From JSCHELDE@STEEVAST.RUG.AC.BE Tue Jun 29 09:59:00 1993 Date: Tue, 29 Jun 1993 09:59 +0000 (N) From: JSCHELDE@steevast.rug.ac.be Subject: helix construct To: chemistry@ccl.net Message-Id: <01GZY331DLQO001JO8@BGERUG51.BITNET> Hi all, Can somebody tell me the best way to constuct a helix(polyalanine,..) to use then in M.D. simulations. Thanks. Jean-Luc ====================================================================== Verschelde Jean-Luc Dept for Mathematical Physics Dept for Biochemistry University of Ghent Krijgslaan 281 S9 B9000 Ghent Tel:091/644794 Email:jschelde@steevast.rug.ac.be Fax:091/644989 ====================================================================== From youngdc@cemvax.cem.msu.edu Tue Jun 29 04:11:01 1993 Message-Id: <199306291215.AA05650@oscsunb.ccl.net> Date: Tue, 29 Jun 1993 08:11:01 -0400 From: youngdc@cemvax.cem.msu.edu To: CHEMISTRY@ccl.net Subject: PC tar utility In response to the request for a PC version of the unix tar (tape archiver) command. I beleive you will find one on the anonymous ftp site simtel20.army.mil use the login "anonymous" and your E-mail as the password. This is a real good place to get all sorts of general PC stuff (except games, which they don't deal with). Good Luck YOUNGDC@CEMVAX.CEM.MSU.EDU From browe@ncsa.uiuc.edu Tue Jun 29 03:18:28 1993 Date: Tue, 29 Jun 93 08:18:28 -0500 Message-Id: <9306291318.AA11722@newton.ncsa.uiuc.edu> To: chemistry@ccl.net, deal@hobbes.kzoo.edu, CHEMED-L@UWF.bitnet, From: browe@ncsa.uiuc.edu (Barry Rowe) Subject: Note to Friends of ChemViz Friends of ChemViz. For all of you who have asked about ChemViz, we now have our materials on an ftp site here at NCSA. You may get them by ftping from the ChemViz directory (folder) inside the Education directory at ftp.ncsa.uiuc.edu. The signon is 'anonymous', and you should leave your sigon as the password. The ChemViz directory at NCSA contains programs, training materials, images, and documentation for the NCSA ChemViz project. If you download these materials and find them useful to you, you may then arrange for a Cray account at NCSA to use the materials and the process with your students. ChemViz is an NSF funded grant to use High Powered Computing and Communications to help high school students better visualize abstract concepts of Chemistry. Other supporters are the Benjamin Cummings Company, Apple Computer and NCSA. Our current module allows the student (or teachers) to make images and animations of calculated atomic and molecular orbitals. Currently our project only supports the Macintosh. A color monitor is necessary to view these files. We expect to announce limited MSDOS implementation this summer. The items one needs to use the ChemViz project tools are: A Macintosh with at least 4 MBytes RAM. A Math Coprocessor and more Ram is preferred. The items that you can ftp from NCSA include: ChemViz Paper (available in MacWrite II, Word and HyperCard formats) This explains the project and gives its history. BOOGIE Docs (available in MacWrite II, Word and HyperCard formats) This paper tells how to use our materials and gives support information. ChemViz Training (a folder containing 2 HyperCard stacks -- done by Elaine Schulte, a high school student involved with the ChemViz project) BOOGIE (a 'front end' program that generates input files for NCSA DISCO) NCSA Image (to view animations and images generated with DISCO) Image is available from the main NCSA ftp directory NCSA Collage (to view animations and images generated with DISCO) Collage is available from the main NCSA ftp directory NCSA Telnet (to send BOOGIE files to and from the Cray if connected to Internet) Telnet is available from the main NCSA ftp directory Zterm (to send BOOGIE files to and from the Cray if using a modem) Zterm is available from this directory Sample Images to look at (in this directory) The sample images are in the form of HDF files (NCSA's data format). They can be read with NCSA IMAGE or NCSA Collage. MacMolecule (to observe ball and stick, line and space filling models and for future use with our materials. MacMolecule and examples of images made for it are available in this directory To run files one needs a Cray account and can obtain one by contacting Lisa Bievenue at (217)244-1993 or by email at bievenue@ncsa.uiuc.edu. It is suggested you download the ChemViz Paper first, and then the rest if our materials are appropriate for you. Documentation is in the 3 directories identified as WORD, MacWriteII and HyperCard. If you have any questions please contact Todd Veltman by phoning (217)244-0702 or by email at tveltman@ncsa.uiuc.edu [] [] [] [] [] [] [] [] [] Barry E. Rowe browe@ncsa.uiuc.edu NCSA ChemViz group 240 CAB, 152 E. Springfield Ave. Champaign, IL 61820 ANY PRACTICAL APPLICATION OF PHYSICS OBVIOUSLY INVOLVES MATTER, AND IS THEREFORE CHEMISTRY. [] [] [] [] [] [] [] [] [] From chp1aa@surrey.ac.uk Tue Jun 29 10:24:44 1993 From: Mr Andrew D Allen Message-Id: <9306291359.AA17134@central.surrey.ac.uk> Subject: AMPAC: gpt files To: chemistry@ccl.net Date: Tue, 29 Jun 93 14:59:37 BST I'm having some trouble preventing AMPAC from deleting the .gpt files on completion of geometry optimisations. I need the .gpt files for input of density matricies to Biosyms Insight Any help would be apreciated. Andy. From lith!kestas@infopro.com Mon Jun 28 14:37:41 1993 Subject: LogP calculations? To: Chemistry Mailing List Date: Mon, 28 Jun 1993 21:37:41 -0700 (PDT) From: Kestutis Sliupas Message-Id: <9306282137.AA00198@lith.UUCP> Hi: I was wondering if there was any public domain code available for calculating the octanol / water partition co- efficient? This would be for small molecules, less than say mw350. Archie returned nothing useful searching for 'logp'. -- Regards, Kestas Kestutis Sliupas x (510) 231-1540 (work voice) kestas%lith@infopro.com x (510) 231-1285 (work FAX) USA CA For you Compuserve users >>>> internet:kestas@lith.uucp From EWING@JCVAXA.JCU.EDU Tue Jun 29 06:44:00 1993 Date: Tue, 29 Jun 1993 11:44 EST From: "DAVID W. EWING (216) 397-4742" Subject: Unable to exactly reproduce previous results - MINDO/3 and MNDO To: chemistry@ccl.net Message-Id: <01GZY6SH3KMO8Y4ZVH@jcvaxa> Fellow Comp. Chemers: We cannot reproduce some of the published results on a couple of transition states using MINDO/3 and MNDO. Our bond lengths agree but angles are off by as much as 2 degrees and activation energies are off by nearly 1 Kcal/ mol. The paper to which we are comparing was published in 1988. Are the standard parameters slightly different now (we're using MOPAC 93) such that these differences would be expected? Thank you in advance for any comments! Dave Ewing, a semi-empirical neophyte John Carroll University ewing@jcvaxa.jcu.edu From raman@bioc01.uthscsa.edu Tue Jun 29 07:59:15 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9306291759.AA04906@bioc01.uthscsa.edu> Subject: Re: help: tar file on PC (fwd) To: chemistry@ccl.net Date: Tue, 29 Jun 1993 12:59:15 -0500 (CDT) Forwarded message: From raman Mon Jun 28 19:00:14 1993 Subject: Re: help: tar file on PC To: feng@sgi.chem.temple.edu (Feng Chen) Date: Mon, 28 Jun 1993 19:00:14 -0500 (CDT) > Is there any public domain DOS software availabel that can untar (tar -xvf) > the file which is generate on the UNIX machine on PC. When you say, UNIX machine, I presume you are referring to a workstation (one could imagine a UNIX partition on a PC too! ). Assuming this to be the case, you can do the following: ftp wuarchive.wustl.edu login: ftp passwd: bin cd /mirrors/msdos/filutl/ get detar11.arc quit On the PC you need to Arc to unpack this archive and then you are ready to go. This utility will untar a tar file created on any unix machine and will work on a PC. There is a similar utility for Mac users. You can use Archie to find the same! Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From ajay@cgl.ucsf.edu Tue Jun 29 04:34:31 1993 Message-Id: <9306291834.AA24650@marx.ucsf.EDU> To: CHEMISTRY@ccl.net Subject: Partial Least Squares Date: Tue, 29 Jun 93 11:34:31 -0700 From: ajay@cgl.ucsf.EDU Hi, Is anyone aware of any public domain code that does partial least squares (PLS)? Thanks. ---ajay From SC18%NEMOMUS.BITNET@phem3.acs.ohio-state.edu Tue Jun 29 09:37:43 1993 Date: Tue, 29 Jun 1993 13:37:43 -0400 (EDT) From: SC18000 Subject: Silicon Graphics To: chemistry@ccl.net Message-Id: <29JUN93.14719019.0032.MUSIC@NEMOMUS> Hi Netters, Could someone quickly give me the address and phone number of Silico n Graphics, Inc? I need to speak to people about prices etc. Thanx, Ken Fountain/ sc18@nemomus From lim@rani.chem.yale.edu Tue Jun 29 12:18:23 1993 From: Dongchul Lim Message-Id: <9306292018.AA22223@rani.chem.yale.edu> Subject: Re: PC tar utility To: chemistry@ccl.net (Computational Chemistry) Date: Tue, 29 Jun 93 16:18:23 EDT youngdc@cemvax.cem.msu.edu writes: > In response to the request for a PC version of the unix > tar (tape archiver) command. > > I beleive you will find one on the anonymous ftp site > > simtel20.army.mil > > use the login "anonymous" and your E-mail as the password. > > This is a real good place to get all sorts of general > PC stuff (except games, which they don't deal with). > Some of basic UNIX commands such as ls, mv, df, tar, etc can be found in /pub/pc/utils/unixlike directory of unr.edu. This site doesn't have many DOS programs but directories are well organized. -DCL From wipke@SECS.UCSC.EDU Tue Jun 29 08:53:20 1993 Date: Tue, 29 Jun 1993 15:53:20 PDT From: "W. Todd Wipke" To: chemistry@ccl.net Message-Id: <0096EC1D.FA6F4000.4627@SECS.UCSC.EDU> Subject: Intellectual Property The recent discussion on reproducibility of computational chemistry expts was the basis of starting Tetrahedron Computer Methodology, a journal with disks and an on-line component so that parameters and data and code could accompany the paper in a form that could be directly read by the one doing the manipulation, namely, the computer. Some scientists took the opportunity, but it was easier for many to publish in conventional journals where reproducibility is not required. Ironically, computational chemistry is unique in that we can guarantee reproducibility, yet we neglect it more than other sub disciplines such as synthetic organic. Of course we have many more variables to disclose than in the experimental for carrying out a given reaction, but I believe the real problem is a lack of mature ethics in the field of computational chemistry. Synthetic organic chemists take pride in citing the work of others, even detailed workup procedures or use of particular solvent etc. They are able to read such details in the experimental sections and if they fail to give proper citations, they are promptly chastised by referees. In contrast, computational chemists are often unable to see inside the black box, they find few details in the experimental sections, especially on algorithmic efficiencies, and other such innovations. They seem inclined to give less credit to prior work, perhaps because they gained less than they wished from it, or perhaps because they know the referees can't recognize borrowed code >from the scant experimental. The missing citations not only rot the moral standards, they also impede readers understanding of the relation of the work to prior work, and of course mislead the reader. The question is not "How much do I have to change a code before I can call it my own?", but rather "How can I respect the intellectual property of the author of the code?". Peer pressure on offenders can enforce the ethical standards and lead to improvement. That in turn may lead to more released source code and more collaboration and more reproducible results. It certainly will lead to a more comfortable and rewarding work environment. As I see it, scientific ethics are separate from patent and copyright law. Shortcomings or ambiguities in the latter are no excuse to violate the former. Similarly, the newness of the field of computational chemistry does not excuse it from the well-established common sense scientific ethics that evolved over time with the experimental sciences. Raising the ethical standards and respect for intellectual property will accelerate research in computational chemistry more than anything else we can do. -Todd Wipke Molecular Engineering Laboratory Dept of Chemistry University of California Santa Cruz, CA 95064 wipke@chemistry.ucsc.edu Disclaimer: My employer DOES subscribe to EDUCOM's ethical standards for software. From raman@bioc01.uthscsa.edu Tue Jun 29 13:46:20 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9306292346.AA05558@bioc01.uthscsa.edu> Subject: Re: Silicon Graphics To: SC18%NEMOMUS.BITNET@phem3.acs.ohio-state.edu (SC18000) Date: Tue, 29 Jun 1993 18:46:20 -0500 (CDT) > Could someone quickly give me the address and phone number of Silico > n Graphics, Inc? I need to speak to people about prices etc. 1-800-800-SGI1 or 1-800-800-7441 -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From dave@carbon.chem.csiro.au Wed Jun 30 05:21:44 1993 Message-Id: <199306300021.AA02668@shark.mel.dit.csiro.au> Date: Wed, 30 Jun 93 10:21:44 EST From: (Dr.) Dave Winkler Subject: Re: log P To: lith!kestas@infopro.com, chemistry@ccl.net Dear Kestas, I got a bounce when trying to email you direct. I don't know of any public domain programs for predicting log P. There is a good package called HINT which costs about $200 and can be obtained from Don Kellogg at Virginia Commonwealth University (gkellogg@gems.vcu.edu). It calculates logP and can also generate lipophilicity fields around molecules which can be viewed in a number of commercial modelling packages or used in ComFA analysis. The other 'de facto' standard logP predicyion package is the Medchem suite sold by Daylight Chemical Information Systems in Pomona. I think this costs $10K or so with all the other (excellent) chemical database software. Cheers, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. "Life is what happens to you while you're making other plans" From dave@carbon.chem.csiro.au Wed Jun 30 05:57:34 1993 Message-Id: <199306300057.AA03153@shark.mel.dit.csiro.au> Date: Wed, 30 Jun 93 10:57:34 EST From: (Dr.) Dave Winkler Subject: 10th European QSAR meeting To: tom@sgih.roc.wayne.edu, chminf-l@iubvm.ucs.indiana.edu, chemistry@ccl.net Tom, The info has been hard to find but here it is... 10th European QSAR meeting. September 4-10 Hotel Feria Palace on Montjuic Mountain Barcelona Spain Contact: Prof. Ferran Sanz Institut Municipal d'Invetigacio Medica carrer Dr. Aiguader, 80 E-08003 Barcelona, Spain Fax: 34 3 221 3237 email: qsar10@imim.es Cheers, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. "Life is what happens to you while you're making other plans" From st-amant@cgl.ucsf.EDU Tue Jun 29 13:07:10 1993 Date: Tue, 29 Jun 93 20:07:10 -0700 Message-Id: <9306300307.AA25117@socrates.ucsf.EDU> From: st-amant@cgl.ucsf.edu (Alain St-Amant) To: chemistry@ccl.net, wipke@SECS.UCSC.EDU Subject: Re: Intellectual Property Todd Wipke writes: > The question is not "How much do I have to change a code before I can >call it my own?", but rather "How can I respect the intellectual property of >the author of the code?". Peer pressure on offenders can enforce the ethical >standards and lead to improvement. That in turn may lead to more released >source code and more collaboration and more reproducible results. It >certainly will lead to a more comfortable and rewarding work environment. >As I see it, scientific ethics are separate from patent and copyright law. >Shortcomings or ambiguities in the latter are no excuse to violate the former. I was the asker of that question "How much do I have to change a code before I can call it my own?" and I guess upon reading Dr. Wipke's letter, I guess it did sound kind of unethical the way I put it. Actually, quite unethical. Sorry. However, if it's any justification, the original author that I'm trying to scam is none other than myself. I'm developing a program similar to one I wrote up as a student that ended up commercialized and I was just curious as to whether adopting the same structure, programming style, look and feel, etc. etc. and using old code to verify the veracity of new code would constitute "self"-plagiarism. Hopefully, this clarification will reestablish my good name. :-) I wholeheartedly agree that we shouldn't try to engage in legal technicalities to cheat original authors of their due credit and that we should strive to seek ways to reverse the trend towards the commercialization of software which is only hurting science since source code is no longer being freely exchanged. Sincerely, Alain St-Amant Dept. of Pharmaceutical Chemistry University of California, San Francisco