From cramos@dino.conicit.ve Fri Feb 26 05:02:03 1993 From: cramos@conicit.ve (Cesar Ramos Cedeno (CEDITEC)) Message-Id: <9302260929.AA18686@dino.conicit.ve> Subject: Venezuelan Society of cristalography To: chemistry@ccl.net Date: Fri, 26 Feb 93 5:29:03 AST Foundation of the venezuelan Society of Cristalography ================================================================= > > The Sociedad Venezolana de Cristalografi'a (SVCr) was recently > created (9/2/93) in the II Sessions of Diffraction of X Ray and its > applications that were carried out in the Facultad de Ciencias of > the Universidad Central de Venezuela. > > In the founding meeting participated 40 investigating of field that > word in different institutions of the country (UCV, USB, IVIC, > ULA, UDO, IUT-RC, UNEG, INTEVEP). > > The fundamental objective of the SVCr is to stimulate the cooperative > relationships establishment between the researchers, that are > devoted to the study of the structure of the matter per se or in > order to know or to comprehend the properties and functions of > different systems, and that work in institutions publish or > private, of the country or not. > > In these II Sessions was put from manifesto the extended use of the > diffraction techniques by different investigating of the country. > In they were presented 5 conferences, 17 oral presentations and 8 > posters in the fields of: biology, chemistry, petroleum, metallurgy, > catalysis, ceramic, computation, information systems, etc. > > The organization of the formed recently SVCr is responsibility of > an executive commission, coordinated by the Dr. Mario Capparelli > (Escuela de Qui'mica, Universidad Central de Venezuela - UCV -) and > integrated by the Drs. Rodolfo Vargas (Centro de Biofi'sica y > Bioqui'mica - CBB -, Instituto Venezolano de Investigaciones > Cienti'ficas -IVIC-), Yolanda Ng Lee (Escuela de Fi'sica, UCV), Dora > Gomez (Departamento de Qui'mica, Universidad de los Andes -ULA-), > Ali' Khan and Oscar Gonzalez (Departamento de Fi'sica, Universidad > de Oriente - UDO -), Maximiliano Donat and Arturo Montes (Instituto > Universitario de Tecnologi'a-Region Capital -IUT-RC-), Rao Mokka and > Leonir Gomez ( Universidad Nacional Experimental de Guayana - UNEG > -), Eduardo Greaves (Departamento de Fi'sica, Universidad Simon > Bolivar - USB -). > > The communication with the SVCr can be make by the following > directions: > > Universidad Central de Venezuela > Facultad de Ciencias > Escuela de Fi'sica y Matema'tica > > AP.: 47586, Caracas 1041-A, Venezuela > Email: jmichine@dino.conicit.ve > Fax: 58 2 6629734 > 58 2 6718378 > > > > Instituto Venezolano de Investigaciones Cienti'ficas (IVIC) > Centro de Biofi'sica y Bioqui'mica (CBB) > Laboratorio de Estructura Molecula (LEM) > AP.: 21827, Caracas 1020-A, Venezuela > Email: rvargas@ivic.ivic.ve > rvargas@cbb.ivic.ve > Fax: 58 2 5713143 > > > > Universidad Central de Venezuela > Facultad de Ciencias > Escuela de Qui'mica > AP.: 47074, Caracas 1041-A, Venezuela > Email: mcappare@dino.conicit.ve > > > > From kmoore@ncsc.org Fri Feb 26 04:15:59 1993 Date: Fri, 26 Feb 93 09:15:59 EST From: Kevin Moore Message-Id: <9302261415.AA24415@duck.ncsc.org> To: d3e129@cagle.pnl.gov Subject: X-Window terminal emulator for Mac >>If you need to go to the high performance mac there is a >>better/cheaper solution. I have a NCD color xterminal at home. I can >>run nearly everything that is x-based, xdbx, gnuplot, emacs, xterm, >>etc. work great. The only problem I do have is with Liken which is a >>mac emulator for the sparcstation (and other Unix) box. The cost is >>around $3500 (probably a little cheaper for University?). Grayscale >>is even cheaper. The performance is slow for opening new windows but Ncd also has this software (PC-Xremote) for a PC (an even cheaper solution). It allows the PC to run over a serial line and display X-Windows. It costs about $200. They may have a mac version of the software though I could not find a description of it in the literature that I have. The salesman has told us that you don't want to do anything graphical over anything less than 9600 baud. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ || Kevin Moore North Carolina Supercomputing Center || || Scientific Support Analyst 3021 Cornwallis Rd. || || (919) 248-1179 Research Triangle Park, NC 27709 || ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From alex@baruch.saclay.cea.fr Wed Feb 24 17:19:17 1993 Date: 25 Feb 93 16:19:17-2300 From: "Alexandre MICU P16A" Message-Id: <9302261519.AA16423(a)baruch> To: CHEMISTRY@ccl.net Subject: summary for cheap graphics on SGI Dear Netters, Here are the answers concerning a cheap package for molecular graphics on SGI. Thanks to all of you who replied. from Wolfgang Sauer, >there are several packages around, some 'free' for non-profit use. >Check ScareCrow announced on this list a few days ago !!! >from Peter Shenkin, >Our program, MacroModel, does what you want on SGI, and in addition >does do dynamics, etc. The price to a non-profit organization is >$750 US. >from Tom Slee, >HyperChem on the SGI is currently selling at $3,500 (commercial) >and I believe $700 to educational institutions, in the US, same >price as the PC version. Contact >Autodesk at 1-800-424-9737 for more information. If you are not in >the US or Canada, I can put you in touch with AUtodesk by e-mail. (can't >tell where you are from from the OSC mailing). >from Carlos Simmerling, >I have a program that I developed for viewing proteins on sgi. >It isn't great, but it is free and I will send it to you if you are >interested. It reads only CHARMm-style CRD files for now, I am adding >pdb probably this week or next. Let me know if you want to ftp it. >from Tom Simonson, >Midas from UCSF is a nice cheap graphics package for SGI for proteins et al. >For info try midas@cgl.ucsf.edu or belwer@cgl.ucsf.edu, >or phone (415) 476-5128. It costs $350. From alex@baruch.saclay.cea.fr Wed Feb 24 17:09:17 1993 Date: 25 Feb 93 16:09:17-2300 From: "Alexandre MICU P16A" Message-Id: <9302261509.AA17436(a)baruch> To: CHEMISTRY@ccl.net Subject: summary of answers concerning G90 on HP735 Dear Netters, Thanks to all of you who replied. Here is the summary of the answers I have received to the question: >>3- What do you think about running G90 ( or G92) on HP735 ? >>How much memory do I need for an optimal run ? How fast would it >>be compared to the CRAY2 (or how slow) ? Our lab is in position >>to choose between 4 HP735 and a 2-processors Power Challenge from SGI. >>I would very much appreciate >>your opinions and a discussion "HP against SGI". The answers would be >>summarized, of course. >from Murray Smigel, >First a disclaimer, I work for a computer company, Convex, which >markets HP-735 clusters, usually in conjunction with one of >our C-Series vector machines as the file and queue server. > >We have done quite a bit of comparison of HP-735 vs SGI R-4000 >machines and the answer is that the HP is 2-3 times faster then >the R-4000 for Gaussian 92. The "power challenge" SGI will >use a somewhat faster chip, I believe it will be a 75 Mhz vs >50 Mhz chip, but it will still be slower then the HP. I think >4 HP's are a lot more machine then a 2 head SGI. > >You will need at least 64 MB of memory on the HP's. What kind >of runs do you do? Direct scf, mp2, mp4?? If you do >stuff with a lot of disk i/o, you might want to specify the >"fast and wide" SCSI interface as the older SCSI is not the >fastest disk in the world. > >I do not have direct comparison timings for the Cray 2, but for >most cpu bound things, the HP will be about 1/4-1/3 the speed >of a YMP. If you want, I can run some data sets for you if you >have comparison timings on the Cray 2. Just email them to >me with an estimate of the time, memory and disk requirements > >One other issue, Convex sells a scientific library product, >MLIB which is quite useful for linking Gaussian 92 on the >HP-735. It really speeds up the matrix multiply dominated >steps. >from Mike, (I've lost part of the message and the full name as well as the e-mail address. I apologize and beg to be contacted again; I have few more details to ask for) >We have been running G90 and now G92 on our HP 750 (slower than the >735) for about a year now, and it works quite well. You should probably >have 64 MB memory, but 32 MB would do if you don't do anything else >on the workstation (especially not use the display to login). >We also try to keep about 300 MB free disk space, though many of the >more popular G92 options can be done with little disk space, but >some can not. Our 750 is faster than the Cray X-MP we used to have, >but not be a lot (the 735 would be almost 2x our 750). > >At a first glance, you are getting ~twice as much total computing power from >4 HP 735s that you get from a 2-cpu SGI, but G92 is (partially) >parallelized for SGI so you might get better single-job turnaround >on the SGI by letting both cpus work on the same job. You want to have >local disk on the HPs to avoid doing I/O over the network, >though just loading binaries from a single /g92 directory might still be >acceptable (though you are dead if that single system goes down). > >from Doug Fox, > We are currently working on getting the HP/735 fully supported with >Gaussian 92. Gaussian 90 is not available. > > In general we recommend at least 32MB of memory and 1GB of scratch >disk for Unix workstations. This provides sufficient balance and >resources that you can use all the capabiiilties of Gaussian 92. > From caldwell@utdallas.edu Fri Feb 26 04:00:32 1993 From: "Richard A. Caldwell" To: chemistry@ccl.net Subject: apologies from "beginners" Message-Id: <93Feb26.100035cst.15728@utdallas.edu> Date: Fri, 26 Feb 1993 10:00:32 -0600 I wish those of us who are less experienced than others of us would get over feeling they have to excuse themselves when they ask a "naive question." My sense is that we all have expertise to share and I've been delighted with the responses in the few cases in which I've been involved in such information exchanges on this list. I'd like to encourage "dumb" questions; I think for each of us with guts enough to ask one there are ten who are hesitant but want the same questions answered. The savants have been more than willing to share expertise; so long as they are, the field will prosper by having this forum used in that way. Count me a non-savant who reads and usually learns from responses to such questions whether or not I ask them. Dick Caldwell caldwell@utdallas.edu Department of Chemistry The University of Texas at Dallas From cheney%hersch1@harvard.harvard.edu Fri Feb 26 06:50:18 1993 Date: Fri, 26 Feb 93 11:50:18 EST From: cheney%hersch1@harvard.harvard.edu (jill cheney) Message-Id: <9302261650.AA21674@hersch1> To: chemistry@ccl.net Subject: Computer Program to Evaluate Wigner 3j Coefficients I'm a graduate student at Harvard looking for a program that recursively evaluates a series of 3j coefficients with different values of j1. I found one source in Computer Physics Communications 11, 269 (1976), but the only local copy is a printout of the listing. Reluctant to type in all that code, I wonder if anyone is aware of a more efficient alternative? Thanks! Jill Cheney Griffin From ole.swang@kjemi.uio.no Fri Feb 26 23:08:57 1993 Date: Fri, 26 Feb 1993 22:08:57 +0100 From: ole.swang@kjemi.uio.no Message-Id: <9302262108.AAkelvin16632@kelvin.uio.no> To: chemistry@ccl.net Subject: language question Please don't get offended by this non-chemical question: The latin term "et al." is commonly seen in scietific articles, and to the best of my knowledge it means "and co-workers". The dot in "al." obviously means that the real Latin word is longer than two letters.. What is the full word? Hints on ethymology are also appreciated. Just curious, Ole Swang From hogue@mosquito.den.mmc.com Fri Feb 26 08:05:51 1993 Date: Fri, 26 Feb 93 15:05:51 MST From: hogue@mosquito.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9302262205.AA02238@mosquito.den.mmc.com> To: chemistry@ccl.net Subject: Hydrazine bond length I would like opinions on two observations: 1. The HOMO/LUMO gap between hydrazine and nitrogen tetroxide (two hypergolic rocket fuel components) is about 5 electron volts. Is this a lot or not much for a spontaneous chemical reaction? 2. The N-N bond given by AM1 is 2.7 Anstroms. Cotton and Wilkinson list 1.47 A. Any thoughts on why this would be? The AM1 N-N bon length for N2O4 was right on the money. Thanks in advance, Pat Hogue From newton%gandal.dnet@server.uga.edu Fri Feb 26 12:27:59 1993 Date: Fri, 26 Feb 93 17:27:59 -0500 Message-Id: <9302262228.AA20537@server.uga.edu> From: newton%gandal.dnet@server.uga.edu To: "CHEMISTRY@ccl.net"%SERVER.dnet@server.uga.edu Subject: Thermodynamics from Benson's Rules? Do any programs exist which estimate thermochemical values from an input structure diagram using Benson's additivity rules (or any other scheme)? Gary Newton UGa E-MAIL newton@bscf.uga.edu From wei@hermes.chpc.utexas.edu Fri Feb 26 10:32:59 1993 Date: Fri, 26 Feb 93 16:32:59 -0600 From: wei@hermes.chpc.utexas.edu (Tai-Guang Wei) Message-Id: <9302262232.AA20933@hermes.chpc.utexas.edu> To: CHEMISTRY@ccl.net Subject: Force fields in internal coordinates and normal coordinates Could someone please tell me where I can get a program which converts the force fields in internal coordinates into force fields in normal mode coordinates up to quartic fields? I would like to get source code in either Fortran or C. Thank you very much for your help. Tai-Guang Wei From sam@ncsa.uiuc.edu Fri Feb 26 12:37:42 1993 Date: Fri, 26 Feb 93 18:37:42 CST From: sam@ncsa.uiuc.edu (Sam Milosevich) Message-Id: <9302270037.AA14152@troon.ncsa.uiuc.edu> To: d3e129@cagle.pnl.gov, kmoore@ncsc.org Subject: Re: X-Window terminal emulator for Mac Yes, NCD says PC-Xremote is NOT available for the Apple Macintosh. ---Sam * Sam Milosevich, Research Scientist, Eli Lilly and Company * * E-mail: sam@ncsa.uiuc.edu (NCSA Partners), sam@lilly.com * * X.400: G=Samuel; S=Milosevich; P=Lilly; A=ATTmail; C=US; * > From chemistry-request@ccl.net Fri Feb 26 11:33:10 1993 > Date: Fri, 26 Feb 93 09:15:59 EST > From: Kevin Moore > To: d3e129@cagle.pnl.gov > Subject: X-Window terminal emulator for Mac > > >>If you need to go to the high performance mac there is a > >>better/cheaper solution. I have a NCD color xterminal at home. ... > > Ncd also has this software (PC-Xremote) for a PC (an even cheaper solution). > It allows the PC to run over a serial line and display X-Windows. It > costs about $200. They may have a mac version of the software though I > could not find a description of it in the literature that I have. The > salesman has told us that you don't want to do anything graphical over > anything less than 9600 baud. From wsonnen@rcf.usc.edu Fri Feb 26 08:27:43 1993 Date: Fri, 26 Feb 93 16:27:43 PST From: wsonnen@alnitak.usc.edu (Wayne Sonnen) Message-Id: <9302270027.AA05036@alnitak.usc.edu> To: chemistry@ccl.net Subject: summary: dna charges I wish to thank all who replied to my question about potential-derived charges for dna bases. Below is a copy of my origional post and the replies i received. Wayne Sonnen ****************************************************************** ORIGIONAL QUESTION: ------------------- Dear CC netters, I am interested in obtaining electrostatic potential-derived charges with solvation effects included for dna bases: adenine, guanine, cytosine and thymine. My intention is to use these derived charges in some molecular dynamics studies. I understand that Guassian 92 can perform such calculations using a reaction-field model for the solvent and solving the problem in an iterative procedure. (1) Does anyone have any references in which such calculations have been done for the above dna bases? (2) How realistic are the derived charges on the above bases? I am interested in the charge distribution on the bases as they exist as isolated molecules in water and as they exist in both single and double stranded dna. (3) How would the counterions effect the charge distribution of the bases? Comments and/or opinions are very welcome. I will summarize responses and post it on the network. Although for discussion purposes, it might be best to reply to chemistry@ccl.net. Thank you, Wayne Sonnen wsonnen@alnitak.usc.edu ***************************************************************** Wayne I seen your message on the computational chemistry mailing list. I would be quite interested in seeing the replies. I would appreciate it if you forwarded them on to me please. The last time I sent a message to the list, a lot of people responded to me personally rather than sending replies to the list. If you have any general references on the subject of accurate charges and electrostatic potentials of the DNA bases, I would be very interested. The paper that I have been using is Pullman & Pullman Quart. Rev. Biophys. *14* 289-380 (1981), I suspect this is probably slightly out of date now. Brian Denny Pharmacy Dept. Aston University Birmingham B4 7ET United Kingdom ******************************************************************** Wayne - Consult the following: Pranata, J.; Wierschke, S.G.; Jorgensen, W.L. JACS v.113 pp.2810-2819 (91). - Erin erin@rani.chem.yale.edu **************************************************************** Dear Dr. Sonnen: I noticed your inquiry about potential derived charges on the network. Perhaps you will be interested in my program package for deriving net atomic charges and multipoles. A description follows. -Don Williams Program PDM93, Potential Derived Multipoles, is now available. The following is a brief description of this program. Molecules interact with each other via their electric potential. PDM93 finds optimized net atomic charges and other site multipole representations of the molecular electric potential based on a variety of models. The program is easy to use, flexible and powerful. Results are obtained in a single iteration and a complete error treatment is made which includes estimated standard deviation and correlation of variables. The program is written in Fortran 77 and runs on Unix, Vax, and other computers with F77 capability. Program PDM93 has a unique combination of features: o general sites, not necessarily at atomic locations o each site may have any combination of monopole, dipole, or quadrupole o bond dipole model is supported o restricted (along the bond direction) bond dipole model is supported o provision for site dipole vectors in sp2 or sp3 directions o selected fixed atomic charges o selected groups of atoms with fixed charge o atomic charge equalities or symmetry relations o rotational invariance of site charges o provision for optional foreshortening of X-H bonds o comparison with Mulliken charges and Mulliken electric potential o direct input from Gaussian-92 o generalized input from other quantum mechanics programs o automatic generation of electric potential grid points o provision for custom generation of grid points o on-line program manual o comprehensive examples are provided For further information contact Dr. Donald E. Williams, Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA. If you need more detailed information about the program package, copies of the manuals and demonstration calculations are available on request. Tel: (502)588-5975 Fax: (502)588-8149 E-mail: dewill01@ulkyvx.bitnet ----------------------------------------------------------------------- Ordering information Program package consisting of manuals, Fortran-77 source files, and demonstration example files....................................$2,000 Special discount price is available to academic institutions ........$495 Choose the preferred method of shipment: Via ftp, purchaser furnishes valid ftp address................n/c Via magnetic media, specify type..............................$20 DC6150 tape cartridge, unix tar format or MP120 tape cartridge (8mm), Vax backup format or 9-track 1600 bpi ascii tape or 9-track 6250 bpi ascii tape Make check payable to the University of Louisville ********************************************************************* Wayne, Don Truhlar and I are somewhat less enamored of ESP charges than portions of the community. Nevertheless, you may find our recent publication on polarization as it contributes to the solvation of the DNA bases of interest. Chem. Phys. Lett. 1992, 198, 74. Best regards, Chris -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 (612) 624-0859 ************************************************************************ Salut Wayne, .....personal stuff deleted..... I am very much interrested by your question concerning the charges on the bases pairs. This is a very important point. I know a few references : - Kollman of course, he has develloped two force field as you know ! (if you want any references don't hesitate to ask me ) - Jorgensen :jacs - 1991 - 113 - p.2810 - Clementi : (sorry, I didn't keep the reference, it's somewhere in international Journal of quantum chemistry, probably 92, but perhaps 91, or 93) This reference should be of interest for you. - and you have also gromos !?! I hope this helps, and if you receive some interesting replies, I would appreciate if you could forward them to me Pauffinger@boltzmann.wesleyan.edu ********************************************************************* Dear colleague : Solvent effects by means the methodology of the Reaction Field approach for ellipdsoidal cavities and going to a multipole moment of 6th order can be included from a recent package anounced in QCPE Bull. (1992), 12 , 69. There you can also find references to the methodo- logy employed and some applications, ( a paper concerning some isomeric equilibria in solution of enamines, which is in press at J.Am.Chem.Soc. may be sent on request). Concerning influence of cations, the effects can be quite large, to get some idea on the behaviour of cations in water, I could recommend you : J.Phys.Chem. 1991, 95, 8928 and references therein. Expecting this will be useful for you, Sincerely yours, Enrique Sanchez Marcos