From wdi@ccl.net Tue Feb 28 07:42:56 1995 Received: from schiele for wdi@ccl.net by www.ccl.net (8.6.9/930601.1506) id HAA02130; Tue, 28 Feb 1995 07:02:00 -0500 Received: by schiele (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@ccl.net id MAA11111; Tue, 28 Feb 1995 12:58:20 +0100 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9502281258.ZM11109@schiele> Date: Tue, 28 Feb 1995 12:58:17 +0100 Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: GDCh-CIC Mailing List Due to some convoluted problems involving access permissions, nfs crossmounts and a non-standard mail system there were some problems from Saturday to Tuesday morning (local time) with the mailing list manager for the GDCh-CIC mailing list. Please check if you were a victim: The sympton is a compete loss of mail sent from some places when trying to subscribe to the GDCh-CIC mailing list via majordomo@eros.ccc.uni-erlangen.de with 'subscribe gdch-cic' in the mail body. So please if you did not receive any answer (i.e. a message indicating success or failure of subscription and the info file) subscribe again. We apologize for the inconvenience. Once more the info file for the mailing list: *************************************************************************** Diese Mailing-Liste mit dem Namen 'gdch-cic' befindet sich unter der Adresse 'eros.ccc.uni-erlangen.de' im Computer-Chemie-Centrum der Universitaet Erlangen-Nuernberg. Sie ist ein elektronisches Diskusssionsforum der Fachgruppe 'Chemie Information Computer' (CIC) in der GDCh, der Gesellschaft Deutscher Chemiker. Die Liste dient zur Zeit primaer als Koordinierungs- und Austauschstelle zur Projektierung des Informationsprojektes, das gemeinsam mit den Verbaenden der Physiker, Mathematiker und Informatiker konzipiert wird. Im Moment ist die Liste unmoderiert, d.h. jeder Bezieher der Liste kann ungefiltert Beitraege hineingeben, die sofort an alle Subskribenten weitergegeben werden. Auch die Mitgliedschaft ist frei. Es nicht nicht zwingend notwendig, Mitglied der GDCh oder der CIC zu sein, obwohl wir beides empfehlen. Wenn Sie Mitglied der CIC werden wollen und bereits GDCh Mitglied sind, schicken Sie bitte eine Nachricht an Prof. Gasteiger (gasteiger@eros.ccc.uni-erlangen.de), den Vorsitzenden der Gruppe. Wenn Sie Mitglied der GDCh werden wollen, koennen Sie dies leider noch nicht ueber elektronische Medien. Bitte fragen Sie einen Kollegen, der Mitglied ist und Sie einfuehrt. Da dies ein deutsches Forum ist, ist die bevorzugte Sprache der Meldungen Deutsch. Bitte senden Sie Ihre Meldungen an 'gdch-cic@eros.ccc.uni-erlangen.de', nicht an 'majordomo'. Die 'majordomo' Adresse dient auschliesslich zum An- und Abmelden und fuer weitere Serviceleistungen. Benutzen Sie bitte eine aussagekraeftige 'Subject:' Zeile im Mailheader. Vor diese Zeile wird automatisch 'GDCH-CIC:' eingefuegt, so dass Meldungen aus dieser Quelle leicht in den Mailboxen der Empfaenger zu finden sind. Zur Zeit werden alle Nachrichten archiviert. Wir koennen keine unbegrenzte Aufbewahrung garantierten, aber es stehen auf jeden Fall die Nachrichten der letzten Wochen fuer Spaeteinsteiger zum nachtraeglichen Studium zur Verfuegung. Um diese gespeicherten Nachrichten zu erhalten, schicken Sie bitte das Kommando 'get gdch-cic aktuell' im Hauptteil der Nachricht an 'majordomo@eros.ccc.uni-erlangen.de'. An die Liste angekoppelt ist ein Archiv aktueller Dokumente, die die CIC betreffen, zum Beispiel Protokolle und Reports. Eine Uebersicht erhalten Sie mit dem Kommando 'index gdch-cic' im Hauptteil einer Nachricht an 'majordomo@eros.ccc.uni-erlangen.de'. Auch diese Texte stehen Ihnen ueber ein 'get' Kommando zur Verfuegung. Wenn Sie techische Fragen haben oder Probleme mit dem Bezug der Liste oder der Verbreitung Ihrer Meldungen, wenden Sie sich bitte an 'gdch-cic-owner@eros.ccc.uni-erlangen.de'. Erlangen, 24.2.95 -- 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 From JeanLuc.Verschelde@rug.ac.be Wed Mar 1 11:07:41 1995 Received: from mserv.rug.ac.be for JeanLuc.Verschelde@rug.ac.be by www.ccl.net (8.6.10/930601.1506) id LAA20592; Wed, 1 Mar 1995 11:07:34 -0500 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA09336 (5.67b/IDA-1.5 for ); Wed, 1 Mar 1995 17:06:00 +0100 Received: by allserv.rug.ac.be (5.x/SMI-SVR4) id AA06160; Wed, 1 Mar 1995 17:07:09 +0100 Date: Wed, 1 Mar 1995 17:07:09 +0100 (MET) From: Jean-Luc Verschelde To: OHIO SUPER Subject: simplex Message-Id: Hi all, Where can I find minimization algorithms? The simplex procedure would be nice. Jean-Luc From chiremv!andromeda!jeffb@uunet.uu.net Sat Mar 4 11:22:47 1995 Received: from relay3.UU.NET for chiremv!andromeda!jeffb@uunet.uu.net by www.ccl.net (8.6.10/930601.1506) id LAA28049; Sat, 4 Mar 1995 11:22:45 -0500 Received: from uucp6.UU.NET by relay3.UU.NET with SMTP id QQyfpx15333; Sat, 4 Mar 1995 11:22:51 -0500 Received: from chiremv.UUCP by uucp6.UU.NET with UUCP/RMAIL ; Sat, 4 Mar 1995 11:22:45 -0500 Received: from andromeda by chiron.com (4.1/SMI-4.1) id AA13655; Thu, 2 Mar 95 18:41:55 PST Received: by andromeda (931110.SGI/911001.SGI) for chiremv!uunet!ccl.net!chemistry-request id AA18456; Thu, 2 Mar 95 18:22:22 -0800 Date: Thu, 2 Mar 95 18:22:22 -0800 From: chiremv!andromeda!jeffb@uunet.uu.net (Jeff Blaney) Message-Id: <9503030222.AA18456@andromeda> To: uunet!ccl.net!chemistry@uunet.uu.net Subject: Re: CCL:Conformational Analysis > I have been working with steroid conformational analysis in connection > with receptor modeling. I have generated several (typically 100) structures > (conformers) for each steroid using DGEOM program. Now I need to pick out > those conformers that are unique. (DGEOM generated structures might converge > to same minimum upon minimization). Any ideas on how to do that using > commercial modeling software or other shareware programs? The new release of DGEOM (DGEOM95) contains an option to filter conformations based on RMS deviation. There is also a new version of COMPARE (supplied with DGEOM95) which uses Jarvis-Patrick clustering to cluster conformers based on RMS deviation. You can use either approach to generate a unique set of conformers to an arbitrary cutoff based on RMS. Jeff Blaney Chiron From mmccar@postman.essex.ac.uk Tue Mar 7 10:02:51 1995 Received: from postman.essex.ac.uk for mmccar@postman.essex.ac.uk by www.ccl.net (8.6.10/930601.1506) id KAA08132; Tue, 7 Mar 1995 10:00:18 -0500 Received: from postman.essex.ac.uk by postman.essex.ac.uk with SMTP (PP) id <04660-0@postman.essex.ac.uk>; Tue, 7 Mar 1995 14:59:50 +0000 From: Mccarron M Date: Tue, 7 Mar 95 14:59:48 GMT Message-Id: <20272.9503071459@solb1.essex.ac.uk> To: chemistry Subject: CHARMM Has anybody out there got any explanatory free enrgy component analysis scripts e.g. BLOCK COMP .... thanks in advance mmccar@essex.ac.uk From chiremv!andromeda!jeffb@uunet.uu.net Wed Mar 8 07:48:56 1995 Received: from relay3.UU.NET for chiremv!andromeda!jeffb@uunet.uu.net by www.ccl.net (8.6.10/930601.1506) id HAA25107; Wed, 8 Mar 1995 07:48:55 -0500 Received: from uucp6.UU.NET by relay3.UU.NET with SMTP id QQyged24883; Wed, 8 Mar 1995 07:48:58 -0500 Received: from chiremv.UUCP by uucp6.UU.NET with UUCP/RMAIL ; Wed, 8 Mar 1995 07:48:54 -0500 Received: from andromeda by chiron.com (4.1/SMI-4.1) id AA27903; Wed, 8 Mar 95 01:22:26 PST Received: by andromeda (931110.SGI/911001.SGI) for chiremv!uunet!ccl.net!chemistry-request id AA29845; Wed, 8 Mar 95 01:02:41 -0800 Date: Wed, 8 Mar 95 01:02:41 -0800 From: chiremv!andromeda!jeffb@uunet.uu.net (Jeff Blaney) Message-Id: <9503080902.AA29845@andromeda> To: uunet!ccl.net!chemistry@uunet.uu.net Subject: Re: CCL:DGEOM95 Status: RO > Where I can get DGEOM95 the program? Thanks in advance. I sent the new DGEOM release, DGEOM95, to QCPE today (March 7). It should be available shortly. You can reach QCPE at qcpe@ucs.indiana.edu. Jeff Blaney Chiron 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 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.