From cgbzd@alinga.newcastle.edu.au Mon Oct 3 03:16:48 1994 Received: from alinga.newcastle.edu.au for cgbzd@alinga.newcastle.edu.au by www.ccl.net (8.6.9/930601.1506) id CAA27269; Mon, 3 Oct 1994 02:26:51 -0400 Received: (from cgbzd@localhost) by alinga.newcastle.edu.au (8.6.9/8.6.9) id QAA07903 for chemistry@ccl.net; Mon, 3 Oct 1994 16:26:39 +1000 From: DLUGOGORSKI B Z Message-Id: <199410030626.QAA07903@alinga.newcastle.edu.au> Subject: MAC <-> DOS for MS WORD files To: chemistry@ccl.net Date: Mon, 3 Oct 1994 16:26:38 +1000 (EST) X-Mailer: ELM [version 2.4 PL24alpha3] Content-Type: text Content-Length: 465 Would anyone on the net know how to read MAC files on a DOS/MSWindows PC? The files were created on a MAC computer using MS WORD 5.x. Any pointers to commercial/public domain software will be greatly appreciated. Many thanks. -- Bogdan Dlugogorski E-mail: cgbzd@alinga.newcastle.edu.au Department of Chemical Engineering Phone: +61 49 21 6176 University of Newcastle Fax: +61 49 21 6920 Callaghan, NSW 2308, AUSTRALIA From toukie@zui.unizh.ch Mon Oct 3 05:17:23 1994 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.9/930601.1506) id EAA28559; Mon, 3 Oct 1994 04:37:58 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA17122; Mon, 3 Oct 94 09:37:56 +0100 X-Nupop-Charset: British Date: Mon, 3 Oct 1994 09:32:54 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <34374.toukie@zui.unizh.ch> To: chemistry@ccl.net Subject: Organic chemistry Internet group? Ladies and Gentlemen: Some timne ago on CCL I read a posting informing us that there existed an organic chemistry newsgroup that could be reached at orgchem@extreme.chem.rpi.edu However, after sending a note to that e-mail address, I received a message that that address does not exist. Therefore, I request all readers of CCL to kindly advise me whether there does in fact exist a newsgroup dedicated to matters of organic chemis- try; if so, could you please send me the complete e-mail address for this newsgroup? I thank all responders in advance for their kind cooperation in the above matter. Yours respectfully, (Dr.) S. Shapiro Institut fuer orale Mikrobiologie und allgemeine Immunologie Zentrum fuer Zahn-, Mund-, und Kieferheilkunde der Universitaet Zuerich Plattenstrasse 11 Postfach CH-8028 Zuerich, Switzerland Internet: toukie@zui.unizh.ch FAX-nr: ( ... + 1) 261'56'83 From savary@sc2a.unige.ch Mon Oct 3 10:16:57 1994 Received: from UNI2B.UNIGE.CH for savary@sc2a.unige.ch by www.ccl.net (8.6.9/930601.1506) id JAA03062; Mon, 3 Oct 1994 09:35:14 -0400 Received: from PCC2333F (129.194.51.63) by uni2b.unige.ch (PMDF V4.3-8 #2502) id <01HHUD2FINS00026AL@uni2b.unige.ch>; Mon, 3 Oct 1994 14:34:26 WET-DST Date: Mon, 03 Oct 1994 14:34:25 +0100 From: savary@sc2a.unige.ch (Francois Savary) Subject: Mn force constants X-Sender: savary@sc2a.unige.ch To: CHEMISTRY@ccl.net Message-id: <01HHUD2FUG5U0026AL@uni2b.unige.ch> X-Envelope-to: CHEMISTRY@ccl.net MIME-version: 1.0 X-Mailer: Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Dear Co-listers, Here is a question from a collegue: Does anybody know references on Manganese(II)-aminoacid force constants for Charmm force-field. Thanx in advance Francois Savary ---------------------------------------------------------------------------- Francois Savary University of Geneva Department of Physical Chemistry CHIFI Weber 30 quai Ernest-Ansermet CH-1211 Geneva 4 Lab : 112 Phone : +4122 702 65 32 Fax : +4122 702 65 18 e-mail : savary@sc2a.unige.ch HTML : http://scsg9.unige.ch/tabmat.html (in french) : http://scsg9.unige.ch/eng/toc.html (in english) ---------------------------------------------------------------------------- From walterse@mis.fuhscms.edu Mon Oct 3 11:17:02 1994 Received: from mis.fuhscms.edu for walterse@mis.fuhscms.edu by www.ccl.net (8.6.9/930601.1506) id LAA05679; Mon, 3 Oct 1994 11:12:24 -0400 Message-Id: <199410031512.LAA05679@www.ccl.net> Subject: recycling old computers... To: CHEMISTRY@ccl.net (Computational Chem. List) Date: Mon, 3 Oct 1994 10:16:01 -0600 (CST) From: "Dr. D.Eric Walters" X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 8bit Content-Length: 746 Hi, I recently "inherited" two Evans & Sutherland PS330 systems. I'm trying to figure out the best possible use of these once mighty dinosaurs. I would welcome your suggestions, including any useful public domain software which would still run on them, or anyone interested in buying them for parts, or whatever. Best regards, Eric Walters * D. Eric Walters, Ph.D., Associate Professor, Biological Chemistry * Finch University of Health Sciences/The Chicago Medical School * 3333 Green Bay Road, North Chicago, IL 60064 * ph 708-578-3000, x-498;fax 708-578-3240; email: walterse@mis.fuhscms.edu * "A man would do nothing if he waited until he could do it so well that * no one would find fault with what he had done." --Cardinal Newman From case@scripps.edu Mon Oct 3 11:26:18 1994 Received: from scripps.edu for case@scripps.edu by www.ccl.net (8.6.9/930601.1506) id LAA05671; Mon, 3 Oct 1994 11:12:09 -0400 Received: from lanczos.scripps.edu by scripps.edu (5.61/1.34) id AA07009; Mon, 3 Oct 94 08:11:44 -0700 Received: by lanczos.Scripps.EDU (4.1/SMI-4.1/TSRI1.0) id AA01018; Mon, 3 Oct 94 08:10:32 PDT Date: Mon, 3 Oct 94 08:10:32 PDT From: case@scripps.edu (David Case) Message-Id: <9410031510.AA01018@lanczos.Scripps.EDU> To: chemistry@ccl.net, bhardy@convex.ox.ac.uk Subject: Re: CCL:CHARMM/Amber File Conversion Barry Hardy wrote: > Can anyone suggest a program/tool that can convert CHARMM input > files (coordinates, parameters, topology) to Amber and vice-versa? > If not, what is the most efficient work-around? I've worked on converting CHARMM input files into AMBER format, but it's not easy. Here are some of the issues you will face: (1) The CHARMM energy function includes Urey-Bradley interactions (1-3 "bonds") and a different way of maintaining planarity about trigonal centers than amber does, so you will have to modify the AMBER code to include the new functionality. (2) CHARMM uses four-letter codes to indicate atom types, but AMBER allows only two-letter codes, so you will have to make a mapping of these codes. (3) CHARMM force fields before about version 22 only used some of the torsion angles in a molecule in the force field. Adapting to this would require more changes to the AMBER code, which I never attempted, but which probably would not be too hard. (4) CHARMM generally handles the cut-off of non-bonded forces in a different way than AMBER, so that if you really want to reproduce the CHARMM force field inside amber, more code modifications are required. But the good news is that it mosly can be done. Here's what I did: (a) made the mapping of item (2) above, and the code changes in item (1); (b) edited the "all.in" file in AMBER to make the atom types and charges correspond to those in charmm. The atom types can be handled with a "sed"-script, but I ended up doing the charges by hand, although it would probably be possible to automate that as well. (c) wrote a perl script to convert CHARMM parameter and topology files into an AMBER "parm.dat" file. This code is pretty well commented, but was not written with distribution to other users in mind. I am happy to provide those interested a copy of the perl script. The output files it produces contain information covered by a license agreement under which I obtained CHARMM, and is therefore not available for redistribution. The code changes to AMBER will probably be included in the next AMBER release. BUT, the whole thing has not yet been properly debugged and tested, so there are a lot of caveat emptors here. I would be interested to know if anyone has skinned this particular cat in a different way. I believe that the "vice-versa" part (converting AMBER input to CHARMM) is in considerably better shape. ...hpe this helps....dave case ===================================================================== David A. Case | internet: case@scripps.edu Dept. of Molecular Biology, MB1 | bitnet: case%scripps.edu@sdsc The Scripps Research Institute | fax: 619-554-3789 10666 N. Torrey Pines Rd. | phone: 619-554-9768 La Jolla CA 92037 USA | ===================================================================== From shenkin@still3.chem.columbia.edu Mon Oct 3 12:16:55 1994 Received: from still3.chem.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.9/930601.1506) id MAA07560; Mon, 3 Oct 1994 12:06:50 -0400 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@ccl.net id AA14067; Mon, 3 Oct 94 12:06:31 -0400 From: "Peter Shenkin" Message-Id: <9410031206.ZM14065@still3.chem.columbia.edu> Date: Mon, 3 Oct 1994 12:06:04 -0400 In-Reply-To: "Dr. D.Eric Walters" "CCL:recycling old computers..." (Oct 3, 10:16am) References: <199410031512.LAA05679@www.ccl.net> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: "Dr. D.Eric Walters" , CHEMISTRY@ccl.net (Computational Chem. List) Subject: Re: CCL:recycling old computers... Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Oct 3, 10:16am, Dr. D.Eric Walters wrote: > Subject: CCL:recycling old computers... > I recently "inherited" two Evans & Sutherland PS330 systems. > I'm trying to figure out the best possible use of these > once mighty dinosaurs.... We used the "box" from one of these as a coffee table in our conference room for a few years. It worked moderately well for this, though eventually we located a real table, which works even better. We also pulled the boards. They are quite pretty. We thought about framing and hanging them, but after they sat around for a year we finally figured we'd never get around to this and threw them out. Besides, picture frames that big are expensive. Though neither of these applications worked out for us in the long run, I offer them as two of many possibilities. -P. -- *********** World music: What bluegrass is to a Bulgarian. ********** *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* * New York, NY 10027; shenkin@columbia.edu; (212) 854-5143 * **** If Sammy the Bull can turn Rat, who can feel safe any more? ***** From smb@smb.chem.niu.edu Mon Oct 3 12:26:12 1994 Received: from mp.cs.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.6.9/930601.1506) id LAA05969; Mon, 3 Oct 1994 11:19:04 -0400 Received: from cz2.chem.niu.edu by mp.cs.niu.edu with SMTP id AA09955 (5.67b/IDA-1.5 for <@mp.cs.niu.edu.chem.niu.edu:chemistry@ccl.net>); Mon, 3 Oct 1994 10:19:07 -0500 Received: from smb.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @mp.cs.niu.edu.chem.niu.edu:chemistry@ccl.net) id AA05736; Mon, 3 Oct 94 10:14:31 -0500 Received: by smb.chem.niu.edu (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:chemistry@ccl.net) id AA20253; Mon, 3 Oct 94 10:14:30 -0500 Date: Mon, 3 Oct 94 10:14:30 -0500 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9410031514.AA20253@smb.chem.niu.edu> To: chemistry@ccl.net Subject: Electronic Computational Chemistry Conference Abstracts Available The preview stage of the Electronic Computational Chemistry Conference is now available for access by the WWW. The url for the Conference is http://hackberry.chem.niu.edu:70/0/ECCC/homepage.html (An ascii version of the abstracts are available by anonymous ftp to hackberry.chem.niu.edu as /pub/ECCCabstracts.txt) This page will give you access to all of the submitted and accepted abstracts for the ECCC. There is also a current registration list. While it is too late to submit an abstract to the ECCC, you can still register for the conference, which will allow you to participate in the discussions of the papers. Full information on the conference, including how to register is available by: 1) WWW - URL http://hackberry.chem.niu.edu:70/0/ECCCinformation.txt 2) gopher to hackberry.chem.niu.edu port 70 3) anonymous ftp to to hackberry.chem.niu.edu as /pub/ECCCinformation.txt Questions and/or comments can be sent directly to me. Steve \ Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From BLOEB@tacora.puc.cl Mon Oct 3 15:16:57 1994 Received: from tacora for BLOEB@tacora.puc.cl by www.ccl.net (8.6.9/930601.1506) id OAA11237; Mon, 3 Oct 1994 14:35:28 -0400 From: Received: from tacora.puc.cl by tacora.puc.cl (PMDF #12315) id <01HHUCZ9HJDS90NRIA@tacora.puc.cl>; Mon, 3 Oct 1994 14:31 PDT Date: Mon, 3 Oct 1994 14:31 PDT Subject: Inorganic Chemistry net To: chemistry@ccl.net Message-id: <01HHUCZ9HJDS90NRIA@tacora.puc.cl> X-Organization: Pontificia Universidad Católica de Chile X-VMS-To: IN%"chemistry@ccl.net" Does anybody know about the existence of an Inorganic Chemistry net, similar to CCL? Thanks for any information in regard to this point. Barbara Loeb l. Faculty of Chemistry P.Catholic University of Chile BLOEB@TACORA.PUC.CL From debra.moreno@chemistry.gatech.edu Mon Oct 3 16:17:08 1994 Received: from gatech.edu for debra.moreno@chemistry.gatech.edu by www.ccl.net (8.6.9/930601.1506) id QAA12885; Mon, 3 Oct 1994 16:11:10 -0400 Received: from chemistry.gatech.edu (chem-mail.chemistry.gatech.edu) by gatech.edu with SMTP id AA15034 (5.65c/Gatech-10.0-IDA for ); Mon, 3 Oct 1994 16:12:16 -0400 Received: from chem-wrlab.chemistry.gatech.edu by chemistry.gatech.edu (AIX 3.2/UCB 5.64/4.03) id AA13922; Mon, 3 Oct 1994 16:10:36 -0400 Message-Id: <9410032010.AA13922@chemistry.gatech.edu> X-Sender: moreno@chem-mail.chemistry.gatech.edu (Unverified) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 3 Oct 1994 16:13:24 -0500 To: chemistry@ccl.net From: debra.moreno@chemistry.gatech.edu (Debra Moreno) Subject: CHARMm As a newcomer to molecular modeling and MM2 calculations, I am in search of the manufacturer of the program CHARMm. If anyone has that information I would greatly appreciate it. Aslo, is anyone familiar with the program so as to give an opinion of it, especially regarding the way it handles metals? Thanks. Debra A. Moreno debra.moreno@chemistry.gatech.edu