From SAVARY@sc2a.unige.ch Wed May 4 03:22:27 1994 Received: from chx400.switch.ch for SAVARY@sc2a.unige.ch by www.ccl.net (8.6.4/930601.1506) id CAA29162; Wed, 4 May 1994 02:54:34 -0400 From: X400-Received: by mta chx400.switch.ch in /PRMD=switch/ADMD=arcom/C=CH/; Relayed; Wed, 4 May 1994 08:53:53 +0200 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Wed, 4 May 1994 08:53:25 +0200 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Wed, 4 May 1994 10:52:08 +0200 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Wed, 4 May 1994 10:52:03 +0200 X400-Received: by /PRMD=SWITCH/ADMD=ARCOM/C=CH/; Relayed; Wed, 4 May 1994 10:52:03 +0200 Date: Wed, 4 May 1994 10:52:03 +0200 X400-Originator: SAVARY@sc2a.unige.ch X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=SWITCH/ADMD=ARCOM/C=CH/;<01HBXOKESLTE000069@sc2a.unige.c] X400-Content-Type: P2-1984 (2) Content-Identifier: csd->pdb avai... Alternate-Recipient: Allowed Message-ID: <01HBXOKESLTE000069@sc2a.unige.ch> To: CHEMISTRY@ccl.net Subject: csd->pdb availaible X-Envelope-to: CHEMISTRY@ccl.net X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear Netters, The latest version of the CSD->PDB program is now available on www.ccl.net archives. The files can be retrieved in the following way: via email: send a message select chemistry cd software/csd_to_pdb get README get csdpdb.c quit to MAILSERV@ccl.net and files will be sent automatically your mailbox. via gopher/WWW: gopher www.ccl.net 73 software csd_to_pdb README csdpdb.c or URL: gopher://www.ccl.net:73/11/software/csd_to_pdb via anonymous ftp: ftp www.ccl.net Name: anonymous Password: your_email_address ftp> cd /pub/chemistry/software/csd_to_pdb ftp> get csdpdb.c ftp> README ftp> quit Francois Savary -------------------------------------------------------------- Francois Savary Department of Physical Chemistry University of Geneva 30, quai Ernest-Ansermet CH-1211 Geneva 4 phone : +4122 702 65 32 fax : +4122 702 65 18 e-mail : savary@sc2a.unige.ch -------------------------------------------------------------- From longshot@chem.duke.edu Wed May 4 04:22:27 1994 Received: from duke.cs.duke.edu for longshot@chem.duke.edu by www.ccl.net (8.6.4/930601.1506) id DAA29342; Wed, 4 May 1994 03:36:53 -0400 Received: from london.chem.duke.edu by duke.cs.duke.edu (5.65/3.9G/4.1.3) id AA01228; Wed, 4 May 94 03:36:53 -0400 Received: from canada.chem.duke.edu by london.chem.duke.edu (5.64/1.19LP/4.1.1) id AA11645; Wed, 4 May 94 03:36:52 -0400 Received: by canada.chem.duke.edu (5.64/2.12L/4.1) id AA06658; Wed, 4 May 94 03:36:50 -0400 Date: Wed, 4 May 94 03:36:50 -0400 From: longshot@chem.duke.edu (Brad Isbister) Message-Id: <9405040736.AA06658@canada.chem.duke.edu> To: chemistry@ccl.net Subject: Re: Amber 4.0 help Thanks to all of you who replied! The fact that so many of you recognized my error suggests that everyone else does this at least once. ;) A summary of my question: When I tried to use AMBER 4.0 to minimize a solute in a periodic box of water, the program hadd a fatal error and gave the message: COORDINATE RESETTING CANNOT BE ACCOMPLISHED, DEVIATION IS TOO LARGE NITER, NIT, LL, I AND J ARE : 0 2 1 1 2 A summary of the answer: Don't use SHAKE constraints before the initial minimization. The constraints on bond lengths by the SHAKE algorithm can conflict with the minimization forces >from strong VdW repulsion (too close). Once SHAKE is turned off, everything should work out fine. To use SHAKE in MD, turn it on AFTER the initial minimization. Once the extreme VdW contacts have been eliminated, SHAKE constraints will not cause any conflicts. Further questions about AMBER can be answered through the AMBER mailing list: >From ross@cgl.ucsf.edu > >There is a mail reflector for users and people interested in >Amber. A major part of the traffic is the bugfix announcements. > >Mail sent to the reflector is automatically sent to all who have >joined the list. > >You can address all members by sending mail to either of the >following addresses: > > amber@cgl.ucsf.edu > amber@ucsfcgl.bitnet > >and mail to either > > amber-request@cgl.ucsf.edu > amber-request@ucsfcgl.bitnet > >for administrative requests. ---------------------------------Clip N Save------------------------------------ Brad Isbister Duke University longshot@chem.duke.edu Department of Chemistry Computational/Biophysical chemistry E.J. Toone group From MOSES@cmchem.chem.cmu.edu Wed May 4 10:23:54 1994 Received: from cmchem.chem.cmu.edu for MOSES@cmchem.chem.cmu.edu by www.ccl.net (8.6.4/930601.1506) id KAA03815; Wed, 4 May 1994 10:04:42 -0400 Date: Wed, 4 May 1994 10:03:24 -0400 (EDT) From: "D.J. Moses, 412-279-6700, 412-279-2118 (Fax)" To: chemistry@ccl.net CC: MOSES@cmchem.chem.cmu.edu Message-Id: <940504100324.21e00341@cmchem.chem.cmu.edu> Subject: Joint Gaussian-Spartan Workshop ----------------------------------------------------------------------------- GAUSSIAN, INC. Carnegie Office Park Building 6 Pittsburgh, PA 15106 USA Phone - 412-279-6700 Fax - 412-279-2118 EMail - info@gaussian.com Digital Sponsors Two Joint Gaussian-Spartan Workshops Digital Equipment Corporation is sponsoring two introductory workshops covering the Spartan and Gaussian programs. The workshops will be conducted jointly by Wavefunction, Inc. and Gaussian, Inc. Details about the workshops are summarized below: Dates: Session 1 June 27th and 28th (Monday and Tuesday) Session 2 June 29th and 30th (Wednesday and Thursday) The two sessions cover identical content. Location: Digital US Customer Training Center Maynard, Massachusetts Course Fee: $250.00 per student Instructors: Dr. Lonnie Burke, Wavefunction, Inc. Dr. Douglas Fox, Gaussian, Inc. Dr. Michael Frisch, Gaussian, Inc. Dr. Warren Hehre, Wavefunction, Inc. Computing Resources: DEC Alpha AXP workstation running OSF/1 (one per student) The workshops will cover a variety of topics, including the following: * Overview of Electronic Structure Methods, including their theoretical background. Methods covered will include semi-empirical, Hartree-Fock, and Density Functional Theory models as well as G1 and G2 theory. * Gaussian and Spartan calculation types and prediction capabilities, including Spartan's extensive visualization features. * Practical advice for approaching chemical problems with electronic structure theory and estimating resource requirements for various types of calculations. The workshops will provide students with a large amount of hands-on experience using both programs. The course fee covers all instruction, laboratory sessions and course materials (including Gaussian's textbook Exploring Chemistry with Electronic Structure Methods). Each workshop is limited to 15 students. To register or to obtain additional information, contact the Workshop Coordinator at Gaussian, Inc.: Voice: 412-279-6700 Fax: 412-279-2118 Mail: Gaussian, Inc. Carnegie Office Park, Bldg. 6 Pittsburgh, PA 15106 Information may also be obtained via electronic mail to info@gaussian.com. However, email may NOT be used for registration. ----------------------------------------------------------------------------- This notice is sent without warranty of any kind, expressed or implied. Gaussian is a trademark of Gaussian, Inc. All other trademarks are the property of their respective holders. Specifications and availability subject to change without notice. From eisenmen@rz.charite.hu-berlin.de Wed May 4 12:22:35 1994 Received: from comcom.rz.charite.hu-berlin.de for eisenmen@rz.charite.hu-berlin.de by www.ccl.net (8.6.4/930601.1506) id LAA09894; Wed, 4 May 1994 11:52:03 -0400 Message-Id: <199405041552.LAA09894@www.ccl.net> Received: by comcom.rz.charite.hu-berlin.de (16.6/15.6) id AA21379; Wed, 4 May 94 17:29:54 +0200 From: Frank Eisenmenger Subject: minimizer To: chemistry@ccl.net Date: Wed, 4 May 94 17:29:53 MESZ Mailer: Elm [revision: 66.25] Hi everyone, could you help me with an address for anonymous ftp-server(s) providing good (=usable for a non-mathematician), public domain UNCONSTRAINED LOCAL OPTIMIZER using analytical first derivatives ? Thanks in advance, Frank Eisenmenger +------------------------------------------------------------------------+ | Institute of Biochemistry | | Medical Faculty of the Humboldt University (Charite) | | | | Hessische Str. 3-4 | | 10115 Berlin, Germany | | | | Phone: +49-30-28468-612 or -239 FAX: +49-30-28468-600 | | E-mail: eisenmen@comcom.rz.charite.hu-berlin.de | +------------------------------------------------------------------------+ From georgia@Huckel.chem.uga.edu Wed May 4 13:22:35 1994 Received: from Huckel.chem.uga.edu for georgia@Huckel.chem.uga.edu by www.ccl.net (8.6.4/930601.1506) id MAA11915; Wed, 4 May 1994 12:28:24 -0400 Received: by Huckel.chem.uga.edu (920110.SGI/901025.SGI.UNSUPPORTED.PROTOTYPE) (for chemistry@ccl.net) id AA23346; Wed, 4 May 94 12:25:51 -0400 From: georgia@Huckel.chem.uga.edu (Georgia McGaughey) Message-Id: <9405041625.AA23346@Huckel.chem.uga.edu> Subject: NAD+ To: chemistry@ccl.net Date: Wed, 4 May 94 12:25:50 EDT X-Mailer: ELM [version 2.3 PL11] A fellow "lab mate" has the following question: I am using the AMBER force field to examine various properties of NAD+ bound to a protein as a cofactor. However, there are missing parameters - particularly for the nicotinamide portion of the structure. Does anyone have these parameters? Please respond directly to "me": georgia@huckel.chem.uga.edu Thanks in advance, GA -- "Classical music is not just for the rich. The poor also like caviar, only no one offers it." Arthur Moreira Lima Computational Center for Molecular | TEL: (706) 542-4205 Structure and Design | FAX: (706) 542-9454 Department of Chemistry | E-MAIL: University of Georgia, Athens, GA 30602 | georgia@Huckel.chem.uga.edu From PHYSPLMP@MIZZOU1.missouri.edu Wed May 4 17:23:09 1994 Received: from MIZZOU1.missouri.edu for PHYSPLMP@MIZZOU1.missouri.edu by www.ccl.net (8.6.4/930601.1506) id RAA27778; Wed, 4 May 1994 17:18:32 -0400 From: Message-Id: <199405042118.RAA27778@www.ccl.net> Received: from MIZZOU1 by MIZZOU1.missouri.edu (IBM VM SMTP V2R2) with BSMTP id 3175; Wed, 04 May 94 16:16:22 CDT Received: by MIZZOU1 (Mailer R2.10 ptf000) id 0206; Wed, 04 May 94 14:58:40 CDT Date: Wed, 04 May 94 14:55:52 CDT To: jmiller@SANDCASTLE.COSC.BROCKU.CA cc: CHEMISTRY@ccl.net Subject: Re: CCL:Molecular Modeling Programs In-Reply-To: jmiller@SANDCASTLE.COSC.BROCKU.CA -- Thu, 28 Apr 94 09:38:24 -0400 I would be interested in the responses you received. I have some students in m y computational chemistry class who are interested in trying some systems which include metals and I have no experience with these systems. Thanks in advance- Pat Plummer Dept of Chem. University of Missouri-Columbia From kallick@nemesis.medc.umn.edu Wed May 4 19:22:40 1994 Received: from nemesis.medc.umn.edu for kallick@nemesis.medc.umn.edu by www.ccl.net (8.6.4/930601.1506) id SAA29693; Wed, 4 May 1994 18:53:23 -0400 From: Received: by nemesis.medc.umn.edu (920330.SGI/890607.SGI) (for chemistry@ccl.net) id AA18470; Tue, 4 May 71 17:42:44 -0500 Date: Tue, 4 May 71 17:42:44 -0500 Message-Id: <7105042242.AA18470@nemesis.medc.umn.edu> To: chemistry@ccl.net Subject: silicon graphics monitor Hello CCLers, My Silicon Graphics monitor fails the 'convergence' test; i.e., its fuzzy. Using degauss doesn't help, and I don't have a maintenance contract nor technical support (YET). Does anyone know how to fix this? Thanks Deborah Kallick Department of Medicinal Chemistry University of Minnesota Minneapolis, MN 55455 kallick@nemesis.medc.umn.edu phone 612 626 1962 fax 612 626 4429 From kallick@gwinn.medc.umn.edu Wed May 4 19:24:37 1994 Received: from gwinn.medc.umn.edu for kallick@gwinn.medc.umn.edu by www.ccl.net (8.6.4/930601.1506) id SAA29704; Wed, 4 May 1994 18:55:41 -0400 From: Received: by gwinn.medc.umn.edu (911016.SGI/890607.SGI) (for chemistry@ccl.net) id AA10095; Wed, 4 May 94 17:54:14 -0500 Date: Wed, 4 May 94 17:54:14 -0500 Message-Id: <9405042254.AA10095@gwinn.medc.umn.edu> To: chemistry@ccl.net Subject: silicon graphics monitor Hello CCLers, Sorry if this is a duplicate message. The first one has the wrong date stamp. My Silicon Graphics monitor fails the 'convergence' test; i.e., its fuzzy. Using degauss doesn't help, and I don't have a maintenance contract nor technical support (YET). Does anyone know how to fix this? Thanks Deborah Kallick Medicinal Chemistry University of Minnesota 308 Harvard St. S.E. Minneapolis, MN 55455 email: kallick@gwinn.medc.umn.edu From chiremv!chiremv.chiron.com!davids@uunet.UU.NET Wed May 4 21:22:39 1994 Received: from relay1.UU.NET for chiremv!chiremv.chiron.com!davids@uunet.UU.NET by www.ccl.net (8.6.4/930601.1506) id UAA00759; Wed, 4 May 1994 20:56:06 -0400 Received: from uucp3.uu.net by relay1.UU.NET with SMTP (5.61/UUNET-internet-primary) id AAwomt11941; Wed, 4 May 94 20:56:04 -0400 Received: from chiremv.UUCP by uucp3.uu.net with UUCP/RMAIL ; Wed, 4 May 1994 20:56:05 -0400 Received: by chiron.com (4.1/SMI-4.1) id AA25354; Wed, 4 May 94 17:17:51 PDT Date: Wed, 4 May 94 17:17:51 PDT From: davids@chiremv.chiron.com (David C. Spellmeyer) Message-Id: <9405050017.AA25354@chiron.com> To: chemistry@ccl.net Subject: Symposium Announcement and Call for Papers SYMPOSIUM ANNOUNCEMENT AND CALL FOR PAPERS Applications of Computers in Molecular Diversity and Combinatorial Chemistry to be held at the National American Chemical Society Meeting Anaheim, CA April 2-7, 1995 Sponsored by the Division of Computers in Chemistry This symposium will cover all aspects of computational chemistry applied to the field of molecular diversity and combinatorial chemistry. This includes design and analysis of combinatorial libraries, design of conformationally constrained libraries, computational measures of diversity, and others. New algorithms and applications of existing algorithms are welcome. This symposium is being held in conjunction with the Combinatorial Chemistry symposium sponsored by the Organic Division. The due date for 150 word abstracts is October 15, 1994. For planning purposes, however, please let me know if you plan to submit an abstract no later than July 15, 1994. David C. Spellmeyer Chiron Corporation 4560 Horton Street Emeryville, CA 94608 Voice: (510)-601-3313 Fax: (510)-601-3360 email: davids@chiron.com