From toukie@zui.unizh.ch Wed Mar 13 03:16:05 1996 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.7.1/950822.1) id CAA08879; Wed, 13 Mar 1996 02:56:50 -0500 (EST) From: Received: from rzurs3.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA14817; Wed, 13 Mar 96 08:56:40 +0100 Received: by rzurs3.unizh.ch (AIX 3.2/UCB 5.64/4.03) id AA49292; Wed, 13 Mar 1996 08:56:40 +0100 Message-Id: <9603130756.AA49292@rzurs3.unizh.ch> Subject: Seeking info re MD of CHCl3 &/or PL To: chemistry@www.ccl.net Date: Wed, 13 Mar 1996 08:56:39 +0100 (MET) X-Mailer: ELM [version 2.4 PL24 PGP2] Content-Type: text Dear Colleagues; I should like to know if anybody has references (old or new) to molecular dynamics simulations of the molecule chloroform and/or of a _single_ phospho- lipid molecule (any PL; the precise identity isn't so important) enclosed in a water box (or box of any other solvent). If so, would you be kind enough to share these references with me? Thanks in advance to all responders. Sincerely, S. Shapiro Zuerich toukie@zui.unizh.ch From r2d2@newworld.bridge.net Wed Mar 13 04:16:05 1996 Received: from relay7.UU.NET for r2d2@newworld.bridge.net by www.ccl.net (8.7.1/950822.1) id DAA09085; Wed, 13 Mar 1996 03:39:04 -0500 (EST) Received: from newworld.bridge.net by relay7.UU.NET with ESMTP id QQagvi07818; Wed, 13 Mar 1996 03:39:02 -0500 (EST) Received: (from r2d2@localhost) by newworld.bridge.net (8.7.4/8.7.3) id DAA15828; Wed, 13 Mar 1996 03:37:22 -0500 (EST) Date: Wed, 13 Mar 1996 03:37:22 -0500 (EST) From: Venkat Sivaraman To: CHEMISTRY@www.ccl.net Subject: DNA bending Angles Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL readers. I would like some input in to the computational methods that are used to calculate the bending of DNA molecules. I would also appreciate any pointers to any packages , algorithems that may be available to do some straight forward computations of the DNA bending angles. Thanks in advance. Venkat From czernek@bilbo.chemi.muni.cz Wed Mar 13 08:16:07 1996 Received: from aragorn.ics.muni.cz for czernek@bilbo.chemi.muni.cz by www.ccl.net (8.7.1/950822.1) id HAA13037; Wed, 13 Mar 1996 07:35:16 -0500 (EST) Received: from bilbo.chemi.muni.cz by aragorn.ics.muni.cz with SMTP id AA20004 (5.67a8/IDA-1.4.4 for ); Wed, 13 Mar 1996 13:35:01 +0100 Received: (from czernek@localhost) by bilbo.chemi.muni.cz (8.7.1/8.7.1) id NAA17777; Wed, 13 Mar 1996 13:35:08 +0100 (MET) From: Jiri Czernek Message-Id: <199603131235.NAA17777@bilbo.chemi.muni.cz> Subject: atomic calculations with QZ of Thakkar & al. To: chemistry@www.ccl.net Date: Wed, 13 Mar 1996 13:35:08 +0100 (MET) Cc: czernek@bilbo.chemi.muni.cz (Jiri Czernek) X-Mailer: ELM [version 2.4 PL24] Content-Type: text Dear Netters , For H, C, N, O and F I wanted to use Quadruple Zeta basis set described in A.J. Thakkar, T. Koga, M. Saito, and R.E. Hoffmeyer "Double and Quadruple Zeta Contracted Gaussian Basis Sets for Hydrogen through Neon", Int. J. of Quantum Chemistry: Quantum Chemistry Symposium _27_, 343-354 (1993) . I typed in the exponents and contraction coefficients from tables in the article. I'm aware of, and afraid of, possible typos in my input file and/or in the publication. To test against them I ran atomic calculations using GAUSSIAN94 . ( # ROHF/Gen Geom=Coord SCF=InCore SCF=Conver=8, and tried both Guess=Huckel andCore, and also SCF=VeryTightLinEq, but the results were the same in all cases) For carbon 3P and nitrogen 4S I obtained THE SAME values like given in the article (-37.688422 and -54.400602 respectively). For fluorine 2P I obtained HIGHER energy (-99.407251 instead of -99.408490) so I thought it was due to some error in the input of basis set. BUT for oxygen 3P I obtained LOWER energy (-74.810794 vs -74.808842), even LOWER THAN HF-LIMIT (which is reported to be -74.809398) ! I'm a novice in the field of ab initio calculations so most probably I made some trivial mistake. Please help me! Cordially , George From owner-chemistry@ccl.net Wed Mar 13 10:16:07 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id JAA15431; Wed, 13 Mar 1996 09:58:05 -0500 (EST) Received: from phem3 for R29CLOSE@ETSU.EAST-TENN-ST.EDU by bedrock.ccl.net (8.7.1/950822.1) id JAA00133; Wed, 13 Mar 1996 09:58:05 -0500 (EST) From: Received: from ETSU.EAST-TENN-ST.EDU (MAILER@ETSU) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01I2AAZRMTTC8WXXH2@phem3.acs.ohio-state.edu>; Wed, 13 Mar 1996 09:58:01 EST Received: from ETSU.EAST-TENN-ST.EDU (NJE origin R29CLOSE@ETSU) by ETSU.EAST-TENN-ST.EDU (LMail V1.2a/1.8a) with BSMTP id 6086; Wed, 13 Mar 1996 09:56:45 -0500 Date: Wed, 13 Mar 1996 09:35:34 -0500 (EST) Subject: Crystal Packing To: chemistry@ccl.net Message-id: <01I2AAZRMTTE8WXXH2@phem3.acs.ohio-state.edu> Organization: East Tennessee State University X-Envelope-to: chemistry@ccl.net Content-transfer-encoding: 7BIT I have uploaded the source code for my crystal packing program with CCL. The program can be found at: ftp://ccl/ccl.net/pub/chemistry/software/SOURCES/FORTRAN/drawcrys In this directory there are seven files. The FORTRAN code for my program is called DRAWCRYS.FOR. A complied version of this program is just DRAWCRYS. This was complied by MS FORTRAN Powerstation. These programs are based on modifications of the old Oak Ridge crystallo- graphic program ORFEE. I've included the ORFEE source code and the complete instruction manual. There is also a complete OFREE input file based on cytidylic acid. This is called CYTIDYL.ORF. To make sure ORFEE is working, I've included a test output file called CYTIDYL.OUT. There is a brief description of the program in a README file. This is only a first attempt at solving this problem. Please let me know about any problems that develop in using this program. I will try to incorporate suggested improvements in a revision. Thanks for Jan Labanowski, our fearless List Administrator, for help getting this far, and for calming my nerves this morning after I was flammed. Regards, Dave Close. From owner-chemistry@ccl.net Wed Mar 13 14:16:09 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id NAA19708; Wed, 13 Mar 1996 13:52:00 -0500 (EST) Received: from bioc1.msi.com for rgiaimo@iris1.msi.com by bedrock.ccl.net (8.7.1/950822.1) id NAA04920; Wed, 13 Mar 1996 13:51:46 -0500 (EST) Received: from iris1.biosym.com by bioc1.msi.com (5.64/0.0) id AA00712; Wed, 13 Mar 96 10:56:22 -0800 Received: by iris1.msi.com (940816.SGI.8.6.9/930416.SGI) for CHEMISTRY@ccl.net id KAA11722; Wed, 13 Mar 1996 10:51:14 -0800 Date: Wed, 13 Mar 1996 10:51:14 -0800 From: rgiaimo@msi.com (Rick Giaimo ) Message-Id: <199603131851.KAA11722@iris1.msi.com> To: CHEMISTRY@ccl.net Subject: Re: CCL:Crystal Packing Dave -- Cerius2 (from MSI) can do everything that you describe here, including selection across unit cell boundaries with distance criteria. Adding atoms to a crystal can be done with XYZ, ABC, or UVd coordinates. Symmetric and periodic copies are constructed according to the spacegroup and unit cell paramaters specified for the crystal. Multiple cells can be visualized. Selection can find all of the atoms within the radius specified, across cell boundaries, if necessary. -- Rick. > Reply to Hiroshi Ogura: > I am amazed at how many people have written this group in the past > few years about generating crystal structures. Each time someone > responds with a hint about using a commercial package like Sybil or > HyperChem. > > I don't have access to either of these programs, so have been > working on this problems over the past few weeks. My solution was > to take the old Oak Ridge packages like ORFEE and ORTEP and modify > them to generate any number of unit cells. The appeal of using these > packages is that one doesn't have to reinvent any codeing for mole- > cular transformations. > So far I have a simple FORTRAN program that takes the xyz coordinates > from a crystal paper and generates the unit cell. For the old timers > you know that the notation for the first molecule is 55501. If there > are 4 molecules in the unit cell, these are just specified as 55502, > 55503 and 55504. One can then move these up an axis (say b) by > just specifying 565xx, etc. Real simple. > My program does this and then outputs a file to BABEL. I then > use BABEL to generate an ALCHEMY file. I use ALCHEMY to view the > molecule. It works. But I can't streamline it because I don't > have the BABEL source code. If I did, I could compile the whole. > routine. So there are several steps involved, but it seems to work. > I am sure that the people with commercial packages think this is > all a waste of time. I realize that commercial packages can generate > a unit cell from the xyz coordiates, but can they really generate > several unit cells? This is really what's important if your looking > for nearest neighbors. I looked at several packages that could not > determine, for example, all the atoms 4-5 Angstroms from a particular > part of any molecule. Since ORFEE is so good at doing this, I decided > to modify the program rather that buy something that may or may not > really work. > If this is of interest to anyone, write me and I will send you the > FORTRAN code. > Regards, Dave Close. > > Richard Giaimo Molecular Simulations rgiaimo@msi.com From markm@portal.vpharm.com Wed Mar 13 15:16:09 1996 Received: from portal.vpharm.com for markm@portal.vpharm.com by www.ccl.net (8.7.1/950822.1) id PAA21160; Wed, 13 Mar 1996 15:10:39 -0500 (EST) Received: by portal.vpharm.com (AIX 3.2/UCB 5.64/4.03) id AA20583; Wed, 13 Mar 1996 14:51:11 -0500 From: markm@portal.vpharm.com (Mark Murcko) Message-Id: <9603131951.AA20583@portal.vpharm.com> Subject: Final call -- ACS Orlando de novo design session To: chemistry@www.ccl.net Date: Wed, 13 Mar 1996 14:51:10 -0500 (EST) X-Mailer: ELM [version 2.4 PL21] Content-Type: text ===== FINAL CALL FOR PAPERS ===== Session on De Novo Ligand Design American Chemical Society Annual Meeting Orlando, Florida, August, 1996 I am still looking for presentations (both oral and posters) on the subject of the design and use of ligand design software. Previously unpublished methods, as well as novel applications of de novo methods, are especially welcome. If you would like to present a talk or a poster at this session, please *** send an abstract *** by Monday, March 18th *** to the address shown below. Thanks. Dr. Mark Murcko Senior Scientist Vertex Pharmaceuticals markm@vpharm.com From P8946019@vmsuser.acsu.unsw.EDU.AU Wed Mar 13 20:16:21 1996 Received: from vmsuser.acsu.unsw.EDU.AU for P8946019@vmsuser.acsu.unsw.EDU.AU by www.ccl.net (8.7.1/950822.1) id UAA24305; Wed, 13 Mar 1996 20:06:04 -0500 (EST) From: Received: from vmsuser.acsu.unsw.EDU.AU by vmsuser.acsu.unsw.EDU.AU (PMDF V4.3-13 #6323) id <01I2BTNV2RGG8WXF0E@vmsuser.acsu.unsw.EDU.AU>; Thu, 14 Mar 1996 12:06:17 +1000 Date: Thu, 14 Mar 1996 12:06:17 +1000 Subject: STO integration code To: chemistry@www.ccl.net Message-id: <01I2BTNV43OI8WXF0E@vmsuser.acsu.unsw.EDU.AU> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Does anybody know where I might be able to find code (source or compiled) for doing integrals over Slater Type Orbitals? Hugh From irikura@ENH.NIST.GOV Wed Mar 13 21:16:22 1996 Received: from ENH.NIST.GOV for irikura@ENH.NIST.GOV by www.ccl.net (8.7.1/950822.1) id UAA24492; Wed, 13 Mar 1996 20:30:51 -0500 (EST) Received: from chlorine (chlorine.nist.gov) by ENH.NIST.GOV (PMDF V5.0-5 #10952) id <01I2AX127XS000NLNO@ENH.NIST.GOV> for chemistry@www.ccl.net; Wed, 13 Mar 1996 20:29:01 -0400 (EDT) Date: Wed, 13 Mar 1996 20:31:12 -0500 From: Karl Irikura Subject: Final call for papers: Computational Thermochemistry X-Sender: irikura@enh.nist.gov To: chemistry@www.ccl.net Message-id: <01I2AX12B5IQ00NLNO@ENH.NIST.GOV> MIME-version: 1.0 X-Mailer: Windows Eudora Version 2.1.1 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT =============================================================== Abstract deadline: April 19 on official ACS abstract form. ACS abstract forms may be requested from (1) http://www.acs.org/memgen/meetings/abrqst.htm (2) Ann Nelson (a_nelson@acs.org) (3) one of the organizers. =============================================================== -- Final call for papers -- COMPUTATIONAL THERMOCHEMISTRY American Chemical Society COMP Division 212th National Meeting Orlando, Florida August 25-29, 1996 ...including any computer-based means for predicting the thermochemical properties of a substance. This encompasses everything from group methods to high-level ab initio calculations. Potential topic areas include: * Advances in Group Contribution Techniques * New Software to Predict Thermochemistry * New Computational Techniques * Validation of Predictive Methods * Applications of Techniques to Practical Problems The following speakers have accepted invitations to the symposium: A. D. Becke (Queen's University) S. W. Benson (University of Southern California) J. W. Bozzelli (New Jersey Institute of Technology) C. J. Cramer/D. G. Truhlar (University of Minnesota) L. A. Curtiss (Argonne National Laboratory) D. A. Dixon (Pacific Northwest National Laboratory) E. S. Domalski (National Institute of Standards and Technology) R. S. Drago (University of Florida) K. Harrison (University of Southern Alabama) A. J. Holder (University of Missouri) T. J. Lee (NASA Ames Research Center) M. L. Mavrovouniotis (Northwestern University) C. F. Melius (Sandia National Laboratories) G. A. Petersson (Wesleyan University) P. Politzer (University of New Orleans) D. W. Rogers (Long Island University) P. E. M. Siegbahn /M. R. A. Blomberg (University of Stockholm) T. Ziegler (The University of Calgary) Please contact one of the organizers if you would like to present a paper. Dr. Karl K. Irikura Dr. David J. Frurip National Institute of Standards & Technology The Dow Chemical Company (301) 975-2510 (517) 636-2446 fax 301-926-4513 fax 517-638-6027 irikura @ enh.nist.gov dfrurip @ dow.com ---------------------------------------------- Dr. Karl K. Irikura Chemical Kinetics and Thermodynamics Division National Institute of Standards and Technology Gaithersburg, MD 20899 ----------------------------------------------