From surjit@chemistry.iitd.ernet.in Tue Jul 15 00:07:11 1997 Received: from kriti.iitd.ernet.in for surjit@chemistry.iitd.ernet.in by www.ccl.net (8.8.3/950822.1) id XAA27143; Mon, 14 Jul 1997 23:49:16 -0400 (EDT) Received: from chemistry.iitd.ernet.in (netearth) by kriti.iitd.ernet.in (5.x/SMI-SVR4) id AA08427; Tue, 15 Jul 1997 09:18:14 +0530 Received: by chemistry.iitd.ernet.in; id AA29947; Tue, 15 Jul 1997 09:18:52 +0530 Received: by chemistry; Tue, 15 Jul 1997 09:18:52 +0530 id AA29947; Tue, 15 Jul 1997 09:18:52 +0530 Date: Tue, 15 Jul 1997 09:18:51 +0530 (IST) From: Surjit Dixit Subject: Re: CCL:AMBER and contiuum solvent models To: Jeffrey.Nauss@UC.Edu Cc: chemistry@www.ccl.net In-Reply-To: <9707141134.ZM12124@beryllium.crs.uc.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > > Have contiuum solvent models been implemented in AMBER for MD simulations? If > so, is the code available? > Yes, it has been done. Fritsch, V., and E. Westhof. 1991. Three-center hydrogen bonds in DNA: molecular dynamics of poly(dA).poly(dT). J. Am. Chem. Soc. 113:8271-8277. But that was AMBER3. Best regards, Surjit. ____________________________ Surjit B.Dixit PhD Candidate Telephone:+91 11 666979 Extn.:7602 Chemistry Department, Facsimile:+91 11 6862037 Indian Institute of Technology, Email : surjit@chemistry.iitd.ernet.in Hauz Khas, surjit@netearth.iitd.ernet.in New Delhi 110016, India. From ccl@www.ccl.net Sun Jul 13 20:06:57 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id TAA18981; Sun, 13 Jul 1997 19:38:38 -0400 (EDT) Received: from europe.std.com for jle@world.std.com by bedrock.ccl.net (8.8.6/950822.1) id TAA11273; Sun, 13 Jul 1997 19:38:36 -0400 (EDT) Received: from world.std.com by europe.std.com (8.7.6/BZS-8-1.0) id TAA19034; Sun, 13 Jul 1997 19:38:33 -0400 (EDT) Received: by world.std.com (5.65c/Spike-2.0) id AA23677; Sun, 13 Jul 1997 19:38:31 -0400 Date: Sun, 13 Jul 1997 19:38:31 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199707132338.AA23677@world.std.com> To: chemistry@ccl.net Subject: re: What languages will be here tomorrow... Alex Turner ; Mon, 14 Jul 1997 09:17:53 +0100 (BST) Date: Mon, 14 Jul 1997 09:17:52 +0100 (BST) From: Val Gillet X-Sender: li1vg@stoat To: chemistry@www.ccl.net Subject: Call for papers Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CALL FOR PAPERS: COMPUTATIONAL APPROACHES TO THE DESIGN AND ANALYSIS OF COMBINATORIAL LIBRARIES The Molecular Graphics and Modelling Society and the Chemical Structure Association are organising a joint conference on the computational analysis of molecular diversity, to be held in Sheffield, UK 14-16 April 1998. Contributions are now sought in areas such as: the design of diverse and focussed libraries; algorithms and methods for the selection of database subsets; the representation and searching of combinatorial libraries and analogous virtual databases; the design and use of both in-house and commercial software for diversity analysis; diversity indices; compararison of property-based and fingerprint-based (dis)similarity measures; and the integration of diversity analysis with other computational tools, such as docking and QSAR. People wishing to present their work should submit a 500-word abstract (preferably by email) to Dr V.J. Gillet, Department of Information Studies, University of Sheffield, Sheffield S10 2TN, UK (tel. 044-114-2222652, fax 044-1142780300, email v.gillet@sheffield.ac.uk) by 1st October 1997. From MAILER-DAEMON@www.ccl.net Mon Jul 14 09:07:12 1997 Received: from schiele for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.8.3/950822.1) id IAA21816; Mon, 14 Jul 1997 08:58:36 -0400 (EDT) Received: by schiele (950911.SGI.8.6.12.PATCH825/940406.SGI.AUTO) id OAA00022; Mon, 14 Jul 1997 14:58:25 +0200 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9707141458.ZM20@eros.ccc.uni-erlangen.de> Date: Mon, 14 Jul 1997 14:58:21 -0600 In-Reply-To: Wang Jiansuo "CCL:Where is software on interconversion of chemical structure systems based on WLN???" (Jul 14, 16:52) References: Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: Wang Jiansuo Subject: Re: CCL:Where is software on interconversion of chemical structure systems based on WLN??? Cc: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On Jul 14, 16:52, Wang Jiansuo wrote: > Subject: CCL:Where is software on interconversion of chemical structure sy > Dear netter, > Wiswesser Line Notation(WLN) is a widely-used method of chemical I HOPE NOT! This kind of notation is an abomination. Are there any software packages around which stil use this represenation? This format was designed at a time when storage space was extremely expensive. It produces very compact representations, at the cost of ridiculously convoluted and self-contradicting encoding rules. If you need to use a line notation, you should employ the widely supported SMILES system. If, however, you have some legacy database, you have my deepest sympathy and a lot of work to do. > structure presentation.I am looking for programs that interconve between > WLN and Connection Table or other structure presentation systems.Any > information of yours is appreciated. > Thanks in advance. > Your sincerely, > >-- End of excerpt from Wang Jiansuo -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From jkl@ccl.net Mon Jul 14 23:07:14 1997 Received: from bedrock.ccl.net for jkl@ccl.net by www.ccl.net (8.8.3/950822.1) id WAA26805; Mon, 14 Jul 1997 22:11:42 -0400 (EDT) Received: from krakow.ccl.net for jkl@ccl.net by bedrock.ccl.net (8.8.6/950822.1) id WAA14329; Mon, 14 Jul 1997 22:11:40 -0400 (EDT) From: Jan Labanowski Received: for jkl@ccl.net by krakow.ccl.net (8.8.3/920428.1525) id WAA00587; Mon, 14 Jul 1997 22:11:38 -0400 (EDT) Date: Mon, 14 Jul 1997 22:11:38 -0400 (EDT) Message-Id: <199707150211.WAA00587@krakow.ccl.net> To: chemistry@www.ccl.net Subject: xvibs.c now works with dummies in ACES2 Cc: jkl@ccl.net Dear vacationers and vacationists... The xvibs.c (a program to extract vibrational modes from output files of Aces2, Gamess, and Gaussian is revisited... Thanks to Eric V. Patterson and Bradley Smith the serious features (some call them bugs) of xvibs.c acting on ACES2 output were uncovered. I did not check the thing for dummy atoms and symmetry. And I should have had... Now, this seems to be fixed, so grab the new version of xvibs.c >from ftp:/www.ccl.net/pub/chemistry/software/SOURCES/C/xvibc and report new unknown features which I just introduced {:-)}. Yours, Jan Labanowski jkl@ccl.net From dsmith@CTCnet.Net Mon Jul 14 23:07:20 1997 Received: from home.CTCnet.Net for dsmith@CTCnet.Net by www.ccl.net (8.8.3/950822.1) id WAA26801; Mon, 14 Jul 1997 22:11:19 -0400 (EDT) Received: from fock by home.CTCnet.Net (SMI-8.6/SMI-SVR4) id WAA14867; Mon, 14 Jul 1997 22:04:15 -0400 Message-Id: <3.0.1.32.19970714221226.009b8fc0@pop.dasgroup.com> X-Sender: dsmith@pop.dasgroup.com X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Mon, 14 Jul 1997 22:12:26 -0400 To: jtgolab@amoco.com (Joe Golab) From: "Douglas A. Smith Ph.D." Subject: Re: CCL:Reaction Pathway Program Cc: CHEMISTRY@www.ccl.net In-Reply-To: <199707142145.AA14645@interlock.amoco.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Joe: I am not familiar with any program that will suggest ALL reaction pathways... there are just way too many possibilities, which is why we still have synthetic organic chemists. You are probably familiar with Bill Jorgensen's CAMEO program (I hope I have the name correct), which can suggest 'reasonable' synthetic routes to various types of compounds and functionality. There is also a commercial program (not that Bill doesn't sell his programs, ;)) called SYNTREE (I believe). There were some papers about this at either the last ACS National meeting in San Francisco or at the Midland, MI, ACS Regional meeting in May. I can look for more information if you wish, but I am at home and just finishing up a vacation while I write this. Regardless, both of these programs use a combination (I believe) of data bases and "expert" algorithms to select likely reactions. I don't know of anything that will give you all possible routes, except perhaps an aggressive undergraduate who has just finished his/her organic final exam. There was also SYNLIB that came from the late Dan Chodosh... I don't know if anyone picked up that program so I can't tell you if it still exists. This was purely data base based and matched based on user-defined descriptors, if I remember correctly from my postdoc days. MDL REACCS and CAS's reaction data base are two others that come to mind. I would also love to hear from anyone else about similar programs. Please post to CCL rather than just to Joe. Doug Smith At 04:43 PM 7/14/97 -0500, you wrote: >Dear CCL Member: > >Do you know of any (engineering, chemistry, biological, etc) program that >given a compound would suggest any and all reaction pathways toward that >compound (no matter how outlandish from a thermodyanmic standpoint)? > >For example, given tolune, the program would suggest: > > 1) benzene + methane -> toluene > 2) methylcyclohexane -> toluene + H2 > 3) methane + heat/pressure -> toluene + H2 > 4) ETC. > >Perhaps this is really a database that is part of a program. Any leads >would be gratefully appreciated! Thanks. > >-- > >:Joe > jtgolab@amoco.com > (630) 961-7878 > > +-------------------------------------------------------------------------+ > | There are two kinds of people, those who finish what they start and ... | > | - Robert Byrne | > +-------------------------------------------------------------------------+ > >-------This is added Automatically by the Software-------- >-- Original Sender Envelope Address: jtgolab@amoco.com >-- Original Sender From: Address: jtgolab@amoco.com >CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator >MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 >Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > > -- Dr. Douglas A. 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