From jkl@ccl.net Thu Mar 9 00:10:49 1995 Received: for jkl@ccl.net by www.ccl.net (8.6.10/930601.1506) id XAA08793; Wed, 8 Mar 1995 23:11:55 -0500 Date: Wed, 8 Mar 1995 23:11:55 -0500 From: Jan Labanowski Message-Id: <199503090411.XAA08793@www.ccl.net> To: chemistry@ccl.net Subject: CINF -- ACS Anaheim abstracts available in CCL archives Cc: jkl@ccl.net Dear Netters, Thanks to Guenter Grethe from MDL Information Systems for this contribution. The abstracts for the DIVISION OF CHEMICAL INFORMATION (CINF) program at the SPRING ACS Meeting in Anaheim, CA are available in CCL archives. They are saved as: /pub/chemistry/info/cinf-acs-anaheim You can get there via ftp (www.ccl.net), gopher (gopher.ccl.net 73) WWW: http://www.ccl.net/chemistry.html, or you can get them via e-mail by sending a message: select chemistry cd info get cinf-acs-anaheim quit to MAILSERV@ccl.net Jan Labanowski jkl@ccl.net P.S. By the way... Did you write your letter of support for CCL? If not, I am still waiting. You can find more info on this in the directory: /pub/chemistry/ccl-proposal in CCL archives. -- Dr. Jan K. Labanowski, Senior Research/Supercomputer Scientist/Specialist, etc. Ohio Supercomputer Center, 1224 Kinnear Rd, Columbus, OH 43212-1163 ph:(614)-292-9279, FAX:(614)-292-7168, E-mail: jkl@ccl.net JKL@OHSTPY.BITNET From lutz@ricx.royal-institution.ac.uk Thu Mar 9 05:11:00 1995 Received: from sun2.nsfnet-relay.ac.uk for lutz@ricx.royal-institution.ac.uk by www.ccl.net (8.6.10/930601.1506) id EAA11869; Thu, 9 Mar 1995 04:40:21 -0500 Via: uk.ac.royal-institution.ricx; Thu, 9 Mar 1995 09:38:07 +0000 From: Lutz Ackermann Date: Thu, 9 Mar 95 09:34:34 GMT Message-Id: <5408.9503090934@ricx.ri.ac.uk> To: chemistry@ccl.net Subject: searching: CADPAC manual on the Internet? Hi, I am looking for the latest CADPAC-manual in PostScript format. Does anybody know, if it's some place on the internet? Thanks a lot! L. Ackermann From lutz@ricx.royal-institution.ac.uk Thu Mar 9 05:18:18 1995 Received: from sun2.nsfnet-relay.ac.uk for lutz@ricx.royal-institution.ac.uk by www.ccl.net (8.6.10/930601.1506) id EAA11866; Thu, 9 Mar 1995 04:40:15 -0500 Via: uk.ac.royal-institution.ricx; Thu, 9 Mar 1995 09:33:51 +0000 From: Lutz Ackermann Date: Thu, 9 Mar 95 09:30:19 GMT Message-Id: <5374.9503090930@ricx.ri.ac.uk> To: chemistry@ccl.net Subject: 3D Banstr. code? Hello Netters, a collegue of mine asked me about a 3D bandstructure code (something cheap like a EHT-based method prefered). Do you know any, which is available? Please let me know, if you do. Thank you! L. Ackermann <^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^> < Dr. Lutz Ackermann > < Davy-Faraday Research Laboratory > < The Royal Institution of Great Britain > < 21 Albemarle Street > < London W1X 4BS > < UK > < > < e-mail: lutz@ricx.ri.ac.uk > vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv From yasuike@kokinw0.iw.chem.keio.ac.jp Thu Mar 9 09:11:11 1995 Received: from kokinw0.iw.chem.keio.ac.jp for yasuike@kokinw0.iw.chem.keio.ac.jp by www.ccl.net (8.6.10/930601.1506) id IAA13968; Thu, 9 Mar 1995 08:11:24 -0500 From: Received: by kokinw0.iw.chem.keio.ac.jp (4.2/Sony4.2MX) id AA10224; Thu, 9 Mar 95 22:10:58 JST Date: Thu, 9 Mar 95 22:10:58 JST Message-Id: <9503091311.AA10224@kokinw0.iw.chem.keio.ac.jp> To: chemistry@ccl.net Cc: yasuike@iw.chem.keio.ac.jp Subject: Include me,please X-Mailer: mnews [version 1.16PL4] 1993-09/22(Wed) Dear Coordinator of CCL, I'd like to participate in your Mailing list. I'm a student at Keio University in Japan. In Japan,Theoretical chemistry is not popular in private university. But Keio University (the oldest private university in Japan) has Theoretical Chemistry devision. I belong to it. I'm interested in your mailing-list. My English is poor. But I'd like to not only accept information but also serve information. Of cource,I must learn English more. I thank your great efforts to maintain CCL. Good-bye! TOMOKAZU YASUIKE : Theoretical Chemistry,Department of Chemistry Faculty of Science and Technology,KEIO University,Japan My e-mail address is yasuike@iw.chem.keio.ac.jp -------------------------- From liang@chvxmw.chem.ncsu.edu Thu Mar 9 10:11:06 1995 Received: from chvxmw for liang@chvxmw.chem.ncsu.edu by www.ccl.net (8.6.10/930601.1506) id JAA15796; Thu, 9 Mar 1995 09:46:40 -0500 From: Message-Id: <199503091446.JAA15796@www.ccl.net> Date: Thu, 9 Mar 1995 09:42:35 -0500 To: Chemistry@ccl.net Subject: Re: 3D band structure code X-VMS-To: SMTP%"Chemistry@ccl.net" Hello, you may get EHMACC from QCPE, which was originally developed in R. Hoffmann's group by M.-H. Whangbo. A new version for IBM-PC is under way. Let me know if you want more info on this special version. Weigen From grfamini@cbdcom.apgea.army.mil Thu Mar 9 13:11:10 1995 Received: from cbdcom.apgea.army.mil for grfamini@cbdcom.apgea.army.mil by www.ccl.net (8.6.10/930601.1506) id NAA21185; Thu, 9 Mar 1995 13:07:38 -0500 Date: Thu, 9 Mar 95 12:59:34 EST From: George R Famini To: chemistry@ccl.net Subject: COMP Program for Chicgao Message-ID: <9503091259.aa00319@cbdcom.apgea.army.mil> Enlcosed is the American Chemical Society's Division of Computers in Chemistry schedule of symposia for the national meeting in August (Chicago). If you are interested in presenting a paper, please contact the appropriate organizer prior to sending an abstract. Several symposia are already filled. The deadline for abstracts to be submitted is 19 April. I would like to shy away from emailed abstracts, so if you need abstract forms, please contact either ACS directly, or me. George Famini COMP Program Chair American Chemical Society Computers in Chemistry Division Chicago Meeting, August 20-24 1995 Program Chair: George R. Famini, U.S. Army Edgewood Research, Development and Engineering Center, SCBRD-ASI, Aberdeen Proving Ground, MD 21010; Voice: (410)671-2552; Fax: (410)671-2014; email: grfamini@apgea.army.mil. Four (4) copies of 150-word abstract (Original on ACS Abstract Form) are due by April 19, 1995 to respective session or symposium chairpersons. * Computation in NMR Spectroscopy: Data Collection, Processing, Analysis, Refinement and Display - Dr. Mary Baum, Associate Director, Corporate and Foundation Relations, Development Office, Princeton University, 5 New South Building, P.O. Box 39, Princeton, NJ 08544-0039; phone: (609)258-5955; fax: (609)258-1159; email: mbaum@princeton.edu; Dr. Robert von Tersch, U.S. Army Medical Research Institute of Chemical Defense, Commander, USAMRICD, ATTN:SGRD-UV-PB/CPT R. L. von Tersch, Aberdeen Proving Ground, MD 21010-5425; Voice: (410)671-1309; fax: (410)671-1960 ; email: vontersch_rl@mricd1.apgea.army.mil. * QSAR and Related Techniques - Dr. George R. Famini, U.S. Army Edgewood Research, Development and Engineering Center, SCBRD-ASI, Aberdeen Proving Ground, MD 21010; Voice: (410)671-2552; Fax: (410)671- 2014; email: grfamini@apgea.army.mil. * Force Fields: Metholodogy and Parameterization - Dr. Kenneth Lipkowitz, Indiana University Purdue University, Indianapolis 46202; voice: (317)274-6883; email: lipkowitz@chem.iupui.edu. * New Parameters in Semi-Empirical Molecular Orbital Theory - Dr. John McKelvey, Research Labs, Eastman- Kodak Co., Rochester, NY, 14650; Voice: (716)477-3335; email: mckelvey@Kodak.com. . * Homology Model Building and Docking - Dr. Jeffrey Blaney, Chiron Corporation, Emeryville, CA 94608; voice: (510)601-3313; fax: (510)601-3360; email: jeffb@chiremv.chiron.com. * Chemistry on the Infobahn - Dr. Thomas Pierce, Rohm and Haas Co. P.O. Box 219 Bristol, PA 19007; Voice: (215) 785-8989; FAX (215) 781-4204; email: thpierce@rohmhaas.com, Steven Bachrach, Department of Chemistry, Northern Illinois University, DeKalb, Il 60115;voice: (815)753-6863; Fax: (815)753-4802; email: smb@smb.chem.niu.edu, Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; voice: (44) 171 594 5774 or 594 5809. Fax: (44) 171 594 5804; email: rzepa@ic.ac.uk via Eudora 2.03, World-Wide-Web URL: http://www.ch.ic.ac.uk/rzepa.html. * The Collaboratory- Dr. Douglas Smith, Concurrent Technologies Corporation, 1450 Scalp Avenue, Johnstown, PA 15904; voice: (814) 269-2545; fax: (814)269-2798; email: theochem@ctc.com Bioinformatics - Dr. Michael Liebman, Amoco Technology Group, Amoco Research Center, Mail Code F- 2, Warrenville Rd and Mill St, Box 3011, Naperville, IL 60566; voice: (708) 961-7850; fax: (708) 420-3845; email: mliebman@amoco.com. Computational Evaluation of the Synthetic Feasibility of Compounds - Yvonne Martin,Computer Assisted Molecular Design Project, D-47E, AP9A-LL, Abbott Laboratories, One Abbott Park Road, Abbott Park, IL 60064,voice: (708) 937-5362fax: 708 937-2625; email: MARTIN%cmda@randb.abbott.com. * General Computational Chemistry - Poster and/or Oral Sessions - Dr. George R. Famini, US Army Edgewood Research, Development and Engineering Center, SCBRD- ASI, APG, MD 21010; voice: 410)671-2552; Fax: (410)671-2014; email: grfamini@apgea.army.mil. From grfamini@cbdcom.apgea.army.mil Thu Mar 9 16:11:17 1995 Received: from cbdcom.apgea.army.mil for grfamini@cbdcom.apgea.army.mil by www.ccl.net (8.6.10/930601.1506) id PAA24865; Thu, 9 Mar 1995 15:48:26 -0500 Date: Thu, 9 Mar 95 15:44:24 EST From: George R Famini To: chemistry@ccl.net Subject: Revised COMP listing Message-ID: <9503091544.aa25230@cbdcom.apgea.army.mil> It seems my inability to use email is matched only by my inability to proofread. Enclosed is the UPDATED COMP symposia schedule for Chicago. George Famini American Chemical Society Computers in Chemistry Division Chicago Meeting, August 20-24 1995 Program Chair: George R. Famini, U.S. Army Edgewood Research, Development and Engineering Center, SCBRD-ASI, Aberdeen Proving Ground, MD 21010; Voice: (410)671-2552; Fax: (410)671-2014; email: grfamini@apgea.army.mil. Four (4) copies of 150-word abstract (Original on ACS Abstract Form) are due by April 19, 1995 to respective session or symposium chairpersons. * Computation in NMR Spectroscopy: Data Collection, Processing, Analysis, Refinement and Display - Dr. Mary Baum, Associate Director, Corporate and Foundation Relations, Development Office, Princeton University, 5 New South Building, P.O. Box 39, Princeton, NJ 08544-0039; phone: (609)258-5955; fax: (609)258-1159; email: mbaum@princeton.edu; Dr. Robert von Tersch, U.S. Army Medical Research Institute of Chemical Defense, Commander, USAMRICD, ATTN:SGRD-UV-PB/CPT R. L. von Tersch, Aberdeen Proving Ground, MD 21010-5425; Voice: (410)671-1309; fax: (410)671-1960 ; email: vontersch_rl@mricd1.apgea.army.mil. * QSAR and Related Techniques - Dr. George R. Famini, U.S. Army Edgewood Research, Development and Engineering Center, SCBRD-ASI, Aberdeen Proving Ground, MD 21010; Voice: (410)671-2552; Fax: (410)671- 2014; email: grfamini@apgea.army.mil. * Force Fields: Metholodogy and Parameterization - Dr. Kenneth Lipkowitz, Indiana University Purdue University, Indianapolis 46202; voice: (317)274-6883; email: lipkowitz@chem.iupui.edu. * New Parameters in Semi-Empirical Molecular Orbital Theory - Dr. John McKelvey, Research Labs, Eastman- Kodak Co., Rochester, NY, 14650; Voice: (716)477-3335; email: mckelvey@Kodak.com. . * Homology Model Building and Docking - Dr. Jeffrey Blaney, Chiron Corporation, Emeryville, CA 94608; voice: (510)601-3313; fax: (510)601-3360; email: jeffb@chiremv.chiron.com. * Chemistry on the Infobahn - Dr. Thomas Pierce, Rohm and Haas Co. P.O. Box 219 Bristol, PA 19007; Voice: (215) 785-8989; FAX (215) 781-4204; email: thpierce@rohmhaas.com, Steven Bachrach, Department of Chemistry, Northern Illinois University, DeKalb, Il 60115;voice: (815)753-6863; Fax: (815)753-4802; email: smb@smb.chem.niu.edu, Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; voice: (44) 171 594 5774 or 594 5809. Fax: (44) 171 594 5804; email: rzepa@ic.ac.uk via Eudora 2.03, World-Wide-Web URL: http://www.ch.ic.ac.uk/rzepa.html. * The Collaboratory- Dr. Douglas Smith, Concurrent Technologies Corporation, 1450 Scalp Avenue, Johnstown, PA 15904; voice: (814) 269-2545; fax: (814)269-2798; email: theochem@ctc.com Bioinformatics - Dr. Michael Liebman, Amoco Technology Group, Amoco Research Center, Mail Code F- 2, Warrenville Rd and Mill St, Box 3011, Naperville, IL 60566; voice: (708) 961-7850; fax: (708) 420-3845; email: mliebman@amoco.com. Computational Evaluation of the Synthetic Feasibility of Compounds - Yvonne Martin,Computer Assisted Molecular Design Project, D-47E, AP9A-LL, Abbott Laboratories, One Abbott Park Road, Abbott Park, IL 60064,voice: (708) 937-5362fax: 708 937-2625; email: MARTIN%cmda@randb.abbott.com. * General Computational Chemistry - Poster and/or Oral Sessions - Dr. George R. Famini, US Army Edgewood Research, Development and Engineering Center, SCBRD- ASI, APG, MD 21010; voice: 410)671-2552; Fax: (410)671-2014; email: grfamini@apgea.army.mil. From chiremv!andromeda!jeffb@uunet.uu.net Thu Mar 9 01:49:19 1995 Received: from relay3.UU.NET for chiremv!andromeda!jeffb@uunet.uu.net by www.ccl.net (8.6.10/930601.1506) id BAA10167; Thu, 9 Mar 1995 01:49:17 -0500 Received: from uucp4.UU.NET by relay3.UU.NET with SMTP id QQyggx13089; Thu, 9 Mar 1995 01:49:17 -0500 Received: from chiremv.UUCP by uucp4.UU.NET with UUCP/RMAIL ; Thu, 9 Mar 1995 01:48:58 -0500 Received: from andromeda by chiron.com (4.1/SMI-4.1) id AA20500; Wed, 8 Mar 95 18:31:01 PST Received: by andromeda (931110.SGI/911001.SGI) for chiremv!uunet!ccl.net!chemistry-request id AA02619; Wed, 8 Mar 95 18:11:14 -0800 Date: Wed, 8 Mar 95 18:11:14 -0800 From: chiremv!andromeda!jeffb@uunet.uu.net (Jeff Blaney) Message-Id: <9503090211.AA02619@andromeda> To: chiremv!uunet!ccl.net!chemistry@uunet.uu.net Subject: DGEOM95 Status: R DGEOM95 is now available from QCPE (qcpe@ucs.indiana.edu). DGEOM95 is a distance geometry program for molecular model-building, receptor modeling, conformational analysis, and NMR solution structure determination. DGEOM95's authors are: Jeffrey M. Blaney, Gordon M. Crippen, Andrew Dearing, J. Scott Dixon, and David C. Spellmeyer. A copy of the release notes (relative to the 1990 release of DGEOM) is attached (2 pages). Jeff Blaney Chiron jeffb@chiron.com DGEOM95 Release Notes March, 1995 New Features ------------ * Partial metrization algorithm improves random sampling (Kuszewski, J., Nilges, M., Brunger, A. T. "Sampling and efficiency of metric matrix distance geometry: A novel partial metrization algorithm", J. Biomol. NMR 1992, 2, 33-56). * New lower bound error function improves convergence (Havel, T. F. "An Evaluation of Computational Strategies for Use in the Determination of Protein Structure from Distance Constraints Obtained by Nuclear Magnetic Resonance", Prog. Biophys. Molec. Biol. 1991, 56, 43-78). * Molecular dynamics has been added as a refinement method to supplement conjugate gradient minimization. * Random coordinate generation has been added as an alternative to embedding. * Automatic connectivity generation and double bond assignment (even for conjugated and aromatic systems). This eliminates the need for supplying CONECT records and/or editing them to specify double bonds for most organic structures, including peptides and nucleotides. Automatic connectivity generation will be performed if CONECT records are missing. * Free-format input for CONSTRAINT and ORIENT files. Backwards compatible with original version, except that now a '*' is required for molecule and residue wildcards to mark their fields (previously, a blank was used). Original DGEOM 1990 fixed-format constraint files will still work. * Free-format input of van der Waals and covalent bond radii (the latter are needed for connectivity generation). DGEOM95 preassigns van der Waals and covalent bond radii only for C, N, O, S, P, H, F, Cl, Br, I, and Du (dummy atom, radius = 0.). * 'REJECT' rejects similar structures. 'REJECT' rejects the current structure if its minimum RMSD to all previously accepted structures is less than REJECT's threshold (default = 1.0 angstrom). This ensures that all output structures will have a minimum pairwise RMSD > REJECT's threshold. * New rules to detect conjugated groups (e.g. butadiene, aniline, or phenol-like systems which have restricted rotation about the single bond) and constrain them to be nearly coplanar (+/- 40 degrees); disulfide and hydrazine torsions are constrained to be +/- 90 degrees. Recognizes thioamides and thioesters. * Read atom names beginning with integers and residue numbers with optional chain identifiers from PDB format files. * New 'FLOAT' command available in CONSTRAINTS file for specifying chiral centers that can racemize or 'float', and amide or ester carbonyl carbons that should randomly sample cis and trans. * Warns about newly assigned, weaker constraints that overwrite previously assigned, stronger constraints. * Molecule-molecule, molecule-residue, or residue-residue distance constraints are now all available. * Wildcard selection of all atoms in a molecule with GROUP, MATCH, or PLANAR constraints is now possible. * 'PDBOUT' can now specify the starting output structure number by appending a ':' to the root filename, followed by the desired number. * 'PREFIX' toggles writing the structure number before or after the fileroot when writing out PDB files. * 'SPLIT' writes each molecule to a separate file with filename <#>.pdb. Works as expected with 'PREFIX:'. * Modified all boolean commands to take TRUE/FALSE option; entering a command with no value implies TRUE. * Comment lines can be included in DGEOM95 command files; they begin with '!' or '#' and are echoed to the summary output file. * Chiral constraints can be reinitialized, clearing all previously set chiral constraints (automatic and user-defined) with the new command: CHIRAL INIT. * User-defined random number generator initialization. 'NSEED1' and 'NSEED2' set the 1st and 2nd seeds for the random number generator, and 'NRANDOM' initializes the random number sequence to the NRANDOMth element. * 'ORIENT' command warns if less than 4 atoms are entered for matching. * Program COMPARE includes Jarvis-Patrick clustering (Jarvis, R. A., Patrick, E. A. "Clustering Using a Similarity Measure Based on Shared Near Neighbors", IEEE Trans. Comp. 1973, C22, 1025-1034) and is now completely self-contained. COMPARE reads a series of PDB files, along with (optional) free-format input containing the molecule number, residue number, and names of atoms to match. It calculates all pairwise RMS least-squares fit errors between the structures, generates a distance matrix from the RMS matrix, extracts the set of nearest neighbors from the distance matrix, and clusters the nearest neighbor list using the Jarvis-Patrick algorithm to group the structures into 'families'. Bug Fixes --------- * Fixed bug to allow read/write of 4-character residue names. * Fixed bug which forced the end of a constraints group after reading a comment card or blank line. * Fixed bug in the message warning of more than 4 bonds to a given atom. * Fixed bug involving read/write of the metric matrix to a scratch file. * Fixed bug where automatic chiral constraint generation could overflow the format statement in an internally generated chiral command. * Chiral quartets within RIGID groups are now only set if the abs(chiral volume) < threshold, where threshold ~ max volume for a chiral carbon. Previously, very large volumes between atoms far apart in a structure could lead to severe convergence problems. * Fixed bug in eigenvalue routine for two-dimensional structures. * Fixed bug in torsion picking routine where upper and lower bounds are nearly equal. * Fixed bug in routine to find aromatic rings. * Fixed sulfate/phosphate bug where planar constraint is mistakenly assigned to these groups.