From KATEY@psipsy.uct.ac.za Mon Jan 23 09:39:04 1995 Received: from ucthpx.uct.ac.za for KATEY@psipsy.uct.ac.za by www.ccl.net (8.6.9/930601.1506) id JAA25224; Mon, 23 Jan 1995 09:15:43 -0500 Received: from charongw1.uct.ac.za by ucthpx.uct.ac.za with smtp (Smail3.1.28.1 #43) id m0rWPVu-000KLGC; Mon, 23 Jan 95 16:13 SAST Received: From ITS/WORKQ1 by charongw1.uct.ac.za via Charon-4.0A-VROOM with IPX id 100.950123160743.448; 23 Jan 95 16:14:57 -0200 Message-ID: To: chemistry@ccl.net From: KATEY@psipsy.uct.ac.za Date: 23 Jan 95 16:14:24 SAST-2 Subject: Biosym problem Priority: normal X-mailer: Pegasus Mail v2.3 (R4). I am working with a peptide that I am able to completely construct using the "Builder" module of Biosym. I then set the potentials and save the molecule. Having done this, as soon as I run any form of minimisation using the "Discover" module I am given warnings regarding certain groups not being neutral. My problem is that I don't know how these groups are actually being created by the program, and subsequently don't know how to neutralise them. Thank you in advance for any help regarding this problem. Kate Sunter. From heelisp@delta.newi.ac.uk Mon Jan 23 11:39:05 1995 Received: from delta for heelisp@delta.newi.ac.uk by www.ccl.net (8.6.9/930601.1506) id KAA27144; Mon, 23 Jan 1995 10:51:42 -0500 From: Date: Mon, 23 Jan 1995 15:48:57 +0100 Message-Id: <95012315485753@delta.newi.ac.uk> To: CHEMISTRY@ccl.net Subject: DNA X-VMS-To: SMTP%"CHEMISTRY@ccl.net" Dear all, anyyone out there with software that can construct B-DNA's automatically. I would be greatfull for a B-DNA of sequence TTTTTTTTTTTTT say 10 bases long, and also CCCCCCCCCCCCC, both with complimentary strand. PDB or CSD or CSSR formats. Thanks in advance, Paul Heelis Heelisp@newi.ac.uk From garciae@ucsub.colorado.edu Mon Jan 23 16:39:07 1995 Received: from ucsub.colorado.edu for garciae@ucsub.colorado.edu by www.ccl.net (8.6.9/930601.1506) id QAA04802; Mon, 23 Jan 1995 16:00:01 -0500 Received: (from garciae@localhost) by ucsub.colorado.edu (8.6.9/8.6.9/CNS-3.5) id NAA24769; Mon, 23 Jan 1995 13:59:25 -0700 Date: Mon, 23 Jan 1995 13:59:22 -0700 (MST) From: Garcia Edgardo To: chemistry@ccl.net Subject: CCL: OPLS parameters Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Can anybody send me (or point references) OPLS parameters for P,S and F,Cl,Br,I atoms ? Thanks. Edgardo Garcia Univ. of Colorado Boulder CO USA From janr@tiger.chem.uw.edu.pl Mon Jan 23 16:45:52 1995 Received: from tiger.chem.uw.edu.pl for janr@tiger.chem.uw.edu.pl by www.ccl.net (8.6.9/930601.1506) id PAA04342; Mon, 23 Jan 1995 15:44:24 -0500 Received: by tiger.chem.uw.edu.pl (AIX 3.2/UCB 5.64/4.03) id AA20795; Mon, 23 Jan 1995 21:44:19 +0100 Date: Mon, 23 Jan 1995 21:44:19 +0100 From: janr@tiger.chem.uw.edu.pl (Jan Radomski) Message-Id: <9501232044.AA20795@tiger.chem.uw.edu.pl> To: chemistry@ccl.net Subject: MDL user group or e-mail reflector Cc: janr@tiger.chem.uw.edu.pl ------ Dear Netters, is there anything like MDL's software user support group or some e-mail reflector serving the same purpose in Cyberspace? Jan Radomski From EDGECOMK@QUCDN.QUEENSU.CA Mon Jan 23 17:39:10 1995 Received: from QUCDN.QueensU.CA for EDGECOMK@QUCDN.QUEENSU.CA by www.ccl.net (8.6.9/930601.1506) id RAA05783; Mon, 23 Jan 1995 17:03:17 -0500 Message-Id: <199501232203.RAA05783@www.ccl.net> Received: from QUCDN.QUEENSU.CA by QUCDN.QueensU.CA (IBM VM SMTP V2R2) with BSMTP id 1149; Mon, 23 Jan 95 16:58:30 EST Received: from QUCDN.QUEENSU.CA (NJE origin EDGECOMK@QUCDN) by QUCDN.QUEENSU.CA (LMail V1.1d/1.7f) with RFC822 id 7596; Mon, 23 Jan 1995 16:58:29 -0500 Date: Mon, 23 Jan 1995 16:53 EST From: EDGECOMK@QUCDN.QueensU.CA To: chemistry@ccl.net Subject: Security breach? Could anyone on the list enlighten members about a story in todays New York Times about a massive security problem on practically all computers? The Computer Emergency Response Team is supposed to issue an advisory on the Internet today but I have yet to see the post. Will it lead to draconian methods that may curb network freedom?... as the article tends to imply. Ken Edgecombe From rsjuds@california.sandia.gov Mon Jan 23 21:39:07 1995 Received: from california.sandia.gov for rsjuds@california.sandia.gov by www.ccl.net (8.6.9/930601.1506) id UAA09572; Mon, 23 Jan 1995 20:44:37 -0500 Received: by california.sandia.gov (8.6.9/1.15) id RAA02148; Mon, 23 Jan 1995 17:44:35 -0800 From: rsjuds@california.sandia.gov (judson richard s) Message-Id: <199501240144.RAA02148@california.sandia.gov> Subject: rigid body optimization To: chemistry@ccl.net Date: Mon, 23 Jan 1995 17:44:35 -0800 (PST) Cc: rsjuds@california.sandia.gov (judson richard s) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 839 We are starting to look at rigid body gradient optimization of ligands inside protein cavities. I am looking for information on what the best methods and implementations are. For instance have people used truncated Newton methods vs. CG methods? Are implementations in one commercial package superior to those in another? Does converting to all internal coordinates work much better than using cartesians plus Lagrange multiplier constraints? Any information is useful. I will summarize if there is interest. ----------------------------------------------- | Richard Judson | | Center for Computational Engineering, MS 9214 | | Sandia National Laboratories | | Livermore, CA 94551-0969 | | (510)294-1438 | | (510)294-2234 (FAX) | | email: rsjuds@ca.sandia.gov | | | -----------------------------------------------