From ross@cgl.ucsf.EDU Tue May 11 15:06:56 1993 Date: Tue, 11 May 93 22:06:56 -0700 Message-Id: <9305120506.AA05833@socrates.ucsf.EDU> From: ross@cgl.ucsf.edu (Bill Ross ) To: chemistry@ccl.net Subject: QCPE for free There are already free ftp sites; if people put their free softwhere there instead of QCPE, then the goal will have been achieved. As for the cost, see the recent _Science_ magazine article on the physics preprint repositories. Two obvious 'name' candidates (if their policies allow it): osc (kekule) and netlib. Bill Ross From NMUELLER@EDVZ.UNI-LINZ.AC.AT Wed May 12 09:45:07 1993 Message-Id: <199305120653.AA18390@oscsunb.ccl.net> Date: Wed, 12 May 1993 08:45:07 +0100 To: chemistry@ccl.net From: NMUELLER@edvz.uni-linz.ac.at (Norbert Mueller) Subject: QCPE >The question of accessing QCPE programs via internet has arisen before. The >problem is (correct me if I misstate this, Richard) that QCPE is not supported >by sources other than income derived from the sale of programs, bulletins, >etc. So, if it free and unlimited access were provided via internet, there >would soon be nothing to access. > >Richard Counts has done an excellent job over many years running, maintaining >and expanding QCPE. He deserves a big round of thanks. > >Doug > I agree with this. However I might add two suggestion to improve the efficiency of QCPE: 1) They should accept credit cards! It's really complicated to send a cheque from Europe for their subscription fees and the bank charges frequently exceed the amount transferred. 2) What about providing non-anonymous accounts for the members for downloading. This should be less effort than copying tapes. "The subject is open for discussion" Norbert Mueller Institut fuer Chemie Johannes Kepler Universitaet A-4040 Linz Austria e-mail: NMUELLER@edvz.uni-linz.ac.at (preferred) norbert@soft.uni-linz.ac.at NorbertM (AMDA-Link Linz) ->FirstClass K360171@alijku11.earn \ K360171@alijku11.bitnet > will expire in 1994 K360171@alijku11.edvz.uni-linz.ac.at / From h.rzepa@ic.ac.uk Wed May 12 10:56:02 1993 Message-Id: <9305120957.AA07315@cscmgb.cc.ic.ac.uk> Date: Wed, 12 May 1993 10:56:02 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Re: Net access to self funding databases & archives >Dear Netters, > >There are queries from time to time along the lines of..."why can't we get >free >ftp access to QCPE?" or "can you search the Cambridge Crystallographic >Database >via the Internet". The reason why these things cannot be done is that the >organizations maintaining these archives or databases rely on income from >purchases of software/databases to continue operating. > >I've often wondered whether it might be possible to devise a secure way of >allowing this type of access via the net by means of encrypted files, special >access keys or, more obviously special temporary accounts with passwords. >Could some way could be developed where, say QCPE programs, could be available >on a public ftp archive in a 'locked' form with unlocking instructions >provided >once the credit card transaction has been processed? As the director of the >Australian Affiliated Centre for Cambridge Database I know from personal >experience what a hassle it is to ship tapes, disks, manuals etc all over the >world and distribute them within a country. Electronic distribution would be >much simpler if the money side of things could be solved. > >In a less than perfect world I guess this would still lead to net bandwidth >problems if someone tried to ftp Gaussian in one lump! I notice that several companies are now issuing virtually free CD-ROMs containing several hundred programs etc. You pick what you want, phone up with money, and they issue the de-encryption keyword. I dare say that QCPE, Cambridge etc might adopt this system, now that the cost of pressing CD-ROM masters is dropping. Mind you, with say QCPE, the original authors receive NO Money, and QCPE was supposed to cover just the distribution cost + admin cost of the organisation itself. The CD-ROM route would substantially reduce the distribution costs to the point where the QCPE admin cost would be by far the major component. Could they generate sufficient income to survive? I would be quite happy to pay 1-2 hundred dollars for say 2-3 CD-ROMS every year. If 5000 people did the same, QCPE would flourish! Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 1.3.1, Tel:+44 71 225 8339, Fax:+44 71 589 3869. From 009LGZS@witsvma.wits.ac.za Wed May 12 08:50:49 1993 Message-Id: <199305121200.AA22868@oscsunb.ccl.net> Date: Wed, 12 May 93 13:53:56 RSA From: Leslie Glasser <009LGZS@witsvma.wits.ac.za> Subject: 'shell model' for ionic crytals To: Comp Chem Group Dear Readers: I am attempting to introduce the 'shell model' of an ion into the modelling of some ionic crystal structures; this was originally introduced by Dick and Overh auser. There are many references to the model, but I have not been able to fi nd an adequate description from which I can implement it. The best reference that I have is A. Wall And G D Price, Amer Miner 73, 224-231 (1988) where the model is outlined too superficially for me to follow. Could someone direct me to a suitable, more complete description, or explain wh at is required to be done to set up the model. With my grateful thanks, Leslie Glasser ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (Prof.) Leslie Glasser Dept. of Chemistry E_MAIL: 009LGZS@WITSVMA.WITS.AC.ZA University of the Witwatersrand Tel: (011)-716-2070 WITS 2050 FAX: (011)-339-7967 South Africa ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From topper@haydn.chm.uri.edu Wed May 12 05:03:34 1993 Date: Wed, 12 May 93 09:03:34 -0400 From: topper@haydn.chm.uri.edu (Robert Q. Topper) Message-Id: <9305121303.AA03441@haydn.chm.uri.edu> To: chemistry@ccl.net Subject: QCPE Here's another vote for internet access to QCPE on a paying basis. QCPE can only ship tapes in a couple of formats (or at least that was the case last time I heard), and a lot of potential users don't have ready access to machines which understand those tape formats, so they find it difficult to order the codes. Then they REALLY find it difficult to install them...in other words, the activation barrier to ordering codes from QCPE would be lowered if one could pay to access them over the net. Another suggestion; FREE online access to the QCPE CATALOG, perhaps through gopher. Or perhaps this already exists...? rqt ******************************** * Robert Q. Topper, Ph.D. * * Department of Chemistry * * University of Rhode Island * * Kingston, RI 02881 USA * ******************************** * topper@haydn.chm.uri.edu * * (401) 792-2597 [office] * * (401) 792-5072 [FAX] * ******************************** "And the lonely voice of youth cries...what is truth?" -Johnny Cash From ssidner@unmc.edu Wed May 12 03:20:53 1993 Date: Wed, 12 May 93 08:20:53 CDT From: ssidner@unmc.edu (Steve Sidner) Message-Id: <9305121320.AA27453@molecular.unmc.edu> To: chemistry@ccl.net Subject: Re: QCPE on Internet > From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" > Subject: QCPE on Internet > To: chemistry@ccl.net > > The question of accessing QCPE programs via internet has arisen before. The > problem is (correct me if I misstate this, Richard) that QCPE is not supported > by sources other than income derived from the sale of programs, bulletins, > etc. So, if it free and unlimited access were provided via internet, there > would soon be nothing to access. Since QCPE's budget is significantly less than the Superconducting Super Collider, yet the utility greater (certainly, to most of the computational chemistry community), it seems a shame that someone like NSF couldn't fund this. Heck, I bet QCPE could be funded for a year for a day's worth of one of the supercomputer centers. > Richard Counts has done an excellent job over many years running, maintaining > and expanding QCPE. He deserves a big round of thanks. I agree heartily! I think Internet access would help alot, though. Just being able to grep and browse the documentation would help enourmously. There is such a wealth of information, constantly being updated, in the Catalog, that the paper copies just don't do it justice. Maybe we could hold a Bake Sale... Steve Sidner Eppley Institute, University of Nebraska Medical Center 600 S. 42nd St., Omaha, NE, 68198-6805, U.S.A. (402) 559-4921, FAX: (402) 559-4651 ssidner@unmc.edu ssidner@unmcvm.bitnet From culmer@stardent.chem.UTOLEDO.edu Wed May 12 05:44:43 1993 Date: Wed, 12 May 1993 09:44:43 -0400 (EDT) From: culmer@stardent.chem.UTOLEDO.edu (Charles W. Ulmer II) Subject: Tools, tools, tools, and more tools. To: chemistry@ccl.net Message-Id: <9305121344.AA01891@stardent.chem.utoledo.edu> Chemistry tools and more....They already exist. What more do you want the tools to do? The AVS Chemistry Viewer probably does or can do whatever you wish. For Example: Read Files: Gaussian, Mopac, BGF, MDL, PDB, XYZ Write Files: Same as above. Selected Features: 1) Edit and build molecules 2) Display AO's, MO's, Electron Density, Dipole Moment, Connolly Surface, Vibrational Modes, and Electrostatic Potential 3) Perform various operations on one or two density matrices 4) Perform a localization transformation on MO's 5) Converts Bohr to Ang. and back 6) Much, much more.... Plus, you get the versatility of AVS. This means that you get real-time rotation, graphing abilities, 3D rendering, imaging, animation, and the ability to window across the net.... I can't begin to go into all the capabilities that the AVS Chemistry Viewer gives to you in an e-mail message. But, I am teaching a course on advanced topics and applications of the Chemistry Viewer at the AVS '93 Conference in Orlando on May 24-26. I do not work for Molecular Simulations, Inc., who distributes this product. I am a 4th year Grad. Student and end user of a very nice product that I wish I would have had when I first started. How many times have you sifted through Gaussian Frequency output to determine if you had a transition state? Why not animate the frequency and see it? The only draw-back is that you must also have AVS. This is not really a draw-back though, since AVS is so powerful. -- Charles W. Ulmer culmer@stardent.chem.utoledo.edu D.A.Smith Group culmer@uoft02.utoledo.edu University of Toledo Toledo, OH, 43606 WE ARE PERHAPS NOT FAR REMOVED FROM THE TIME WHEN WE SHALL BE ABLE TO SUBMIT THE BULK OF CHEMICAL PHENOMENA TO CALCULATION. -- JOSEPH LOUIS GAY-LUSSAC MEMOIRES DE LA SOCIETE D'ARCUEIL, 2, 207 (1808) From DSMITH@uoft02.utoledo.edu Wed May 12 04:48:23 1993 Date: Wed, 12 May 1993 09:48:23 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: QCPE access - another comment To: chemistry@ccl.net Message-Id: <01GY30D7YEA6007PNM@UOFT02.UTOLEDO.EDU> Several people have already offerred interesting and important comments on the issue of QCPE access. Let me respond to a few which raised issues I feel are important. First, QCPE might be made available in a manner similar to CAS Online, but with a lot of work and cost. Remember, CAS is not cheap, and is a huge operation. I am not sure of the current situation at QCPE, but I seem to recall that the entire operation was Richard Counts, one full time assistant and maybe one part timer. If someone took over QCPE (which I am not suggesting unless Richard wants to retire), then account numbers, dial-in or internet access, and all of the other advantages to a CAS-like system could be realized. But it would probably cost the users more than the current system. Second, as to free ftp sites/depositories for codes (e.g. kekule@ccl.net) are a major investment of time and effort on the part of the person who maintains the site. (Recall some of Jan's comments from a year or so ago?) I also know this first hand, as I run the MacroModel mail exploder and ftp archives (for more information, send mail to dsmith@uoft02.utoledo. edu requesting information on MMODINFO) and I get swamped occassionally >from this small exploder. Finally, notice that Richard Counts and others from non-commercial sites (e.g. Jan Labanowski, if you will excuse my naming a name) are staying out of this discussion. They do read this mail exploder, as they have posted and replied before. The issue may be too sensitive or close to home for them to add their comments, lest they be viewed as self-serving. Again, to all who serve the internet community - Richard, Jan, and others at other mail exploders and ftp sites, and to your technicians (if any) who keep the hardware and software running - THANKS. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From DSMITH@uoft02.utoledo.edu Wed May 12 05:40:02 1993 Date: Wed, 12 May 1993 10:40:02 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: anonymous ftp correction - 3D To: chemistry@ccl.net Message-Id: <01GY32HTDBCY007PNM@UOFT02.UTOLEDO.EDU> Sorry for the mistake and the wasted bandwidth, but there was a minor error in my earlier posting. If you want to get the summary of Stereoviewing in molecular modeling, you can follow the instructions I sent with one exception - you cannot use the -l switch to your ls command. ls by itself works, as does dir. This host is a VAX VMS machine. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From scott@paganini.biocad.com Wed May 12 00:36:05 1993 Date: Wed, 12 May 93 07:36:05 -0700 From: scott@paganini.biocad.com (Scott Kahn) Message-Id: <9305121436.AA03936@paganini.biocad.com> To: CHEMISTRY@ccl.net Subject: RE: Hydrogen bonds to Cl acceptor ? The only two numbers that I have for H bonds to Cl acceptors are: HCl --- HF delE = -1.3 Kcal/mol; RCl--H = 3.50 A HCl --- HCl delE = -1.5 Kcal/mol; RCl--H = 3.80 A Both employ assumed geometies, and are calculations at the RHF/STO-3G level. The primary reference is Kollman et al, 1974 (sorry, I got this from a table in an H bonding book to which I no longer have access!). Does anyone know of a **comprehensive** and up-to-date table of experimental and/or theoretical H bond strengths? ------ Scott D. Kahn, BioCAD Corporation (415) 903-3917 Email : scott@biocad.com From gene@eastrg1.cray.com Wed May 12 07:39:12 1993 Date: Wed, 12 May 93 11:39:12 EDT From: gene@eastrg1.cray.com (Eugene Fleischmann) Message-Id: <9305121539.AA09892@sodium.cray.com> To: chemistry@ccl.net Subject: RE: Rigid-Body Minimizations? > From mmodinfo-error@uoft02.utoledo.edu Tue May 11 23:45:08 1993 > Resent-Date: Tue, May 11, 1993 22:18 > Resent-From: mmodinfo-error@uoft02.utoledo.edu > Subject: Rigid-Body Minimizations? > To: mmodinfo@uoft02.utoledo.edu > Reply-To: "Michael A. Peterson" > Resent-Message-Id: <01GY2F7KFKGI007P1U@UOFT02.UTOLEDO.EDU> > X-Envelope-To: gene@eastrg2.cray.com > X-Vms-To: IN%"mmodinfo@uoft02.utoledo.edu" > Content-Transfer-Encoding: 7BIT > > Dear MMODers: > > I would like to do rigid-body minimizations (intramolecular minimizations--no > relaxation of _internal_ degrees of freedom of either of two molecules) using > MacroModel 3.1X on a SGI. Evidently mmod used to be able to do this (VAX > version 2(?), anyways) or something similar. I am able to keep a single > molecule fixed and relax the internal degrees of freedom of the second molecule, > but this is not what I want. Can mmod 3.1X do rigid-body minimizations? If so, > how? Will 4.0 do it? Thanks. > > > Michael A. Peterson > ipmp500@indyvax.iupui.edu > Dept. of Chemistry > Indiana Univ-Purdue Univ at Indianapolis > > I think you mean "inter-molecular" minimization, involving the 6 degrees of freedom relating one molecular species to another. Gene Fleischmann ++++++++++++++++++++++++++++++++++++++++ Eugene D. Fleischmann, Ph.D. Computational Chemist Cray Research, Inc. (301)595-2695 gene@eastrg2.cray.com ++++++++++++++++++++++++++++++++++++++++ From mes@atlas.chemistry.uakron.edu Wed May 12 09:36:01 1993 Date: Wed, 12 May 93 13:36:01 EDT From: mes@atlas.chemistry.uakron.edu (Mary Ellen Scott) Message-Id: <9305121736.AA25583@atlas.chemistry.uakron.edu> To: chemistry@ccl.net Subject: Hydrogen bonding Dear netters, I am looking for information on how hydrogen bonds to fluorine. (O-H...F-C). Is anyone doing calculations in this area. I'll summarize the response. Thanks, Mary Ellen From ross@cgl.ucsf.EDU Wed May 12 03:59:03 1993 Date: Wed, 12 May 93 10:59:03 -0700 Message-Id: <9305121759.AA05291@socrates.ucsf.EDU> From: ross@cgl.ucsf.edu (Bill Ross ) To: chemistry@ccl.net Subject: QCPE Steve Sidner: I bet QCPE could be funded for a year for a day's worth of one of the supercomputer centers. Based on working at a supercomputer center and reading the _Science_ article about the physics resource I mentioned, the cost is more like a few minutes of a whole supercomputer center's budget for a year of storage + administration. If QCPE was electronic and automated, the costs we are worrying about would disappear. > Richard Counts has done an excellent job over many years > running, maintaining > and expanding QCPE. He deserves a big round of thanks. I agree heartily! Me too. Bill Ross From avs@iris95.biosym.com Wed May 12 04:19:07 1993 Message-Id: <9305121819.AA02548@iris95.biosym.com> To: chemistry@ccl.net Subject: Re: Tools, tools, tools, and more tools. Date: Wed, 12 May 93 11:19:07 -0700 From: avs@iris95.biosym.com > From: culmer@stardent.chem.UTOLEDO.edu (Charles W. Ulmer II) > Subject: Tools, tools, tools, and more tools. > > Chemistry tools and more....They already exist. What more do you want the > tools to do? The AVS Chemistry Viewer probably does or can do whatever you > wish. For Example: > The only draw-back is > that you must also have AVS. This is not really a draw-back though, since > AVS is so powerful. > > -- > > Charles W. Ulmer culmer@stardent.chem.utoledo.edu > D.A.Smith Group culmer@uoft02.utoledo.edu > University of Toledo > Toledo, OH, 43606 > When most people talk of tools, they are asking for tools that can be incorporated in their own programs. They are looking for source code that can be plugged into their own programs with little or no modification. Certainly, avs chemistry viewer does not fit that bill. Also, many in academics look for vendor independent platform independent products. BTW, avs is not the only product that does all that you mentioned. There are many other commercial programs that do the same....including of course insightII from Biosym :-) **************************************************** Ajay Shah Biosym Technologies avs@biosym.com **************************************************** Have You Heard of the Symmetry Death of the World ? **************************************************** From jas@medinah.atc.ucarb.com Wed May 12 09:37:23 1993 Message-Id: <9305121834.AA20818@medinah.atc.ucarb.com> Date: Wed, 12 May 1993 14:37:23 -0500 To: chemistry@ccl.net From: jas@medinah.atc.ucarb.com (Jack Smith) Subject: Re: Net access to self funding databases & archives >> >>There are queries from time to time along the lines of..."why can't we get >>free >>ftp access to QCPE?" or "can you search the Cambridge Crystallographic >>Database >>via the Internet". The reason why these things cannot be done is that the >>organizations maintaining these archives or databases rely on income from >>purchases of software/databases to continue operating. >> >>I've often wondered whether it might be possible to devise a secure way of >>allowing this type of access via the net by means of encrypted files, special >>access keys or, more obviously special temporary accounts with passwords. >>Could some way could be developed where, say QCPE programs, could be >>available >>on a public ftp archive in a 'locked' form with unlocking instructions >>provided >>once the credit card transaction has been processed? As the director of the >>Australian Affiliated Centre for Cambridge Database I know from personal >>experience what a hassle it is to ship tapes, disks, manuals etc all over the >>world and distribute them within a country. Electronic distribution would be >>much simpler if the money side of things could be solved. >> >>In a less than perfect world I guess this would still lead to net bandwidth >>problems if someone tried to ftp Gaussian in one lump! > >I notice that several companies are now issuing virtually free CD-ROMs >containing several hundred programs etc. You pick what you want, >phone up with money, and they issue the de-encryption keyword. I >dare say that QCPE, Cambridge etc might adopt this system, now that >the cost of pressing CD-ROM masters is dropping. Mind you, >with say QCPE, the original authors receive NO Money, and >QCPE was supposed to cover just the distribution cost + admin >cost of the organisation itself. The CD-ROM route would substantially >reduce the distribution costs to the point where the QCPE admin >cost would be by far the major component. Could they generate >sufficient income to survive? I would be quite happy to pay 1-2 >hundred dollars for say 2-3 CD-ROMS every year. If 5000 people did >the same, QCPE would flourish! > Further questions and comments: 1) Suppose OSC (or similar non-profit institution), as a QCPE subscriber, put all the UNLICENSED programs it acquired on an anonymous FTP server? Could they "legally" do this? Are there any implied contractual agreements between QCPE, the program authors and the end users that prevent this (for programs that do not involve a license agreement of course)? 2) Suppose that maintaining an FTP server is far less time-consuming and less expensive overall (due to lower material and mailing costs), then does it make sense not to do so just to protect a job? No offense to Richard Counts (who does deserve a great deal of gratitude, respect and a commensurate salary), but surely someone with his expertise would rather devote more time to testing, porting, documenting, benchmarking and such, than cutting tapes and stuffing mailers. 3) How about a robust news service like HPCwire (CCwire? or CCreader?) at a respectable subscription rate, with someone like Counts as the editor, to replace or supplement the QCPE Bulletin and generate revenue to support both the news service and FTP server? It looks like hardware and software vendors are quite willing to subsidize such services (provided they get their plugs in). [ For those not familiar with HCPwire, I'd be glad to post a sample of their new service. ] 4) How about an un-scientific poll on how many would be willing to pay for QCPE Internet access if a subscription mechanism could be worked out? If so, how much? Should it be a flat fee or based on volume of service? Should there be both acacemic and industrial rates? What should be the redistribution rights of subscribers? Should program authors have any say? And so on... -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JACK A. SMITH ...................................................................... Union Carbide Corp. || Phone: (304) 747-5797 Catalyst Skill Center || FAX: (304) 747-5571 P.O. Box 8361 || S. Charleston, WV 25303 || Internet: jas@medinah.atc.ucarb.com -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From shepard@dirac.tcg.anl.gov Wed May 12 09:23:52 1993 Date: Wed, 12 May 93 14:23:52 CDT From: shepard@dirac.tcg.anl.gov (Ron Shepard) Message-Id: <9305121923.AA14315@dirac.tcg.anl.gov> To: chemistry@ccl.net Subject: QCPE and encryption schemes There are encryption schemes that allow secure transactions between two parties in which each party has a public key, which is known to everyone, and a private key, which is secret. The sending party, QCPE, encrypts the files with the QCPE private key and the public key of the receiver, who is a registered subcriber. The subscriber decodes the transmission with the QCPE public key and their own private key. Only the designated receiver can do this -- an encryption must be done for each transmission. This isn't as convenient as traditional anonymous FTP, but it might be a practical alternative given the necessity of raising financial support for QCPE. Perhaps it could be automated on the QCPE side, like the email interface to netlib, so that requested software is available on weekends, etc. -Ron Shepard shepard@tcg.anl.gov From feng@lisboa.ks.uiuc.edu Wed May 12 09:26:37 1993 From: Zhou Feng Message-Id: <9305121926.AA01216@lisboa.ks.uiuc.edu> Date: Wed, 12 May 93 14:26:37 -0500 To: chemistry@ccl.net Subject: calculating dielectric constant from MD simulation I am looking for a good method to abstract apparent dielectric constant from molecular dynamics simulation data. The system is a membrane-water interface, which is heterogenious. Is there a good method available now for such problems? I am particularly looking for a few good references. THanks. --- Feng Zhou +-------------------------------------------------------------------- |Theoretical Biophysics feng@lisboa.ks.uiuc.edu |University of Illinois Tel: (217)-244-1612 |3121 Beckman Institute Fax: (217)-244-6078 |405 N Mathews, Urbana, IL61801 NeXTmail Ok +-------------------------------------------------------------------- From dan@omega.chem.yale.edu Wed May 12 12:28:59 1993 From: Dan Severance Message-Id: <9305122029.AA26411@omega.chem.yale.edu> Subject: Re: Tools, tools, tools, and more tools. To: CHEMISTRY@ccl.net Date: Wed, 12 May 93 16:28:59 EDT Organization: Laboratory for Computational Chemistry Chuck Ulmer writes: > > Chemistry tools and more....They already exist. What more do you want the > tools to do? The AVS Chemistry Viewer probably does or can do whatever you > wish. For Example: > ..... > Unfortunately, I don't remember the details, but these tools require you purchase and AVS license, plus the chemistry viewer, which turns out to be a hefty chunk of change even with academic prices. Also, one must use a graphics workstation, which many, but not all of us have. The UNIX tools have traditionally been usable from text terminals (i.e. when you are dialed in from home), so at least a non-graphics option for tools would be nice. The main sticking point I see with AVS is the cost. The original poster was (I think) hoping for a cooperative effort to develop public domain tools that everyone could use, regardless of budgetary constraints. Then data and coordinates can be sent for point A to point B with no concern over differing data formats, and electronic communication between researchers can take another step forward. Dan Severance dan@omega.chem.yale.edu Yale University From jkl@ccl.net Wed May 12 12:42:24 1993 From: Jan Labanowski Date: Wed, 12 May 1993 16:42:24 -0400 Message-Id: <199305122042.AA05791@krakow.ccl.net> To: chemistry@ccl.net Subject: QCPE, Supercomputer Center and Archie Dear Spiders, I wanted to stay out of the QCPE discussion, but it seems that the system did not make a good politician yet. 1. Do we need centralized resources/archives. IMHO we need. The QCPE is an example of a very successful one. The information you get is timely. The manuals you get are often as good as the ones from commercial sources. But most important, it is kept together, indexed, and maintained, and rules about the minimal standard of submitted software are enforced. The QCPE Bulletin gives news, and some publications there are better than in leading journals. It is amazing how much you can do with so little resources. The reasons why the files are not available on the network, is in my opinion, not related to the traditional way of thinking of QCPE board, but to the fact that it would be MUCH MORE EXPENSIVE to make them available on-line. The Internet security is a joke. Believe me, a person with a good knowledge of networking software can crack anything one way or the another, unless there is a 24 hours a day supervision. Can the networks be made safe? Of course they can, but who wants it? Do you want an open Internet or a restricted one? Who will pay for enforcing security on the net? If QCPE decided to allow on line controlled access to the archives, they need 10 people to maintain it. Ask vendors of databases about the nightmares to provide secure access to the databases and to protect user related information and ensure validation. Until this moment when we replace all communication software and protocols on the Internet, the secure access is a joke, and I would not punch my credit card number to any message, encrypted or not. Moreover... The fact that you do not pay for the ftp/e-mail access, does not mean that it is cheap. Sending 100 Mbytes on the net is much more expensive than sending a tape to the most obscure place on the globe. And once the access to the QCPE or whatever archives is commercialized, then someone has to pay for it, since the Feds or local government or institution will not subsidize it (why should they... it is no longer a "free" exchange of information). 2. There is a lot of software scattered on the net in different archives. I welcome suggestions what I could put in the archives on www.ccl.net. You can use archie to find out about stuff all over the world. I included some short info on archie on www.ccl.net in pub/chemistry as archie-info. However, though in principle, I could buy the whole QCPE distribution an place it on www.ccl.net I will not do it, since I neither have time, nor resources to do it. And most importantly, I think that QCPE does a better job than I could ever do. And my last year April Fool's Day joke really scared some people. And though you have the list and archives for free, it is not so free to me (believe it or not...). 3. As to budgets of Supercomputer Centers, they are not as large as some may think (I am talking about publicly accessible supercomputer centers). Of course, we will soon have no supercomputer centers, because workstations are so terrific and cheap. Nobody however seems to realize that once you have your workstation, you will have to buy/install/maintain all your software on it and there will be nobody to ask around. And also, if you do not believe that DIRECT MP4 can be easily done, you will have to buy yourself a nice farm of big disks which will cost you 10 times more than your CPU. In short, we better watch out so we do not throw out the baby with the bath water. Jan Labanowski Your Uncoordinator. jkl@ccl.net From BOYD_DONALD_B@Lilly.com Sun May 12 11:51:53 1993 Date: 12 May 1993 16:51:53 -0500 (EST) From: "DONALD B. BOYD" Subject: QCPE for free? To: chemistry@ccl.net Message-Id: <01GY3F1IUFLU8WZ76V@INET.D48.LILLY.COM> Although it is understandable that users want to avoid the paperwork of writing a check and avoid the wait of receiving a tape in shipment, it could kill the goose that laid the golden egg to make QCPE programs free. QCPE is a self-supporting organization and, I might add, has done so very selflessly. If people have ideas on how to maintain QCPE as a viable and reliable depository in this age of electronic mail, they should offer them. I don't think QCPE has outlived its usefulness. Code developers come and go, change jobs, etc., but some institution needs to be in place to maintain a permanent repository. Don Boyd From: BOYD DONALD B (MCVAX0::QSAR) To: VMS MAIL ADDRESSEE (INT::"chemistry@ccl.net") cc: BOYD DONALD B (MCVAX0::QSAR) From ghammond@igor.une.edu.au Thu May 13 20:46:28 1993 Message-Id: <9305131546.AA12184@igor.une.edu.au> To: schuetz@iacrs2.unibe.ch (Martin Schuetz) Subject: Re: Visualization of MOPAC MO's... Date: Fri, 14 May 93 01:46:28 -0500 From: ghammond@igor.une.edu.au I was just looking back through some old mail and found your request for MO visualisation. What did you find out? I'd be grateful for any information you could supply. Thanks Gerard Hammond ghammond@metz.une.edu.au From jle@world.std.com Wed May 12 17:01:35 1993 Date: Wed, 12 May 1993 21:01:35 -0400 From: jle@world.std.com (Joe M Leonard) Message-Id: <199305130101.AA16190@world.std.com> To: chemistry@ccl.net Subject: Conf anal of cyclic ene's Folks, When studying cyclic species with 1-2 double bonds (like cyclooctene or larger), using the various searching methods out there, are folks concerned about the cis-trans isomerization question? In other words, do folks want to know about the min-E conformations of cyclooctene OR the min-E conformations of cis-cyclooctene and/or trans-cyclooctene? Thanks in advance! Joe Leonard jle@world.std.com From raman@bioc01.uthscsa.edu Wed May 12 15:06:30 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9305130106.AA12534@bioc01.uthscsa.edu> Subject: Re: Hydrogen bonding To: mes@atlas.chemistry.uakron.edu (Mary Ellen Scott) Date: Wed, 12 May 1993 20:06:30 -0500 (CDT) Emsley et al. ( J. Am. Chem. Soc., 103, 14 [1981]) found evidence for strong hydrogen bonding of F- by amides (R-CO-NH2) by 'ab initio calculations and from NMR and IR studies of reactions products of strong solutions of amides and F-. This is one of the most interesting and conclusive studies that I know of; but if you are interested in hydrogen bonding of F- in the case of biological systems, see the work by Joe Kraut et al. ( J. Biol. Chem. 259, 12984 [1984]). Hope this helps. -- 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 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** All Science is either Physics or stamp collecting -E.Rutherford ****************************************************************************** From EWING@JCVAXA.JCU.EDU Wed May 12 16:17:00 1993 Date: Wed, 12 May 1993 21:17 EST From: "DAVID W. EWING (216) 397-4742" Subject: Second posting - 1993 Morley Medal Symposium To: chemistry@ccl.net, neomig@charles.polymer.uakron.edu Message-Id: <01GY3OTEIV5C8Y5MGX@jcvaxa> 1993 Morley Medal Symposium Honoring Professor Gilles Klopman, 1993 Morley Medalist The Morley Medal is given annually by the Cleveland Section ACS to a chemist for outstanding contributions to chemistry while residing in an area within a 250 mile radius of Cleveland. A bronze medal and $1000 are presented at the section's May meeting. This year we are pleased to announce that the awardee is Professor Gilles Klopman of Case Western Reserve University. The following is the program that will be given in his honor at John Carroll University in Cleveland on May 19. Please note that while attendance at the symposium is open to all, reservations for dinner (which includes the social hour) are required. For directions or more information contact Dave Ewing at ewing@jcvaxa.jcu.edu. A sponsor of this event is Technical Software, Inc., which distributes, among other products, HyperChem. Wednesday, May 19, 1993 John Carroll University, Room 256 Science Center 1:25 Welcoming Remarks Prof. David Ewing, Chairman, Cleveland Section ACS Prof. Herbert Rosenkranz, Symposium Chairman, Department of Environmental and Occupational Health, University of Pittsburgh 1:30 "Predicting the Crystal Structure of Organic Molecular Materials" Dr. Anne Chaka, Lubrizol Corporation 2:30 "Proton Affinities of NH3, H2O and HF: A Quest for the Basis Set Limit" Prof. Janet DelBene, Department of Chemistry, Youngstown State University 3:30 BREAK 3:45 "Construction of 3D QSARs for Antitumor DNA Intercalators" Prof. Anton Hopfinger, Department of Pharmacy, University of Illinois at Chicago 4:45 MORLEY MEDAL ADDRESS "Structure and Bioactivity of Chemicals" Prof. Gilles Klopman, 1993 Morley Medalist Department of Chemistry, Case Western Reserve University 6:00 Social Hour, Faculty Lounge, Administration Building Featuring displays by Technical Software, Inc. 7:00 Dinner, Faculty Dining Room, Student Activities Center ----> For reservations call 397-4241 by noon Mon., May 17 $18.00 (Students $8.00) 8:00 Presentation of the Morley Medal 8:15 "The Belgianization of a Chemistry Department" Prof. Irvin Krieger, Department of Chemistry, Case Western Reserve University From rickr@scripps.edu Wed May 12 11:37:58 1993 Date: Wed, 12 May 93 18:37:58 PDT From: rickr@scripps.edu (Rick Ross) Message-Id: <9305130137.AA00682@ppg.Scripps.EDU> To: chemistry@ccl.net Subject: CALLFORPAPERS LAST CALL FOR POSTER PAPERS Theoretical and Computational Chemistry Poster Session 25th Central Regional Meeting American Chemical Society Sheraton Station Square, Pittsburgh, Pennsylvania Poster session will be held on Monday evening, October 4, 1993 Poster papers are requested in all areas of fundamental and applied theoretical and computational chemistry. The Theoretical and Computational Chemistry Poster Session will follow a Theoretical Chemistry Symposium on the afternoon of October 4, 1993 and will precede a symposium on Theoretical Organic Chemistry on October 5, 1993. ****************************************************************** *********DEADLINE FOR SUBMISSIONS: MAY 17, 1993 ***************** ****************************************************************** Four copies of an abstract, with the original on a standard ACS form, must be submitted by May 17, 1993 to the program chairman: Dr. Steven H. Peterson Westinghouse Science and Technology Center 1310 Beulah Road Pittsburgh PA 15235 When submitting abstracts to the program chairman above, please note that you would like to present the poster in The Theoretical and Computational Chemistry Poster Session. This session has been arranged by the Pittsburgh and Northeastern Ohio Modeling Interest Groups. For further general information please contact Dr. Rick Ross, PPG Industries, P.O Box 9, Allison Park, PA 15101. e-mail: rickr@ppg.scripps.edu. FAX: (412) 492-5509. Phone: (412) 492-5359. From dave@carbon.chem.csiro.au Thu May 13 07:08:34 1993 Message-Id: <199305130208.AA17818@shark.mel.dit.csiro.au> Date: Thu, 13 May 93 12:08:34 EST From: (Dr.) Dave Winkler Subject: Vote for paid Internet access to QCPE etc To: chemistry@ccl.net I for one would be happy to pay an annual subscription for internet access to QCPE, with further payment for any software/docs I download (or as one subscriber suggested 1-2 CD-ROMS per year). As most other software houses charge industry more than academia I suggest QCPE did the same. I add my gratitude to Richard for his oustanding effort. 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 lim@rani.chem.yale.edu Wed May 12 18:17:08 1993 From: Dongchul Lim Message-Id: <9305130217.AA21393@rani.chem.yale.edu> Subject: Re: Tools, tools, tools, and more tools. To: chemistry@ccl.net (Computational Chemistry) Date: Wed, 12 May 93 22:17:08 EDT avs@iris95.biosym.com writes: > > From: culmer@stardent.chem.UTOLEDO.edu (Charles W. Ulmer II) > > Chemistry tools and more....They already exist. What more do you want the > > tools to do? The AVS Chemistry Viewer probably does or can do whatever you > > wish. For Example: > > > The only draw-back is > > that you must also have AVS. This is not really a draw-back though, since > > AVS is so powerful. > > When most people talk of tools, they are asking for tools that can be > incorporated in their own programs. They are looking for source code > that can be plugged into their own programs with little or no modification. > > Certainly, avs chemistry viewer does not fit that bill. Also, many in > academics look for vendor independent platform independent products. > > BTW, avs is not the only product that does all that you mentioned. > There are many other commercial programs that do the same....including > of course insightII from Biosym :-) > It would be nice to put these tools (I mean source code) together as a library, for example, "chemlib", as compared to "netlib" or "statlib". We won't need QCPE soon, if we keep depositing our code to anon ftp sites such as www.ccl.net, preferably in a library form, so that the code can be reused without much modification. One of most frequently asked questions seems to be how to convert between different file formats. If we had a library for this one, we could simply write the following pseudo code (in this case, using C) to convert gaussian zmatrix to cartsian coordinates. #include #include "chemlib.h" main(argc,argv) int argc; char **argv; { Gauss gauss; Cart cart; readgausszmatrix(argv[1],&gauss); gausstocartesian(gauss,&cart); printcartesian(cart); } This way we won't have to repeat tedious works which someone might have done already. The question is how much we are willing to share our source code... -Dongchul Lim Department of Chemistry Yale University From wsonnen@rcf.usc.edu Wed May 12 12:43:27 1993 Date: Wed, 12 May 93 19:43:27 PDT From: wsonnen@alnitak.usc.edu (Wayne Sonnen) Message-Id: <9305130243.AA25202@alnitak.usc.edu> To: chemistry@ccl.net Subject: fep/simul_annealing I have a question about resolving a hysteresis problem that i occasionally encounter while performing a free energy perturbation simulation. To clarify my problem more specifically, i perform a FEP starting at state A and perturb the system to state B. Them i reverse the direction and go from B to A. When i do the reverse direction (B to A) i sometimes get very different magnitudes for the free energy difference (of course the sign should be opposite). In performing the B to A simulation i use the end structure from the A to B simulation. My intuition suggests that i should perform an annealling on the end structure of the A to B simulation so that my starting structure for the B to A simulation does not have and biases (eg. "glass like" waters that remain from the first simulation). To do this i thought that an annealling at say 900 degree Kelvin should be sufficient. This is what i plan on starting with to see if the hysteresis problem is resolved. Another option would be to perform a simulated annealling between each step of the FEP (i.e. before i change the fep parameter lambda from for example 0.0 to 0.1 and 0.1 to 0.2,..., 0.9 to 1.0). This procedure seems to me to be the best method of eliminating and biases from previous starting structures. I plan on performing the fep simulations by both methods and comparing results and cpu times involved. Needless to say that if i could afford to perform the fep simulations sufficiently long (in practice too long) then i would not need to do any annealling and i would not observe any hysteresis. My questions are these: (1) Is there a more efficient/better/etc method? (2) Am i getting myself into other troubles by this method? Your opinions are very welcome. Thank you sincerely, Wayne Sonnen wsonnen@alnitak.usc.edu