (JST) Message-ID: <003c01c03cf9$ad60cf20$4b9ae6d2@b159504364> From: "Telkuni" To: Subject: Free MD program for Win95/98 --ADDITION Date: Mon, 23 Oct 2000 23:00:54 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear all CCLers, A few days ago, I submitted the article "Free MD program for Win95/98 --SUMMARY". The orginal question of it is: >I am a novice of MD simulation. >I'm looking for "free" and "for non-Bio" MD programs which are able >to run on Win95/98. >If anyone know such MD programs(and I wish they are also easy to use >for beginners.) , please teach me. >I would like to use them for "MD-learning". Here is one additional software for that summary. The software's name is "Moldy" which is developed by Keith Refson (Keith.Refson@earth.ox.ac.uk). This is also suitable to my purpose. Its URL is http://www.earth.ox.ac.uk/~keith/moldy.html . And, in this site, there is the announcemet of the Moldy's mailinglists. Sorry, I had to include "Moldy" to last summary. Sincerely yours, Telkuni ***************************************** Telkuni Tsuru telmail@d4.dion.ne.jp ***************************************** From chemistry-request@server.ccl.net Mon Oct 23 13:10:47 2000 Received: from narnia2.rutgers.edu (0@narnia2.rutgers.edu [165.230.180.158]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA30450 for ; Mon, 23 Oct 2000 13:10:47 -0400 Received: from eden.rutgers.edu (molly.envsci.rutgers.edu [165.230.5.148]) by narnia2.rutgers.edu (8.8.8/8.8.8) with ESMTP id NAA08845; Mon, 23 Oct 2000 13:10:24 -0400 (EDT) Message-ID: <39F47509.C3B4CAEF@eden.rutgers.edu> Date: Mon, 23 Oct 2000 13:27:37 -0400 From: "Mary O'Connor" X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: Bill Laidig CC: chemistry@ccl.net Subject: Re: CCL:Synthesis and retrosynthesis prediction programs References: <39F43A9B.8310CE9E@pg.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Bill Laidig wrote: > All, > > I am trying to find out about the current status of programs for > synthesis/retrosynthesis. It has been at least 5 years since I have > looked at this area and need to find out about the players, > state-of-the-art, etc. I will summarize what I learn back to the list. > Thanks, Bill Laidig > > -- > ************************************************************************ > * "Like jewels in a crown, the precious stones glittered in the * > * queen's round metal hat." - Jack Handey * > * * > * Bill Laidig * > * The Procter & Gamble Co. tel 513-627-2857 fax - 1233 * > * Miami Valley Laboratories laidig@pg.com (preferred) * > * P.O. Box 538707 laidig.wd@pg.com * > * Cincinnati, OH 45253-8707 * > ************************************************************************ > > -= 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 Dear Bill: Early this year I went to an introductory seminar on a new Beilstein package that specializess in showing these synthetic pathways and has many other features. You can try contacting the Beilstein people, or, for more information, log on to the Rutgers website (New Brunswick), search out a library head honcho, and get more information from them. Try www.libraries.rutgers.edu. Because the package did not have any personal applications for my work, I didn't keep the information. Mary O'Connor Doctoral Candidate Rutgers University New Brunswick, NJ From chemistry-request@server.ccl.net Mon Oct 23 14:28:33 2000 Received: from stillwater.cs.umt.edu (stillwater.cs.umt.edu [150.131.15.39]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA31101 for ; Mon, 23 Oct 2000 14:28:32 -0400 Received: from [150.131.15.54] (dakota.cs.umt.edu [150.131.15.54]) by stillwater.cs.umt.edu (8.9.3+Sun/8.9.3) with ESMTP id MAA08316 for ; Mon, 23 Oct 2000 12:28:18 -0600 (MDT) User-Agent: Microsoft Outlook Express Macintosh Edition - 5.01 (1630) Date: Mon, 23 Oct 2000 12:42:11 -0600 Subject: RE: programs for generation of topological indices From: "Clair W. Cabal" To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit I have received a couple of requests to share the information I received in responses to my query. Thank you very much to those who took the time to send me information. My original message is followed by a summary of the responses: Date: Mon, 16 Oct 2000 13:04:01 -0600 (MDT) From: Clair W Cabal To: chemistry@ccl.net Subject: programs for generation of topological indices All, Please forgive me if this is a redundant request, but in reviewing the archives, I don't see much on this topic since 1995. I am in search of a stand alone program to generate a very large number of toplogical indices for chemical compounds. I know of, but am not familiar with MOLCONN-X, QuaSar-Descriptor and Dr. Basak's POLLY 2.3. A respondent to this query posed in 1995 mentioned a program called EMMA which could handle up to 2,000 descriptors, but I have not received a response to an inquiry about this from the developer at Moscow State University. I would appreciate any feedback about use of the above mentioned programs and any information about others that may have been developed more recently. Thank you. Clair Cabal Research Assistant Machine Learning Research Lab Department of Computer Science University of Montana Missoula, Montana email: cabal@cs.umt.edu fax: (406) 243-5139 --------------------------------------------------------------------------- Date: Tue, 17 Oct 2000 08:58:58 From: "Rob Williams" To: "'Clair W Cabal'" Subject: RE: programs for generation of topological indices Hi Clair, Oxford Molecular distributes a product called TsarBatch. It is a stand-alone version of the descriptor generation parts of their Tsar QSAR product. I wasn't sure from your e-mail whether you were after a program that calculates a very large range of descriptors, or one that calculates standard topological indices for a very large number of structures. TsarBatch is more in the latter of these two categories. You can find more information at: http://www.oxmol.com/software/tsarbatch/ There is a fact sheet that you can download from there. Hope this is of interest to you. Best regards, Rob ------------------------------ Date: Tue, 17 Oct 2000 07:30:06 From: Doug Henry To: "'cabal@cs.umt.edu'" Subject: FW: programs for generation of topological indices The Dragon program was recently posted. It takes Sybyl Mol2 and Hyperchem hin files, and can generate 800+ descriptors. It can be used in conjunction with Babel, but I found the resulting files must have extra blanks removed from the files to be acceptable to Dragon. It can take a directory of molecule files, generate a file with descriptor values, then allows you to add your own "Y" colums to the data: Dear Colleague, We would like to advertise that the new software DRAGON (version 1.0) for the calculation of 853 theoretical molecular descriptors is now free downloadable from our Website. This software has been produced by us, coherently to the Handbook of Molecular Descriptors, by Roberto Todeschini and Viviana Consonni, edited in these days by WILEY - VCH, in the Series of Methods and Principles in Medicinal Chemistry, Vol. 11 (Editors: R.Mannhold, H.Kubinyi, H.Timmerman); pp.680. We have also activated a bibliographic reference service about molecular descriptors at our Website and a special e-mail address (moldes@disat.unimib.it) for the exchange of information of the researchers in this field. Best regards, Roberto Todeschini and Viviana Consonni ---------------------------------------------------------------------------- -------- Milano Chemometrics and QSAR Research Group Department of Environmental Sciences P.za della Scienza, 1 - 20126 Milano (italy) WebSite: http://www.disat.unimib.it/chm/ Dough@mdli.com (just a user) ------------------------------ Date: Wed, 18 Oct 2000 11:38:07 From: "Vladimir A. Palyulin" To: cabal@cs.umt.edu Subject: descriptors Dear Clair Cabal, Just a few days ago Milano Chemometrics group headed by Professor Roberto Todeschini released free version of DRAGON program which computes about 850 descriptors. It can be downloaded from: http://www.disat.unimib.it/chm/ Sincerely, Vladimir Palyulin, Head, Group of Computer Molecular Design, Department of Chemistry, Moscow State University P.S. EMMA program was oriented for DOS and was developed in 1988-1993, now we are working on Windows program which computes thousands descriptors, which are treated with neural networks. ------------------------------ Thanks also to Elena Fioravanzo for forwarding information about DRAGON. I should mention that DRAGON does not just produce topological indices, but generates 14 classes of theoretic descriptors including geometric, information theoretic, constitutional and BCUT descriptors to name a few. I have run some test data with DRAGON and find it to be very easy to use. Now my task is to convert existing data into mol file format! Clair Cabal From chemistry-request@server.ccl.net Mon Oct 23 15:53:51 2000 Received: from email.nist.gov (email.nist.gov [129.6.2.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA31517 for ; Mon, 23 Oct 2000 15:53:50 -0400 Received: from bratsche (bratsche.nist.gov [129.6.194.154]) by email.nist.gov (8.9.3/8.9.3) with SMTP id PAA23074 for ; Mon, 23 Oct 2000 15:53:51 -0400 (EDT) Message-Id: <4.1.20001023150944.00a653d0@mailserver3.nist.gov> X-Sender: irikura@mailserver3.nist.gov X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Mon, 23 Oct 2000 15:52:12 -0400 To: chemistry@ccl.net From: Karl Irikura Subject: verify a far-out MM3 result? Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" I recently obtained the following enthalpy of formation (298 K) for bicyclo[2.1.0]pent-2-ene (C5H6; cyclobutene with a cyclopropane ring fused to the edge opposite the double bond): MM3 545 kJ/mol (expt 333 kJ/mol) It's so far off I wonder if there's some problem with my copy of MM3 (came with Tripos' "Alchemy2000" software). It reports missing bond-equivalent parameters for two bonds (the sp2-sp3 bonds)--could they be worth -106 kJ/mol each? The corresponding bonds in the bicyclopentane are worth +23 kJ/mol each. The results look great for these related molecules: cyclobutene MM3 = 158 expt = 157 kJ/mol cyclopropane MM3 = 54 expt = 53 bicyclo[2.1.0]pentane MM3 = 156 expt = 158 I don't think the experimental value is bad: from G2 I get 320 kJ/mol and from B3LYP//cc-pVTZ//6-31G* I get 331 kJ/mol. I'd be grateful to learn the MM3 result obtained from other software (or even from an independent installation of Alchemy2000). Thanks for any help! Karl ---------------------------------------------- Dr. Karl K. Irikura National Institute of Standards and Technology 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice: 301-975-2510 fax: 301-869-4020 e-mail: karl.irikura@nist.gov http://www.nist.gov/compchem/ ---------------------------------------------- From chemistry-request@server.ccl.net Mon Oct 23 18:14:21 2000 Received: from mercury.chem.nwu.edu (gwuxi@mercury.chem.nwu.edu [129.105.116.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA32219 for ; Mon, 23 Oct 2000 18:14:21 -0400 Received: from localhost by mercury.chem.nwu.edu (8.9.1/8.9.1) with SMTP id RAA03903 for ; Mon, 23 Oct 2000 17:16:15 -0500 (CDT) Date: Mon, 23 Oct 2000 17:16:15 -0500 (CDT) From: Guosheng Wu To: ccl Subject: Help on force field for simplified "atoms" Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear folks, Does any of you have the experience on developing force field for simplified "atoms"? I know there are some papers related with simplified "atom" for CH2 or CH3, but how about biger molecules? For example, if I want to get a simple function V(R) for the interction between C6H6 and C6H6, I may either summarize the LJ(rij) interctions between all of atoms(i in one molecule and j in the other one), or I can do ab initio calculations for different intermolecular distances(R). By both methods I may be able to fit the results into a simple function, say still in LJ(R) form. However, sometimes this mayn't work, or very time-consuming for big molecules. If anyone could give me some suggestions or related reference, I will be very grateful. Thanks a lot! Guosheng Wu -------------------------------------------- Guosheng Wu Dept. of Chem., Northwestern Univ. 2145 Sheridan Road, Evanston, IL, 60208-3113 --------------------------------------------