From smori@chem.s.u-tokyo.ac.jp Mon Nov 18 00:38:25 1996 Received: from utsc.s.u-tokyo.ac.jp for smori@chem.s.u-tokyo.ac.jp by www.ccl.net (8.8.2/950822.1) id AAA00850; Mon, 18 Nov 1996 00:37:05 -0500 (EST) Received: from [133.11.6.112] (smori.chem.s.u-tokyo.ac.jp [133.11.6.112]) by utsc.s.u-tokyo.ac.jp (8.7.6+2.6Wbeta7/3.4W2) with SMTP id NAA02273; Mon, 18 Nov 1996 13:21:03 +0900 (JST) Message-Id: <199611180421.NAA02273@utsc.s.u-tokyo.ac.jp> X-Sender: smori@utsc3.chem.s.u-tokyo.ac.jp X-Mailer: Macintosh Eudora Pro Version 2.1.4-J Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-2022-JP" Date: Mon, 18 Nov 1996 13:24:00 +0900 To: "E. Lewars" From: smori@chem.s.u-tokyo.ac.jp (Seiji Mori) Subject: Re: DYNAMIC, -AL, again Cc: chemistry@www.ccl.net At 10:48 PM 96.11.17, E. Lewars wrote: > Hello, I am a native English speaker who, I hope, knows something about > using words. Basically, _dynamic_ and _dynamical_ mean the same thing. > However, _dynamical_sounds a little oldfashioned. Nowadays, dynamic is >preferred. > E. Lewars > =============== Dear Dr. Lewars, Today I posted my summary about "dynamical correlation" to CCL. Yours (and some responders') are different from my tentative conclusion. (I cited summary I wrote) >Thus, "dynamical correlation" must be used, considering not only OED and >some text books >of QM but also some replies. >Do you agree this summary? Is "dynamic correlation" also acceptable for a technical jargon? Some persons disagreed this as you see in my summary. Sincerely yours, Seiji Mori #################################################### Seiji Mori Graduate student Lab. of Physical Organic Chemistry Department of Chemistry The University of Tokyo Hongo 7-3-1, Bunkyou-ku, Tokyo 113, JAPAN. email:smori@utsc.s.u-tokyo.ac.jp smori@utsc3.chem.s.u-tokyo.ac.jp --- http://www.chem.s.u-tokyo.ac.jp/Students/smori.html #################################################### From gmercier@mail.med.upenn.edu Mon Nov 11 17:12:46 1996 Received: from mail.med.upenn.edu for gmercier@mail.med.upenn.edu by www.ccl.net (8.8.2/950822.1) id QAA19491; Mon, 11 Nov 1996 16:28:09 -0500 (EST) Received: (from gmercier@localhost) by mail.med.upenn.edu (8.6.12/8.6.12) id QAA28854 for CHEMISTRY@www.ccl.net; Mon, 11 Nov 1996 16:28:06 -0500 From: "Gustavo A. Mercier Jr" Message-Id: <199611112128.QAA28854@mail.med.upenn.edu> Subject: P convergence in NPT MD runs - summary To: CHEMISTRY@www.ccl.net Date: Mon, 11 Nov 1996 16:28:05 -0500 (EST) Hi, CClers! A few weeks ago I posted a message regarding convergence on the pressure in NPT simulations. The answers I received are below. In a nutshell, the pressure will not converge as tightly as the temperature. As explained by D. Case (and is detailed in the amber web paged mentioned below), the fluctuations will be large, ca. +/-100-150bars. Mean values close to +/-(1-10) bars can be obtained over long periods, ca. 100 ps. Bye! ***** Answers ******* ******************* If I understand correctly, what you are seeing is what is expected. At equilibrium, the "instantaneous" pressure will have what may seem like large fluctuations. These will never go away, and are related to the compressibility of the solvent. This is in the AMBER FAQ list: see http://www.amber.ucsf.edu/amber/amber.html go to "answers to commonly asked questions", and look for "constant pressure". This contains a disucssion of the behavior that one should expect, which sounds not too far from what you are seeing. ....hope this helps... ...dave case ********** Hi Gustavo, I have also had some problems like yours. I solved it by the following manner: 1.- I slightly increased the temperature for a few picoseconds, with the followinfg coupling constants: temperature 0.05 and pressure 0.5 ps. 2.- After this, I reduced the temperature to the original one, and I used a coupling constants of 0.1 and 0.5 for temperature and pressure respectivelly. If this does not work, I advise you to run a few picoseconds at constant volumen, followed of the steps 1 and 2 such as was described above. Good luck, Javier ******************************************************************************* Dr. Jose Javier Lopez Cascales | Office phone:Int-34-68-307100,ext:2190 * Departamento de Quimica-Fisica | Fax: Int-34-68-364148 * Fac. de Quimica, Uni. de Murcia, | e-mail: javier@fcu.um.es * Campus de Espinardo, 30071 Murcia, | www -> http://leonardo.fcu.um.es/~javier/* Spain | * ******************************************************************************* ************* Gustavo, As for the accuracy of the pressure calculation, it is always difficult to get very accurate value, because pressure is calculated by the virial theorem and it is calculated by subtracting a big value from a big value. The difference between the attractive and repulsive potential curve determines the value and makes the value not accurate. Moreover, you are using NPT ensemble and the particle system interacts with one dynamical system which represents external pressure. Therefore, simple oscillation may appear in the monitoring values. I think that if you add more non-linearity into the interaction between particle system and external pressure system, the equilibriation will be obtained more quickly. Best Regards, ----------------------------------------------------------------------- Masa Katagiri Queen's University of Belfast Atomistic Simulation Group http://titus.phy.qub.ac.uk School of Mathematics and Physics Tel:+44 1232 273528 Belfast BT7 1NN Fax:+44 1232 241958 Northern Ireland E-mail:m.katagiri@qub.ac.uk katagiri@nightmare.qub.ac.uk ----------------------------------------------------------------------- ******** Hi Gustavo, I have observed the same kind of behaviour. Pressure does converge more slowly and fluctuates more widely than Temperature. You could try tighter coupling; i.e. a smaller TAUP value. Note, though, tighter coupling for the Temperature (TAUTP) can lead to anomalous MD; I don't know whether the same thing can happen when the TAUP coupling constant is made very small. Cheers, Vidana C. Epa Biomolecular Research Institute, 343 Royal Parade, Parkville, Vic. 3052, AUSTRALIA. Tel: (61) - 3 - 9342 - 4300 Fax: (61) - 3 - 9342 - 4301 email: vepa@tigger.mel.dbe.csiro.au ******** Hi Gustav, as for the pressure fluctuations, if I were you I should not worry to much about that. The pressure is known to fluctuate enormously, and only the pressures averaged over sufficiently long periods (10-100ps) will have moderate fluctuations. So nothing is wrong in the system, except that if you have to tight coupling (and I think 0.1ps is already below the limit; I'd recommend 0.4ps for the pressure as the lower limit), you will not generate boltzmann-weigthed trajectories. The same holds for the T-coupling; do not couple to tightly. Hope this is of some help, Andrepeter Heiner. ================================================================= | Andreas P. Heiner | voice : +358-9-456 5105 | | VTT/Biotechnology and | fax : +358-9-455 2103 | | Food Research | e-mail: andrepeter.heiner@vtt.fi | | Biologinkuja 1, | | | PO Box 1500, Espoo | | | FIN-02044 VTT Finland | | ================================================================= ------------------------------------------------------------------------- Use a longer coupling constant for the pressure (0.5 or 1.0 ps) The fluctuations in the pressure are also dependent on the way the virial is computed: based on atoms, or based on molecules. The methods are in principle the same and do give the same averages. The atom based virial gives larger fluctuations. In our GROMACS code we have atom based virial and use at least 1.0 ps for the pressure coupling. David van der Spoel --------------------------------------------------------- EMAIL: spoel@chem.rug.nl WWW: http://rugmd0.chem.rug.nl/~spoel PHONE: 31-50-3634327 FAX: 31-50-3634800 MAIL: Nijenborgh 4, 9747 AG Groningen, The Netherlands. --------------------------------------------------------- --------------------------------------------------------- The pressure will never converge as you expect - please see amber41/Questions/pressure, or for the latest version, the version on our web site http://www.amber.ucsf.edu/amber/ Bill Ross --------------------------------------------------------- Gustavo, It is normal for the instananeous pressure to fluctuate wildly when one calculates the pressure from the "atomic" virial (there is a discussion in Allen and Tildesley about different ways to calculate pressure). If you average over 100 ps or so, then the AVERAGE pressure should be within a few atmospheres of your target. Before you invest a lot of CPU in this project, you might want to read a paper that Bernie Brooks, Rich Pastor and I published in JCP last year. JCP, 103, p 4613 (September 15, 1995 issue). There are some serious problems using the Berendsen method with an inhomogenous system, especially is SHAKE is used to maintain rigid water. Scott --------------------------------------------------------- Gustavo, < personal material deleted :-) > As regards your scientific question, I think that big fluctuations are a fact of life with constant pressure simulations - we use the same algorithm, and see the same behavior. Have you tried varying the coupling factor? I doubt that would accomplish a great deal, but I have never done (or seen) a systematic study. I cannot tell you off the top of my head if these big fluctuations are theoretically reasonable for a small ensemble of particles, or if the algorithm is to blame. Regards, Randy All opinions expressed here are mine, not my employer's ///////////////////////////////////////////////////////////////////////// \\ Randy J. Zauhar, PhD | E-mail: zauhar@tripos.com // \\ Tripos, Inc. | : zauhar@cyberjunction.com // \\ 1699 S. Hanley Rd., Suite 303 | Phone: (314) 647-1099 Ext. 3382 // \\ St. Louis, MO 63144 | // ///////////////////////////////////////////////////////////////////////// ** ** ** "If you have conceptions of things that you can have no conception ** ** of, then the conception and the thing appear to co-incide." ** ** --- C.G. Jung ** ************************************************************************* ************* Hola Gus, Perdon por la demora por si alguien te contesto primero. La respuesta facil es: no hay problema con las fluctuaciones de la presion, y son solo producto de la compresibilidad del agua (TIP3). Aca va lo que dicen los expertos sobre el tema: I assume that the pressure should stablize at approximately 1. Except 1) the physics of pressure does not lend itself to instantaneous evaluation/correction and 2) the algorithm used by Amber (scaling the box & translating everything, and then applying SHAKE or letting bond, angle, etc. potentials rectify things) is not the best available. Having most values in the range -100..100 is the best I ever hope for w/ my 8-10000 atom dna/water systems. Note by Dave Case: -- pressure fluctuations are large because the pressure-volume isotherm of a liquid is extremely steep: it takes a large pressure change to yield a small volume change, and conversely: a volume that is instantaneously slightly out of equilibrium yields a large pressure. The fluctuations in pressure are then related to this: in a thermodynamic sense (e.g. Landau & Lifshitz, "Statistical Physics" sec. 114): mean value of (delta p)**2 = -kT(dp/dV) where the derivative is evaluated at constant S (!). Rearranging the above equation, approximating (dp/dV) at constant S by 1/(dV/dp) at constant T, yields (delta p)**2 = kT/(V*beta) or delta p ~= sqrt(1/beta) where beta is isothermal compressibility and I have set kT/V to 1 bar in the final equation. If we use the macroscopic value for beta for water (roughly 4 x 10**-5 bar**-1) we obtain an rms pressure fluctation microscopic ideas: pressure fluctuations in very small volumes would probably be larger than this. Having said this, it must be noted that the procedure used in Amber (based on ideas of Berendsen) does not generate a simple thermodynamic ensemble, and (in addition) should not be expected to yield fluctuations that match the thermodynamic formula cited above. It will be interesting to see if anyone reports a systematic study of these numbers as a function of the type of simulation being done (especially on the volume of the simulated system.) --- ************ ... I have done a large amount of dynamics with periodic boundaries [in charmm]. I believe you can reasonably use about 1 to 100 atmospheres without any real perturbation. My experimental work in my job indicates little pressure effects on most systems of common interest. Besides, the RMS deviation of the pressure in the system is related to the compressability of the system and thus there is a finite and large variation in the internal pressure. The internal pressure of the system will be a strong function of the temperature at which the dynamics are conducted. One approach is to use a boundary which gives a water density very close to standard tables for the given temperature. I have noticed that sometimes this can be incorrect as the second phase (or solute) can have too low of a density. Just recently I have taken a new approach (at least it is new for me). Since standard CHARMm output does not give any idea of the internal pressure or pressure fluctuations for constant volume dynamics, I have started looking at the potential energy of the system as the boundary is decreased. That is, about 5 ps of dynamics are conducted and the average potential energy at the end is recorded. The periodic boundary is then reduced by 0.1 Angstroms and the dynamics restarted for another 5 ps. The procedure is repeated for for several steps of boundary reduction. One will observe a sharp increase in potential energy as the system reaches a pressure of about 1 - 10 atmospheres. This procedure assumes that the initial periodic boundary was too large for the system being studied. In addition, I should mention that the size of my systems range from about 40 Ang on a cubic edge to 60 Ang. on a cubic edge. You may have to take smaller step sizes than I do. --- User dialogue with Dave Case: > in Sander output files (standard name: mdout and mden) values > of the pressure are reported. I'm wandering in which unit > this values are given. I would gess "mbar", but maybe > somebody knows it exactly. A futher problem with the pressure is > that I have got negative values. What does negative values mean? > Is the pressure given as relative pressure? Pressures are reported in bars; negative pressures indicate that the system would like to contract its volume, i.e. that an outward force on the walls of the container would be required to keep the system at its current volume; positive pressure is the opposite: the system would like to increase its volume, and an inward-directed external force would be required to keep the system at its current volume. > As the reported pressure is the absolute pressure I would suggest to > interpret the values in the following way: > > If the instantaneous pressure is greater than PRES0 the system > wants to increase is volume (overpressure); if the instantaneous pressure > is lower than PRES0 but greater than zero the system wants to contract its > volume (subpressure); an instantaneous pressure below zero > is an artifact due to the way the virial term is calculated. I must say that I don't agree with your interpretation.... The pressure is computed from the virial in the standard way. The only influence of PRES0 is on how the volume of the system will respond: if the instantaneous pressure is greater than PRES0, the MD algorithm in Amber will slowly increase the volume of the system; vice-versa if the instantaneous pressure is below PRES0. The *interpretation* of the computed pressure is independent of the value of PRES0. There is nothing "wrong" with negative pressures, and they need not arise from errors or truncations in the virial calculation. The equation of state of a rare gas fluid (for example) has substantial regions of density and temperature where the equilibrium pressure is negative [see, for example, chapter 14 of McQuarrie's "Statistical Mechanics", or other textbooks.] One of the tests I made (many years ago) to verify the correctness of the way Amber calculates pressure terms was to reproduce these equations of state for a Lennard-Jones 6-12 fluid. [One can hope that bugs have not crept in since then!] -- Adrian E. Roitberg ======================================================================== National Institute for | Phone: (301) 975-4469. Fax (301) 330-3447 Standards and Technology | E-mail : adrian@nist.gov Bioprocess Engineering Group | Building 222, A-353 | URL : http://www.chem.nwu.edu/~adrian Gaithersburg, MD 20899 | ======================================================================== -- ("`-/")_.-'"``-._ Gustavo A. Mercier,Jr.,MD,PhD (. . `) -._ )-;-,_() Division of Nuclear Medicine (v_,)' _ )`-.\ ``- Dept. of Radiology _;- _,-_/ / ((,' University of Pennsylvania ((,.-' ((,/ 3400 Spruce St. gmercier@mail.med.upenn.edu Philadelphia, PA 19104 215-662-3069/3091 fax: 215-349-5843 From szilagyi@almosvein.hu Mon Nov 11 12:18:26 1996 Received: from elod.vein.hu for szilagyi@almosvein.hu by www.ccl.net (8.8.2/950822.1) id LAA17571; Mon, 11 Nov 1996 11:57:18 -0500 (EST) Received: by elod.vein.hu (5.65/DEC-Ultrix/4.3) id AA01136; Mon, 11 Nov 1996 17:57:05 +0100 Received: from szilagyi.chemie.uni-marburg.de (pc15114.Chemie.Uni-Marburg.DE) by almos.venet (5.x/SMI-SVR4) id AA25300; Mon, 11 Nov 1996 18:54:24 +0100 Message-Id: <32875A6A.6639@almosvein.hu> Date: Mon, 11 Nov 1996 17:55:06 +0100 From: "Szilagyi, Robert K." Reply-To: szilagyi@almos.vein.hu Organization: =?iso-8859-1?Q?M=FCller?= Laboratory, Dept.Org.Chem., =?iso-8859-1?Q?Uni=2DVeszpr=E9m?=, HU To: chemistry@www.ccl.net Subject: Unit of the force constant within the G94 Dear Members, I am interested in the unit of force constants given in the output file of a Gaussian94 calculation. In the heading part of a frequency analyses the mDyne/A is given, but I receive nearly twice as it would be expected. I am tempting to say, that the unit is mDynd/Bohr instead of mDyn/A. Am I right? -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Robert K. Szilagyi Mueller Laboratory ph.d. student Dept. Organic Chemistry University of Veszprem szilagyi@almos.vein.hu Veszprem, H-8201 POB. 158; Egyetem u. 10. Phone: +36 88 422022 extn. 395 HUNGARY Mobile: +36 20 461413 (temp. susp.) Fax: +36 88 427492 http://mm1.vein.hu/ ====================================================================== ********** All opinions are my own, NOT my employer's ! ********** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From xiannong@pauling.chem.uga.edu Mon Nov 11 12:18:33 1996 Received: from charon.chem.uga.edu for xiannong@pauling.chem.uga.edu by www.ccl.net (8.8.2/950822.1) id LAA17281; Mon, 11 Nov 1996 11:13:14 -0500 (EST) Received: from pauling.chem.uga.edu ( [128.192.5.50]) by charon.chem.uga.edu (8.7.4/8.6.9) with SMTP id LAA13552 for ; Mon, 11 Nov 1996 11:16:38 -0500 Date: Mon, 11 Nov 1996 11:13:11 -0500 (EST) From: Xiannong Chen To: chemistry@www.ccl.net Subject: summary of using bar code system with chemical database Message-ID: Here are all the e-mail I got about using bar code system with chemical database. I thank all the people who helped me. Xiannong =========================================================== Date: Thu, 07 Nov 1996 15:33:44 -0500 From: Heather Hunter To: xiannong@CCMSD.chem.uga.edu Subject: CCL Question Dr. Chen I saw your message on the CCL email this morning. Usually I do not respond to messages, being a commercial software company I think the bulletin board does a great job, and I do not wish to impose on line. Tripos has a desktop product called BioStar that might help you solve your problem of keeping track of your compounds. I can fax over some tech. notes for your if you are interested. Just drop me a email note. Thank you Heather ====================================================== Dear Xiannong, I asked some of my coworkers at MDL about their experiences with using barcodes in ISIS/Base and here is a summary of their responses. I hope this helps you get started. Bob Snyder Product Marketing Manager Database Business Unit MDL Information Systems ======================================================================== >From Bill Hackett (billh@mdli.com): I downloaded a barcode font for Mac from the Net for one of PaulM's customers. There is a font for PC; I've seen references to it. Let me know if you want the Mac font; I've got it on my machine. You can get the PC font in hits from Lycos with the search "macintosh barcode font". After that, its just a matter of changing the font for the numeric data. >From Frank Schaffer (franksch@ag.mdli.com): We have here in the AG developed an inventory system which tracks compounds and bottles containing these compounds as well as ordering for such compounds. It is based on ISISBASE and has indeed a barcoding interface. From this application you can print barcodes for bottles or for labels with user information (user privileges). It uses a barcode reader which is connected between the keyboard and the PC for regular one by one transactions of bottles. The system is also able to interact with a barcode scanner which collects multiple barcodes in it's memory and then sends them to the system (e.g. for updating bottles in a lab). The system also works with a balance to automatically check the contents of bottles. All the communication between this hardware pieces is done via the serial port using an external library (dll) which enables PL to write or read the com ports. >From Michael Edwards (michaele@mdli.com): Several company's have inserted bar code readers into their systems on consulting projects. We have used wedge-types and stand-alone systems. There are a lot of variables and trade off to consider before giving advice. >From Mitch Miller (mitch@mdli.com): Depending on what you want to do with barcodes, it can be pretty simple. If you just want to print barcode labels, or use barcodes to enter compound numbers, it's quite simple. To print barcodes, just set up one box to retrieve the company number in text format with a prefill trigger to take the text value, prepend/append an asterisk (required for 3 of 9, the most popular barcode font). The second box should have the font set to 3 of 9 or whatever. Then just print the form. Barcodes can be used to wand in a compound number just as if you were typing at the keyboard with no customization. ========================================================= -- Dear Xiannong Further to your email message of Thursday 7th November. We at Synopsys Scientific Systems Ltd develop chemical software which transforms Microsoft products into chemically intelligent databases and spreadsheets. The major area of interest to you may be Accord for Access, our chemical, relational, multi-user database. This software allows you to store and search chemical structures by exact, sub-structure and similarity all within the powerful environment of Microsoft Access. This Microsoft Access environment may be the ideal tool you are looking for as a barcoding system. We also develop Accord for Excel, the only true chemical spreadsheet on the market, allowing chemical data analysis all within the powerful environment of Microsoft Excel. If you would like to find out more about our suite of chemical software please contact me on any of the numbers below. I look forward to hearing from you. Yours sincerely Mark G. Vero Sales Executive E-Mail: mark@synopsys.co.uk Tel: +44 113 293 7339 ================================================================= Xiannong Chen wrote: > > Hi, Dear Netters: > > I work for a small pharmaceutical company. We want to use barcode to keep > track of our compounds. We use IsisBase to manage structural as well as > other information. Does anyone have experience with using barcode system > integrated with IsisBase or other database, spreadsheet software? > > Any suggestion about chemical inventary control with any software system > is appreciated. > > THank you very much. I am not on the list. Please sned your response to me > at xiannong@ccmsd.chem.uga.edu > > Xiannong > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: xiannong@pauling.chem.uga.edu > -- Original Sender From: Address: xiannong@CCMSD.chem.uga.edu > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html I have put together a complete barcode system to track all of our commercial chemicals from cradle to grave. We use Daylight software and have barcode scanners in each lab. The barcode readers are hooked up to a pc that processes the data and then sends it over ethernet via an NFS mounted drive to our workstation. This makes it easily expandable as we can drop in new readers and pc anywhere we have ethernet ( which is everywhere in our company now). The data is processed into our ACD database which we buy from Daylight already in their format. I would think this system would be easily adaptable to your system using ISIS. Please call me for more info. -- Wayne Weber (weber@rl.cldx.com) Senior Dyemeister Johnson & Johnson Clinical Diagnostics Phone 716-453-5717 FAX 716-453-5689 From armel@fluo.univ-lemans.fr Tue Nov 12 09:31:20 1996 Received: from ciripa.idris.fr for armel@fluo.univ-lemans.fr by www.ccl.net (8.8.2/950822.1) id IAA23305; Tue, 12 Nov 1996 08:47:55 -0500 (EST) Received: from fluo.univ-lemans.fr (fluo.univ-lemans.fr [193.52.30.128]) by ciripa.idris.fr (8.8.2/8.8.0) with SMTP id OAA21671 for ; Tue, 12 Nov 1996 14:47:25 +0100 Received: from pcb4122.univ-lemans.fr by fluo.univ-lemans.fr (AIX 3.2/UCB 5.64/4.03) id AA16566; Tue, 12 Nov 1996 09:27:15 +0100 Message-Id: <1.5.4.32.19961112083022.00667778@fluo.univ-lemans.fr> X-Sender: armel@fluo.univ-lemans.fr (Unverified) X-Mailer: Windows Eudora Light Version 1.5.4 (32) Date: Tue, 12 Nov 1996 09:30:22 +0100 To: chemistry@www.ccl.net From: Armel Le Bail Subject: Re: CCL:M:HPGL files creasted by MOPAC DENSITY Dear All, Andrea wrote: >I am having a slight problem dealing with the electron density HPGL files >generated by MOPAC DENSITY. I am able to read them into WORD but I would >like to change the colour of the contours - for instance to dotted >and solid both in black for positive and negative electron densities. > >Does anybody know of a way to do this - for instance are there lines >in the HPGL files that I can edit? You can edit HPGL files. Colours are governed by "pen numbers" defined in the HPGL files by: ;SPn; with n=1 or 2 or ... and the color remains valid for all subsequent orders up to the next SP in the HPGL file. Generally SP1 is for black. You have just to edit the file, search for SP and change the pen numbers at your convenience. Armel Armel Le Bail, Laboratoire des Fluorures URA CNRS 449 Faculte des Sciences, Universite du Maine, F-72017 Le Mans, France http://fluo.univ-lemans.fr:8001/ and/or http://pcb4122.univ-lemans.fr/ From ccl@www.ccl.net Tue Nov 12 10:13:03 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.2/950822.1) id KAA24211; Tue, 12 Nov 1996 10:06:14 -0500 (EST) Received: from tlon.unq.edu.ar for seba@tlon.unq.edu.ar by bedrock.ccl.net (8.8.2/950822.1) id KAA18998; Tue, 12 Nov 1996 10:06:12 -0500 (EST) Received: from alien.unq.edu.ar (alien10.unq.edu.ar [170.210.73.80]) by tlon.unq.edu.ar (8.8.2/8.6.10) with SMTP id MAA32537 for ; Tue, 12 Nov 1996 12:13:25 -0300 Date: Tue, 12 Nov 1996 12:13:25 -0300 Message-Id: <199611121513.MAA32537@tlon.unq.edu.ar> X-Sender: seba@tlon.unq.edu.ar X-Mailer: Windows Eudora Versión 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable To: chemistry@ccl.net From: seba@unq.edu.ar (sebastian fernandez) Subject: OPLS parameters for acetonitrilo Hi! Does anybody know OPLS/AMBER parameters for acetonitrilo CH3CN? I would really apperciate any information. Thanks a lot. Sebasti=E1n Fern=E1ndez Alberti Centro de Estudios e Investigaciones Univ. Nacional de Quilmes Saenz Pe=F1a 180, 1876 Bernal, Prov. Buenos Aires Argentina From ccl@www.ccl.net Tue Nov 12 11:13:03 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.2/950822.1) id KAA24668; Tue, 12 Nov 1996 10:57:45 -0500 (EST) Received: from wugate.wustl.edu for reichertd@mirlink.wustl.edu by bedrock.ccl.net (8.8.2/950822.1) id KAA20035; Tue, 12 Nov 1996 10:57:45 -0500 (EST) Received: from mirlink.wustl.edu (mirlink.wustl.edu [128.252.155.1]) by wugate.wustl.edu (8.7.5/8.7.3) with SMTP id JAA21890 for ; Tue, 12 Nov 1996 09:57:46 -0600 Message-Id: <199611121557.JAA21890@wugate.wustl.edu> Date: 12 Nov 1996 09:55:55 -0600 From: "David Reichert" Subject: Multiprocessor Software To: "Comp Chem List" Dear CCLers; A recent summary by Carles Colominas on perfomence benchmarks on various systems, indicted some impressive results for Pentium Pro systems. This got me to wondering wether anyone has been developing modeling software (MM, semi-emp, or ab initio) for multiprocessor PowerPC based systems. Macintosh based systems from Apple, UMAX, and Daystar are all shipping systems with at least 2 180MHz 604e processors with faster ones coming in the near future, and of course there is the BeBox as well with multi-processors. It seems to me that with this kind of CPU power, workstations costing 2 - 4 times as much don't make all that much sense. I'd be interested in hearing people's thoughts and or experiences with these type of systems, and will post a summary if there is any interest. Thanks, David E. Reichert, Ph.D. Mallinckrodt Inst. of Radiology Div. Radiation Sciences phone: (314)362-8461 fax: (314)362-9940 e-mail: reichertd@mirlink.wustl.edu From polowin@hyper.hyper.com Tue Nov 12 11:13:09 1996 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.8.2/950822.1) id KAA24485; Tue, 12 Nov 1996 10:34:40 -0500 (EST) Received: from hyper.hyper.com (hyper.hyper.com [206.51.24.9]) by www.hyper.com (8.6.12/8.6.12) with SMTP id KAA10953; Tue, 12 Nov 1996 10:39:58 -0500 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:CHEMISTRY@www.ccl.net id AA07870; Tue, 12 Nov 96 10:39:51 -0500 Date: Tue, 12 Nov 96 10:39:51 -0500 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9611121539.AA07870@hyper.hyper.com> To: Charilaos Linaras , CHEMISTRY@www.ccl.net Subject: Re: CCL:Energy of Solvation for Proteins > From: Charilaos Linaras > Date: Fri, 8 Nov 1996 12:07:48 -0500 (EST) > > I would like to have your suggestions on any existing > programs for the calculation of the energy of solvation > of proteins. You can do this with any software that can calculate the energy of the solvated structure (including our HyperChem software). Calculate the energy of the system, and save the file. Then delete the protein and calculate the energy of the solvent molecules; bring the file back, delete the solvent, and calculate the energy of the protein without solvation. The difference between the first value and the sum of the latter two is the interaction energy between the protein and the solvent. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ From iris@indigo1.kist.re.kr Wed Nov 13 01:37:20 1996 Received: from indigo1.kist.re.kr for iris@indigo1.kist.re.kr by www.ccl.net (8.8.2/950822.1) id AAA01504; Wed, 13 Nov 1996 00:42:58 -0500 (EST) Received: by indigo1.kist.re.kr (940816.SGI.8.6.9/940406.SGI) for chemistry@www.ccl.net id OAA02912; Wed, 13 Nov 1996 14:43:47 -0800 Date: Wed, 13 Nov 1996 14:43:47 -0800 From: iris@indigo1.kist.re.kr (Taesung Moon) Message-Id: <199611132243.OAA02912@indigo1.kist.re.kr> To: chemistry@www.ccl.net Subject: Determinant of Hessian matrix Dear netters, I have tried to evaluate the determinant of Hessian matrix evaluated using Discover3.0. The Hessian is positive definite at minimun conformation but some determinants are negative in my cases. I carried out full minimization using Quasi-Newton or Newton-Raphson method until maximum derivative is less than 0.00001. For example, --------------------------------------------------------- the determinant of Hessian matrix ---------------------------------- method butane alanine dipeptide --------------------------------------------------------- Quasi-Newton negative positive Newton-Raphson positive negative --------------------------------------------------------- Please let me know the reason. Thanks. ------------------------- moon@kistmail.kist.re.kr. From yschickel@beilstein.com Thu Nov 14 08:37:43 1996 Received: from news.ossinc.net for yschickel@beilstein.com by www.ccl.net (8.8.2/950822.1) id HAA10147; Thu, 14 Nov 1996 07:55:34 -0500 (EST) Received: from news.ossinc.net ([194.152.36.18]) by news.ossinc.net (8.6.12/8.6.9) with SMTP id GAA15786 for ; Thu, 14 Nov 1996 06:57:04 -0700 Date: Thu, 14 Nov 1996 06:57:04 -0700 Message-Id: <199611141357.GAA15786@news.ossinc.net> X-Sender: yschickel@mail.beilstein.com X-Mailer: Windows Eudora Light Version 1.5.2 To: chemistry@www.ccl.net From: Yvonne Schickel Subject: CHEST and Beilstein sign agreement for all UK Higher Education On November 1st 1996, Professor David VandeLinde, Vice Chancellor of the University of Bath, and Professor Dr Clemens Jochum of Beilstein signed a 5 year agreement for the provision of the Beilstein and Gmelin Databases to the UK Higher Education sector. Professor VandeLinde signed on behalf of CHEST (Combined Higher Education Software Team) who negotiated the agreement, and are based at the University of Bath. For further information, please visit the Beilstein Web Pages on URL: http://beilstein.com. *********************************** Yvonne Schickel Sales & Marketing Coordinator Beilstein Informationssysteme GmbH phone: +49-69-7917 410 fax: +49-69-7917 636 e-mail: yschickel@beilstein.com http://www.beilstein.com *********************************** From ccl@www.ccl.net Fri Nov 15 14:37:54 1996 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.2/950822.1) id OAA20206; Fri, 15 Nov 1996 14:28:22 -0500 (EST) Received: from gardel.psc.edu for mmadrid@psc.edu by bedrock.ccl.net (8.8.2/950822.1) id OAA19325; Fri, 15 Nov 1996 14:28:21 -0500 (EST) Received: (from mmadrid@localhost) by gardel.psc.edu (8.7.4/8.7.3 PSC 1996/02/27 lambert) id OAA24071 for chemistry@ccl.net; Fri, 15 Nov 1996 14:28:31 -0500 (EST) From: "Marcela Madrid" Message-Id: <9611151428.ZM24069@gardel.psc.edu> Date: Fri, 15 Nov 1996 14:28:31 -0500 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: chemistry@ccl.net Subject: CCL: Macromolecular Crystallography Workshop The Pittsburgh Supercomputing Center is offering a workshop on "Computational Macromolecular Crystallography", June 25-28, 1997. The workshop will provide hands-on lectures and tutorials for the programs PHASES and X-PLOR(online). Some of the recent features of X-PLOR(online) will be discussed, including probabilistic MAD phasing and torsion-angle molecular dynamics. The theory and practical considerations of isomorphous replacement will be described. Several sample data sets with worked examples will be provided, including a MAD data set. Maximum likelihood structure refinement will be approached through a discussion of the basic theory, a description of the implementation within X-PLOR, and hands-on exercises. Workshop instructors will be Prof. Axel Brunger, Yale University, Prof. Randy Read, University of Alberta, and Prof. William F. Furey, University of Pittsburgh. In addition to the exercises provided, participants are also encouraged to bring their own data, if available, to work on and discuss with the instructors. For more information about this workshop, please check the URL http://www.psc.edu/biomed/workshops/wk-97/crys97/crys97.html To apply for the workshop, please submit the following application materials: PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE Computational Macromolecular Crystallography Application Form Name: ________________________________________________________________ Affiliation: ________________________________________________________________ Address: ________________________________________________________________ (Business) ________________________________________________________________ ________________________________________________________________ (Home) ________________________________________________________________ Telephone: ____________________________ ______________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:___________________ Electronic Mail Address:_______________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: ___________________________________________________ How did you learn about this workshop:_________________________________________ ******************************************************************************** REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vitae. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by May 14, 1997 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein biomed@psc.edu, or (412)268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From sotot@mbox.kyoto-inet.or.jp Sat Nov 16 12:38:05 1996 Received: from gwA.kyoto-inet.or.jp for sotot@mbox.kyoto-inet.or.jp by www.ccl.net (8.8.2/950822.1) id LAA24201; Sat, 16 Nov 1996 11:51:25 -0500 (EST) Received: from mbox.kyoto-inet.or.jp (mbox.kyoto-inet.or.jp [202.245.160.132]) by gwA.kyoto-inet.or.jp (8.7.5/3.4W4-08/19/96) with ESMTP id BAA28878 for ; Sun, 17 Nov 1996 01:51:23 +0900 Received: from [202.245.160.202] (pppL010.kyoto-inet.or.jp [202.245.160.202]) by mbox.kyoto-inet.or.jp (8.7.5/3.4W4-10/02/96) with SMTP id BAA25915 for ; Sun, 17 Nov 1996 01:51:19 +0900 Date: Sun, 17 Nov 1996 01:51:19 +0900 Message-Id: <199611161651.BAA25915@mbox.kyoto-inet.or.jp> To: chemistry@www.ccl.net From: sotot@mbox.kyoto-inet.or.jp (Tomoko Niwa) X-Sender: sotot@mbox.kyoto-inet.or.jp (Unverified) Subject: Re: CCL:Simulated Annealing Return-Receipt-To: sotot@mbox.kyoto-inet.or.jp adre@cdac.ernet.in wrote: > > Dear Sirs : > We are looking for optimization routines incorporating > Simulated Annealing. Are there any web sites or references? > Thank You, > URL for Press, Teukolsky, Vetterling, Flannery, Numerical Recipes in C, 2nd ed p444 is http://nr.harvard.edu/nr/nrhome.html Simulated Annealing program in Fort77 is also available. best regards _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ Tomoko Sotomatsu Niwa, Ph.D. sotot@mbox.kyoto-inet.or.jp R &D Division Nippon Shinyaku Co., Ltd. Nishiohji Hachijo Minami-ku Kyoto, 601 Japan Tel +81-75-321-1111 Fax +81-75-321-9038 _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From uacheva@nic.savba.sk Fri Nov 15 05:19 EST 1996 Received: from nic.savba.sk for uacheva@nic.savba.sk by www.ccl.net (8.8.2/950822.1) id FAA16972; Fri, 15 Nov 1996 05:19:30 -0500 (EST) Received: (from uacheva@localhost) by nic.savba.sk (8.7.3/8.7.3) id LAA28504; Fri, 15 Nov 1996 11:21:13 +0100 (MET) From: Eva Scholtzova Message-Id: <199611151021.LAA28504@nic.savba.sk> Subject: Makefile for G94 on Pentium Pro 200 To: chemistry-request@www.ccl.net Date: Fri, 15 Nov 1996 11:21:13 +0100 (MET) Cc: uacheva@nic.savba.sk (Eva Scholtzova) X-Mailer: ELM [version 2.4ME+ PL26 (25)] Dear Netters, We are urgently looking for Makefile to install Gaussian 94 under Linux on Pentium Pro 200. Another question is as follows: we are looking for Linux driver for IOMEGA ZIP (if exists). Thank you very much in advance. Greetings, Eva -- ############################################################### # Eva Scholtzova # # Ph.D. Student # # Institute of Inorganic Chemistry # # Slovak Academy of Sciences # # Dubravska cesta 9 uacheva@savba.sk # # SK-84236 Bratislava Fax (42-7) 373-541 # # Slovakia Phone (42-7) 378-2835 # ############################################################### From elazhary@theochem.uni-stuttgart.de Mon Nov 18 03:38:29 1996 Received: from artemis.rus.uni-stuttgart.de for elazhary@theochem.uni-stuttgart.de by www.ccl.net (8.8.2/950822.1) id DAA04836; Mon, 18 Nov 1996 03:07:28 -0500 (EST) Received: from tc8.theochem.uni-stuttgart.de (tc8.theochem.uni-stuttgart.de [129.69.55.128]) by artemis.rus.uni-stuttgart.de with SMTP id JAA23187 (8.6.13/IDA-1.6 for ); Mon, 18 Nov 1996 09:06:43 +0100 Message-ID: <199611180806.JAA23187@artemis.rus.uni-stuttgart.de> Received: by tc8.theochem.uni-stuttgart.de (1.38.193.4/16.2/BelWue-2.1) id AA10966; Mon, 18 Nov 1996 09:06:43 +0100 From: "Dr. Adel El-Azhary" Subject: DFT vibrational frequencies of anions To: chemistry@www.ccl.net Date: Mon, 18 Nov 96 9:06:43 MET Mailer: Elm [revision: 70.85] Dear Netters: Does anyone know of vibrational study of anions by the DFT method other than that reported in: S. R. Langhoff, J. Phys. Chem., 100 (1996) 15073. Please send all replies to me and I will summarize to the list. Thank you in advance for your cooperation. Adel El-Azhary Institute for Theortical Chemistry Stuttgart University Stuttgart, Germany e-mail: elazhary@theochem.uni-stuttgart.de From chpajt@bath.ac.uk Mon Nov 18 04:40:11 1996 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.8.2/950822.1) id EAA07332; Mon, 18 Nov 1996 04:03:23 -0500 (EST) Received: from bath.ac.uk (actually host midge.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Mon, 18 Nov 1996 09:02:58 +0000 Date: Mon, 18 Nov 1996 09:02:54 +0000 (GMT) From: A J Turner To: Taesung Moon cc: chemistry@www.ccl.net Subject: Re: CCL:Determinant of Hessian matrix In-Reply-To: <199611132243.OAA02912@indigo1.kist.re.kr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! There are too resons that I can think of. First - the optimiser is not finding a minimum. I cannot say much on this - as I do not know the particular implementation. Second - the hessian is nearly singular - and the numerical noise is causing negative eign values to turn up. My I suggest reoptimisation of the stationary points which you have obtained - using a first order (conj grad or sd) method. Hope it helps Alex ------------------------------------------------------------------- |Alexander J Turner |A.J.Turner@bath.ac.uk | |Post Graduate |http://www.bath.ac.uk/~chpajt/home.html| |School of Chemistry |+144 1225 8262826 ext 5137 | |University of Bath | | |Bath, Avon, U.K. |Field: QM/MM modeling | ------------------------------------------------------------------- From granthan@islandnet.com Mon Nov 18 05:38:29 1996 Received: from mail for granthan@islandnet.com by www.ccl.net (8.8.2/950822.1) id FAA07942; Mon, 18 Nov 1996 05:26:29 -0500 (EST) Received: from i2-24.islandnet.com [198.53.172.24] by mail (Smail3.2) with smtp id m0vPQu5-0006e1C for ; Mon, 18 Nov 1996 02:26:13 -0800 (PST) Message-Id: Date: Mon, 18 Nov 1996 02:26:13 -0800 (PST) X-Sender: granthan@mail.islandnet.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@www.ccl.net From: granthan@islandnet.com (Grant Handford) Subject: tar files Dear CCLer's:- I am a new student of Computational Chemistry and I am just getting started at using a computer for e-mail, Internet, etc. I need to know how to convert compressed tar files into usable form. If you could help me it would be very much appreciated. Thank You. Sincerely, Grant. E-mail:- granthan@islandnet.com From shin@hermes.fju.edu.tw Mon Nov 18 05:40:51 1996 Received: from hermes.fju.edu.tw for shin@hermes.fju.edu.tw by www.ccl.net (8.8.2/950822.1) id FAA07859; Mon, 18 Nov 1996 05:10:19 -0500 (EST) Received: by hermes.fju.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA10771; Mon, 18 Nov 1996 17:43:42 +0800 Date: Mon, 18 Nov 1996 17:43:42 +0800 From: shin@hermes.fju.edu.tw (Shin-Inn Chen) Message-Id: <9611180943.AA10771@hermes.fju.edu.tw> To: chemistry@www.ccl.net Subject: how to execute g94opt utility? dear netters: i have some trouble when using gaussian94. my problem is: how to execute g94opt utility( in user's reference it is "gauopt") i create a template file and execute by command: " g94opt < filename.com > filename.log " the program create fork.com file and then stoped with the followin error messages bsh: fork.logD/,^UH: 0402-011 Cannot create the specified file. Error termination in NtrErr: ntran open failure returned to fopen ------------------------------------------------------------------------------- thanks a lot for your help!!!!!!! E-mail: shin@hermes.fju.edu.tw shin 1996/11/14 From nieder@rs3.thch.uni-bonn.de Mon Nov 18 06:38:31 1996 Received: from IBM.rhrz.uni-bonn.de for nieder@rs3.thch.uni-bonn.de by www.ccl.net (8.8.2/950822.1) id GAA08424; Mon, 18 Nov 1996 06:38:05 -0500 (EST) Received: from rs3.thch.uni-bonn.de by IBM.rhrz.uni-bonn.de (IBM VM SMTP V2R2) with TCP; Mon, 18 Nov 96 12:38:05 MEZ Received: by rs3.thch.uni-bonn.de (AIX 3.2/UCB 5.64/4.03) id AA21783; Mon, 18 Nov 1996 12:37:59 +0100 From: nieder@rs3.thch.uni-bonn.de (Christoph Niederalt) Message-Id: <9611181137.AA21783@rs3.thch.uni-bonn.de> Subject: G94:disc space exceeded during AO/MO transformation To: chemistry@www.ccl.net Date: Mon, 18 Nov 96 12:37:58 MEZ X-Mailer: ELM [version 2.3 PL2] Dear Netters, I'm having a problem with Gaussian94 attempting to run a CIS single point calculation. Using 238 basis functions, the 2GB disc space is exceeded during the transformation of the AO integrals to the MO basis in link l804. The output ends with the message: Semi-Direct transformation. ModeAB= 4 MOrb= 24 LenV= 2893898 LASXX= 31075194 LTotXX= 31075194 LenRXX= 62877810 LTotAB= 31802616 MaxLAS= 40782816 LenRXY= 0 NonZer= 93953004 LenScr= 143823404 LnRSAI= 40782816 LnScr1= 64068122 MaxDsk= -1 Total= 311552152 SrtSym= T File extend in NtrExt1 failed. File extend in NtrExt1 failed If I try the keyword "transformation=fulldirect", I have not enough memory. With the keyword "cis=direct" the transformation is avoided and everything works fine but I need the MO's !!! Can anyone suggest a trick to complete the transformation? Thank you very much for any help, Christoph Niederalt nieder@rs3.thch.uni-bonn.de From Eugene.Leitl@lrz.uni-muenchen.de Mon Nov 18 07:38:31 1996 Received: from sunsrv5.lrz-muenchen.de for Eugene.Leitl@lrz.uni-muenchen.de by www.ccl.net (8.8.2/950822.1) id GAA08495; Mon, 18 Nov 1996 06:51:07 -0500 (EST) Received: from sun2.lrz-muenchen.de by sunsrv5.lrz-muenchen.de; Mon, 18 Nov 96 12:50:13 +0100 Received: by sun2.lrz-muenchen.de (5.x/SMI-SVR4) id AA11639; Mon, 18 Nov 1996 12:50:10 +0100 Date: Mon, 18 Nov 1996 12:50:08 +0100 (MET) From: Eugene Leitl X-Sender: ui22204@sun2 To: Grant Handford Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:tar files In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 18 Nov 1996, Grant Handford wrote: > Dear CCLer's:- > > I am a new student of Computational Chemistry and I am just getting > started at using a computer for e-mail, Internet, etc. I need to know how > to convert compressed tar files into usable form. If you could help me it > would be very much appreciated. Thank You. hint: type man tar at unix prompt. Q&D: If you're using GNU tar: tar xzvf foo.tar.gz (means: eXtract unZip Verbose F?) For vanilla tar: gzip -d foo.tar.gz (means: gnuzip -decompress ) (or gunzip foo.tar.gz) then tar xvf foo.tar hope this helps, 'gene P.S. to create an archive: tar cvf foo.tar YourDirectory then gzip -9 foo.tar to create a compressed version of it. Can also be done with pipes, and GNU tar can do it one go, if you use the z option. > Sincerely, > Grant. > E-mail:- granthan@islandnet.com > From jochen@uni-duesseldorf.de Mon Nov 18 08:38:40 1996 Received: from sirene.rz.uni-duesseldorf.de for jochen@uni-duesseldorf.de by www.ccl.net (8.8.2/950822.1) id IAA08852; Mon, 18 Nov 1996 08:00:37 -0500 (EST) Received: from sunserver1.rz.uni-duesseldorf.de by sirene.rz.uni-duesseldorf.de with SMTP (PP) id <27597-0@sirene.rz.uni-duesseldorf.de>; Mon, 18 Nov 1996 13:48:39 +0000 Received: from localhost by sunserver1.rz.uni-duesseldorf.de (SMI-8.6/SMI-SVR4) id NAA03824; Mon, 18 Nov 1996 13:48:36 +0100 Date: Mon, 18 Nov 1996 13:48:35 +0100 (MET) From: =?ISO-8859-1?Q?Jochen_K=FCpper?= X-Sender: jochen@sunserver1 To: Grant Handford cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:tar files In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 18 Nov 1996, Grant Handford wrote: :> I am a new student of Computational Chemistry and I am just getting :>started at using a computer for e-mail, Internet, etc. I need to know how :>to convert compressed tar files into usable form. If you could help me it :>would be very much appreciated. Thank You. For a Unix system: Use the f. man pages !!! Do either tar xzf or gzip -d // this gives you an uncompressed archive tar xf Greetings ----------------------------------------------------------------------- Jochen Kuepper Heinrich-Heine-Universitaet Duesseldorf jochen@uni-duesseldorf.de Institut fuer Physikalische Chemie I Universitaetsstrasse 26.43.02.29 phone ++49-211-8113681 40225 Duesseldorf fax ++49-211-8115195 Germany ----------------------------------------------------------------------- From mtulio@dragoeiro.uma.pt Mon Nov 18 09:38:32 1996 Received: from phobos.rccn.net for mtulio@dragoeiro.uma.pt by www.ccl.net (8.8.2/950822.1) id JAA09424; Mon, 18 Nov 1996 09:22:27 -0500 (EST) From: Received: from dragoeiro.uma.pt by phobos with SMTP (PP); Mon, 18 Nov 1996 14:20:52 +0000 Received: by dragoeiro.uma.pt (5.4R3.00/200.1.1.4) id AA19198; Mon, 18 Nov 1996 14:18:48 GMT Date: Mon, 18 Nov 1996 14:18:48 GMT Message-Id: <9611181418.AA19198@dragoeiro.uma.pt> Received: from quim96(193.136.232.96) by dragoeiro via smap (V1.3) id sma019168; Mon Nov 18 14:18:21 1996 X-Sender: mtulio@dragoeiro.uma.pt X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: granthan@islandnet.com (Grant Handford) Subject: Re:tar files Cc: CHEMISTRY@www.ccl.net At 02:26 18-11-1996 -0800, Grant Handford wrote: > I need to know how >to convert compressed tar files into usable form. If you could help me it >would be very much appreciated. If you have winzip, just do it as you would do with an ordinary zip file. If you don't try PC/TCP Archiver or similar program. Under Unix just use the tar command: tar -xvf (to extract files) Best regards Mario Tulio Rosado Dept. of Chemistry University of Madeira PORTUGAL From herrmann@hermes.informatik.uni-stuttgart.de Mon Nov 18 09:42:15 1996 Received: from ifi.informatik.uni-stuttgart.de for herrmann@hermes.informatik.uni-stuttgart.de by www.ccl.net (8.8.2/950822.1) id JAA09614; Mon, 18 Nov 1996 09:33:37 -0500 (EST) Date: Mon, 18 Nov 1996 15:33:17 +0100 Message-Id: <199611181433.PAA20284@odysseus.informatik.uni-stuttgart.de> Received: by odysseus.informatik.uni-stuttgart.de; Mon, 18 Nov 1996 15:33:17 +0100 From: Frank Herrmann To: WSMITH@msnet.mathstat.uoguelph.ca CC: chemistry@www.ccl.net In-reply-to: <1B9A5445617@msnet.nw.uoguelph.ca> (WSMITH@msnet.mathstat.uoguelph.ca) Subject: Re: CCL:Molecule Builder Dear netters, several people asked, how to get CSED. You can ftp the CACTVS tool distribution that includes CSED. Here is an excerpt from the "Ftp and Installation Description from the Distribution" from URL http://schiele.organik.uni-erlangen.de/cactvs/toolidx.html ----------------------------------------------------------------- Retrieval of the files via ftp: Prepare a temporary unpacking directory mkdir tmpdir cd tmpdir ftp to schiele.organik.uni-erlangen.de and log in as 'anonymous'. Supply you full email address as password. Go into the /pub directory and retrieve the 'installme' script, i.e. issue the commands ftp schiele.organik.uni-erlangen.de anonymous yourname@youraddress cd pub get installme Next get the correct release from the OS directories (IRIX5.3, SunOS4.1, SunOS5.4 etc). The name of the cactvs tools file is something like 'cactvstools-SunOS4.1-1.2.1.tar.gz'. You need binary mode for transfer. So type for example: type binary cd SunOS4.1 get cactvstools-SunOS4.1-1.2.1.tar.gz quit ----------------------------------------------------------------- best Regards, -------------------------------------------------------------- Frank Herrmann, Computer Scientist, PhD Student Institute of Parallel and Distributed High-Performance Systems (IPVR) University of Stuttgart Breitwiesenstrasse 20-22 D-70565 Stuttgart (Germany) Tel: (49) 711-7816-358, FAX: (49) 711-7816-250 email: Frank.Herrmann@informatik.uni-stuttgart.de From CICARIEJ%A1%RNISD0@mr.nut.roche.com Mon Nov 18 10:38:38 1996 Received: from gatekeeper.roche.com for CICARIEJ%A1%RNISD0@mr.nut.roche.com by www.ccl.net (8.8.2/950822.1) id KAA10173; Mon, 18 Nov 1996 10:31:33 -0500 (EST) Received: by gatekeeper.roche.com (5.65v3.2/fma-120691); id AA08012; Mon, 18 Nov 1996 10:30:46 -0500 Received: from rnuc01.nut.roche.com by mailgate.roche.com; (5.65v3.2/1.1.8.2/20Mar96-0227PM) id AA15870; Mon, 18 Nov 1996 10:31:34 -0500 Received: from mr.nut.roche.com by rnuc01.nut.roche.com (PMDF V5.0-6 #9043) id <01IBZKZVW7HC8WYKMU@rnuc01.nut.roche.com> for chemistry@www.ccl.net; Mon, 18 Nov 1996 10:30:55 -0500 (EST) Received: with PMDF-MR; Mon, 18 Nov 1996 10:30:13 -0500 (EST) Mr-Received: by mta RNIS08; Relayed; Mon, 18 Nov 1996 10:30:13 -0500 Mr-Received: by mta RNUC01; Relayed; Mon, 18 Nov 1996 10:30:51 -0500 Alternate-Recipient: prohibited Date: Mon, 18 Nov 1996 10:30:10 -0500 (EST) From: JANET CICARIELLO-COOK 57165 Subject: Getting structures from SYBYL to FMPro To: chemistry@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-Transfer-Encoding: 7BIT Posting-Date: Mon, 18 Nov 1996 10:30:12 -0500 (EST) Importance: normal Priority: normal Ua-Content-Id: E994IOR29MMQ X400-Mts-Identifier: [;31030181116991/155509@RNISD0] A1-Type: MAIL Hop-Count: 2 Hi All, I am trying to put together an automated (semi-automated?) procedure for our chemists to get their structures from SYBYL (3D-structure, on the SGI) into FileMaker Pro v3.0 (2D-structures, on their Macintoshes). They are currently re-drawing their structures (you can imagine the problem this is, especially with the CombiChem folks) Here's what I've done so far: I have written a SYBYL SPL script to write out a text file where each line is a SMILES string and the corresponding molecule name. This file can easily be transferred to the Mac and read into FileMakerPro (FMPro). I am trying to find a method to convert the SMILES strings into ChemDraw format structures which can be Copy/Pasted into a FMPro picture" field. For various reasons which I cannot go into here, the structures should be ChemDraw format and not PICT format. I can currently (by hand, but would like to AppleScript this) copy the SMILES strings from the FMPro record into a text file, use ISIS ConSystant/Chemeleon to convert to ChemDraw format, open the file in ChemDraw, and Copy/paste the picture back into the FMPro record. (FMPro v3.0 can call AppleScripts as part of it's scripting capabilities - so hopfully the whole conversion procedure can be done from within FMPro by running a FMPro script, making everything else transparent to the chemists) I realize that this is a roundabout procedure and am wondering if anyone has done something similar and/or has any suggestions for a better way of doing this. Also, the ISIS software will only do 2D-SMILES (the stereochemistry is lost). This is ok for now, but I would like to find a way to keep the stereochemistry information from the SMILES strings. Please keep in mind that our chemists all have FMPro and ChemDraw on their Macs, but not ISIS software (this may change, but I am trying to develop this procedure using tools that they are comfortable with and already have) Any AppleScripting hints will also be appreciated, as I am a complete novice at writing AppleScripts. Thanks in advance for your help, and I will summarize responses to the net if there is any interest. Janet p.s. Our e-mail system sometimes put strange things in the "from" field which is not recognized when you "reply" to the e-mail messege. My e-mail address is: janet.cicariello-cook@roche.com From daizadeh@indigo.ucdavis.edu Mon Nov 18 12:38:40 1996 Received: from indigo.ucdavis.edu for daizadeh@indigo.ucdavis.edu by www.ccl.net (8.8.2/950822.1) id MAA11600; Mon, 18 Nov 1996 12:36:54 -0500 (EST) Received: by indigo.ucdavis.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id JAA17979; Mon, 18 Nov 1996 09:39:25 -0800 From: "Iraj Daizadeh" Message-Id: <9611180939.ZM17977@indigo.ucdavis.edu> Date: Mon, 18 Nov 1996 09:39:11 -0800 In-Reply-To: Daniel Mok "Re: CCL:RKR:" (Nov 17, 12:02pm) References: X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: rossi@watson.ibm.com, CHEMISTRY@www.ccl.net, dkwm2@cam.ac.uk, sorkhabi@ucdavis.edum, vivian@chem.unr.edu Subject: Re: CCL:RKR: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. The reference I was alluding to concerning the computer implementation of third RKR on Mathematica is shown below: Senn, P. (1995) {\it Computers in Chemistry}, {\bf 19}, pp. 437-439. Thank you for the interest. Iraj. > > On Sat, 16 Nov 1996, Iraj Daizadeh wrote: > > > Hello and thank you for your response. > > > > The answer to your question is that I believe so. > > > > I have found a paper in Computers in Chemistry (Software Note) which utilizes > > Mathematica to solve this problem. I, however, have not been able to reproduce > > their result using the Mathematica code they included. Somehow they were able > > to manipulate mathematica to circumvent the singularity problem. I would be > > happy to send you the reference if it is of interest to you. > > > > Iraj. > > > > P.S. Surprisingly there exists almost no information concerning the > > computational implementation of this method on the net. Maybe it is trivial? > > > > > > > > On Nov 16, 2:32pm, Daniel Mok wrote: > > > Subject: Re: CCL:RKR: > > > Hi Iraj, The 'third-order RKR' you mentioned, is it the one that make use > > > of data from different isotope to generate the potential curve? > > > > > > Daniel > > > On Fri, 15 Nov 1996, Iraj Daizadeh wrote: > > > > > > > Hello. > > > > > > > > Would anyone know of where I could obtain a program that calculates > > third-order > > > > Rydberg-Klein-Reese (RKR) potential energy (preferably free). > > > > > > > > Iraj Daizadeh > > > > Department of Chemistry > > > > University of California > > > > Davis, CA 95616 > > > > daizadeh@indigo.ucdavis.edu > > > > > > > > -------This is added Automatically by the Software-------- > > > > -- Original Sender Envelope Address: daizadeh@indigo.ucdavis.edu > > > > -- Original Sender From: Address: daizadeh@indigo.ucdavis.edu > > > > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: > > Coordinator > > > > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net > > 73 > > > > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > > > > Web: http://www.ccl.net/chemistry.html > > > > > > > > > > > > > > ******************************************************************************** > > > * Daniel K.W. Mok > > * > > > * E-Mail: dkwm2@cam.ac.uk Phone: 01223-336423 > > * > > > * Office: Dept. of Chemistry, University of Cambridge Fax : 01223-336362 > > * > > > * Lensfield Rd., Cambridge CB2 1EW, UK. > > * > > > ******************************************************************************** > > >-- End of excerpt from Daniel Mok > > > > > > > > ******************************************************************************** > * Daniel K.W. Mok * > * E-Mail: dkwm2@cam.ac.uk Phone: 01223-336423 * > * Office: Dept. of Chemistry, University of Cambridge Fax : 01223-336362 * > * Lensfield Rd., Cambridge CB2 1EW, UK. * > ******************************************************************************** >-- End of excerpt from Daniel Mok From dimitris@3dp.com Mon Nov 18 15:38:35 1996 Received: from boris.3dp.com for dimitris@3dp.com by www.ccl.net (8.8.2/950822.1) id OAA12674; Mon, 18 Nov 1996 14:53:39 -0500 (EST) Received: from europa.3dp.com by boris.3dp.com via SMTP (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA20607; Mon, 18 Nov 96 14:58:19 -0500 Received: by europa.3dp.com (950413.SGI.8.6.12) id OAA03703; Fri, 18 Oct 1996 14:52:22 -0400 From: "Dimitris Agrafiotis" Message-Id: <9610181452.ZM3701@europa.3dp.com> Date: Fri, 18 Oct 1996 14:52:21 -0400 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: new paper on sequence analysis Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii A new paper entitled "A New Method for Analyzing Protein Sequence Relationships Based on Sammon Maps" is to appear in a forthcoming issue of Protein Science. If you would like a pre-print, please send me a note, including your postal address. A postscript version of the paper is also available. The abstract follows below. ___________________________________________________________________ A New Method for Analyzing Protein Sequence Relationships Based on Sammon Maps. Dimitris K. Agrafiotis 3-Dimensional Pharmaceuticals, Inc., 665 Stockton Drive, Exton, PA 19341, USA. Tel: (610) 458-6045, Fax: (610) 458-8249, E-mail: dimitris@3dp.com ABSTRACT Recent advances in gene sequencing and rational drug design have re-emphasized the need for protein analysis, classification, and structure and function prediction. In this paper, we introduce a new method for analyzing protein sequences based on Sammon's non- linear mapping algorithm. When applied to a family of homologous sequences, the method is able to capture the essential features of the similarity matrix, and provides a faithful representation of chemical or evolutionary distance in a simple and intuitive way. The merits of the new algorithm are demonstrated using examples from the protein kinase family. _________________________________________________________________ -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com 3-Dimensional Pharmaceuticals, Inc. | tel: (610) 458-6045 665 Stockton Drive, Suite 104 | fax: (610) 458-8249 Exton, PA 19341 From zhuang@lennon.jci.tju.edu Mon Nov 18 16:38:46 1996 Received: from rafiki.JCI.TJU.EDU for zhuang@lennon.jci.tju.edu by www.ccl.net (8.8.2/950822.1) id QAA13367; Mon, 18 Nov 1996 16:10:23 -0500 (EST) Received: from pumba.JCI.TJU.EDU by rafiki.JCI.TJU.EDU via ESMTP (940816.SGI.8.6.9/940406.SGI) for <@rafiki.JCI.TJU.EDU:CHEMISTRY@www.ccl.net> id QAA17534; Mon, 18 Nov 1996 16:24:48 -0500 Received: from pumba by pumba.JCI.TJU.EDU via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id QAA23347; Mon, 18 Nov 1996 16:24:45 -0500 Sender: lzw@lennon.jci.tju.edu Message-ID: <3290D41D.ABD@lennon.jci.tju.edu> Date: Mon, 18 Nov 1996 16:24:45 -0500 From: Ziwei Huang Organization: Thomas Jefferson University X-Mailer: Mozilla 3.01Gold (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: positions opening Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit POSTDOCTORAL / TECHNICIAN POSITIONS POSTDOCTORAL & TECHNICIAN POSITIONS available immediately in exciting multi-disciplinary research programs to study protein structure/function and to develop novel peptide-based and nonpeptide drugs. You will work with an interdisciplinary team of peptide and organic chemists, computer modelers, structural biologists, and molecular biologists and immunologists. We are looking for applicants in any of the following areas: (1) Molecular Biology or Immunology. Must have experience in expression systems (prokaryotic and eukaryotic), site-directed mutagenesis, cell culture or in vitro assays and receptor binding assays. (2) Synthesis and Structure of Peptides and Peptidomimetics and Combinatorial Chemistry. Must have experience in peptide synthesis (preferably using automated solid phase peptide synthesizer) and HPLC purification, mass spectrometry, NMR and CD spectroscopic study of peptides and peptidomimetics, organic synthesis of non-peptidic compounds, development and application of combinatorial synthetic techniques. (3) Molecular Modeling and Computer-aided Drug Design. Must have experience in computational chemistry, experience in working closely with chemists and biologists, protein structures, peptide and peptidomimetic design, computer docking to search small molecular databases for ligands. A Bachelor's/Master's degree is required for a technician position. Competitive salary and benefits. Send resume including day-time and evening telephone numbers to: Prof. Ziwei Huang Kimmel Cancer Institute Thomas Jefferson University Bluemle Life Sciences Building, Room 802 233 South 10th Street Philadelphia, Pennsylvania 19107 USA FAX: 215-923-2117; E-mail: zhuang@lac.jci.tju.edu. Please visit our homepage for more information about the laboratory Website: http://nana.jci.tju.edu ------------------------------------------------------------------------ From WSMITH@msnet.mathstat.uoguelph.ca Mon Nov 18 18:38:40 1996 Received: from ccshst09.cs.uoguelph.ca for WSMITH@msnet.mathstat.uoguelph.ca by www.ccl.net (8.8.2/950822.1) id SAA14453; Mon, 18 Nov 1996 18:05:26 -0500 (EST) Received: from msnet.nw.uoguelph.ca (msnet.mathstat.uoguelph.ca) by ccshst09.cs.uoguelph.ca with ESMTP (1.40.112.3/16.2) id AA133748352; Mon, 18 Nov 1996 18:05:52 -0500 Received: from MSNET/MAILQ by msnet.nw.uoguelph.ca (Mercury 1.21); 18 Nov 96 18:16:11 GMT-5 Received: from MAILQ by MSNET (Mercury 1.21); 18 Nov 96 18:15:51 GMT-5 From: "William R. Smith" Organization: Dept. of Math & Stats. To: Frank Herrmann , Computational Chemistry List , chemistry@www.ccl.net Date: Mon, 18 Nov 1996 18:15:47 EDT Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re: CCL:Molecule Builder Priority: normal X-Mailer: Pegasus Mail v3.2 (pr2) Message-Id: <2001C5C5876@msnet.nw.uoguelph.ca> Hi, Does anyone know of a simple Windows 3.1/NT/95 product that can be used to build molecules? > > several people asked, how to get CSED. You can ftp the CACTVS tool > distribution that includes CSED. Best Regards, W. R. Smith Professor Dept. of Mathematics and Statistics and School of Engineering University of Guelph FAX: 519-837-0221 Guelph, Ontario Tel: 519-824-4120, ext. 3038 CANADA N1G 2W1