From thomas@salz.phych.ba-freiberg.de Wed Sep 28 03:10:44 1994 Received: from salz.phych.ba-freiberg.de for thomas@salz.phych.ba-freiberg.de by www.ccl.net (8.6.9/930601.1506) id DAA26204; Wed, 28 Sep 1994 03:07:05 -0400 From: Received: by salz.phych.ba-freiberg.de (AIX 3.2/UCB 5.64/4.03) id AA12377; Wed, 28 Sep 1994 09:04:19 +0200 Message-Id: <9409280704.AA12377@salz.phych.ba-freiberg.de> Subject: To jianling liu ! To: chemistry@ccl.net Date: Wed, 28 Sep 94 9:04:18 DFT X-Mailer: ELM [version 2.3 PL2] As an reaction of my request for triangular plots I received a message from mr. jiangling liu. However, the same answer me arrived since this time every day. Because of I don't know his EMail adress, I would like to ask him in this way, to control his Mail-Software ... thomas@salz.phych.ba-freiberg.de From Patrick.Bultinck@rug.ac.be Wed Sep 28 04:10:45 1994 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.9/930601.1506) id DAA26506; Wed, 28 Sep 1994 03:35:24 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA00943 (5.67b/IDA-1.5 for ); Wed, 28 Sep 1994 08:34:40 +0100 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA28397; Wed, 28 Sep 1994 08:35:25 +0100 Date: Wed, 28 Sep 1994 08:35:25 +0100 (MET) From: Patrick Bultinck Subject: SUMMARY : making ECP's To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 6132 Netters, Last week I posted a question on how to make ECP's. A small number of people asked for a summary, so here it is. The number of people who reacted, however, is even smaller ! Thanks to the people who helped me ! ORIGINAL MESSAGE Dear Netters, I would like to know if there are programs that would allow me to make ECP's (Effective Core Potentials) (relativistic as well as non-relativistic) for alkaline and alkaline-earth metal IONS. Please if you know of such programs let me know, alternatively references to articles which give results on ECP's for the requested ions are also gladly accepted ! As always, if there is enough interest, I will post a summary ! Thank you very much, Patrick Bultinck, University of Ghent (Belgium) ANSWERS Hi, Some references to ECPs include the following. The first are the compact effective potential derived according to the scheme of Walt Stevens et al. I think the latter paper describes the s-block metals and may even include some account of core polarization (which has been suggested as important in reproducing things such as the structure of alkaline earth metals). 12. a) "Compact effective potentials and efficient, shared-exponent basis sets for the first- and second-row atoms;" Stevens, W. J.; Basch, H.; Krauss, M. J. Chem. Phys. 1984, 81, 6026. b) "Relativistic compact effective potentials and efficient, shared-exponent basis sets for the third-, fourth-, and fifth-row atoms"Krauss, M.; Stevens, W. J.; Basch, H.; Jasien, P. G. Can. J. Chem. 1992, 70, 612. The Hay-Wadt scheme is described in these papers. 17. "Ab Initio effective core potentials for molecular calculations;" Hay, P. J.; Wadt, W. R. J. Chem. Phys. 1985, 82, 270, 284, 299. Another group which has focused considerably on ECPs are Ross, Pitzer, Ermler and co-workers. The following are for f-block metals, but there should be a ref. to their earlier work since these researchers have developed their ECP scheme for the entire Periodic Table. b) "Ab initio relativistic effective potentials with spin-orbit operators. V. Ce through Lu;" Ross, R. B.; Gayen, S.; Ermler, W. C. J. Chem. Phys. 1994, 100, 8145. b) "Ab Initio Relativistic Effective Potentials with Spin-Orbit Operators. VI. Fr through Pu;" Ross, R. B.; Ermler, W. C.; Chistiansen, P. A. Intern. J. Quantum Chem. 1991, 40, 829. I do not have any handy refs. to the work of Barthelat and co-workers. Hope this is of some help. Tom +===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+=== Thomas R. Cundari Asst. Professor of Chemistry Computational Inorganic Chemistry Lab University of Memphis Memphis, TN 38152 phone: 901-678-2629 fax: 901-678-3447 e-mail: cundarit@memstvx1.memst.edu http://www.memst.edu/chemistry/umchem.html +===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+===+=== > Dear Netters, > > I would like to know if there are programs that would allow me to make > ECP's (Effective Core Potentials) (relativistic as well as > non-relativistic) for alkaline and alkaline-earth metal IONS. > > Please if you know of such programs let me know, alternatively > references to articles which give results on ECP's for the requested ions > are also gladly accepted ! > > As always, if there is enough interest, I will post a summary ! > > Thank you very much, > > Patrick Bultinck, University of Ghent (Belgium) > I'm afraid you will not find any public domain programs to fit ECPs. Each of the groups involved in the development of ECPs normally has their own codes, and it requires quite a bit of know-how to use them. So normally they don't give it away. By the way, what do you mean with ions? Any good ECP that works for the atoms will work for the ions as well. During my thesis in Erlangen (with Paul Schleyer) I cooperated with my former research group in Stuttgart (Hermann Stoll) to make quasirelativistic and nonrelativistic ECPs for Ca, Sr, Ba. The ECPs, valence basis sets, testing, and first applications (to MH2) for Ca, Sr, and Ba have been published in J.Chem.Phys. 1991,94,1360. Note that the first and third s-contraction coefficients for Ba should read -5.928895 and -0.551437, respectively (there is a typo in the paper). The ECPs are of the energy-adjusted type of the Stuttgart group (cf. e.g. Dolg et al. J.Chem.Phys. 1987, 86, 866, and Andrae et al. Theor.Chim.Acta 1990,77,123 for the corresponding ECPs for other transition metals). There was a posting some time ago, on which I already answered and gave some hints on the required core sizes and basis sets. You should be able to find fit in the CCL archives. Unpublished 9-valence-electron ECPs for K, Rb and Cs are also available from the Stuttgart group (I emphasize these small-core ECPs, as you would need core-polarization potentials to get good results out of 1-valence electron ECPs for these atoms). You could contact Prof. Stoll in Stuttgart ( cfaa1019@servus.rus.uni-stuttgart.de ) about the parameters. Successful applications of the alkaline earth 10-valence-electron ECPs may be found in: JACS,1991,113,5606;JACS,1992,114,491;JACS,1992,114,8202;JACS,1992,114,10880; J.Phys.Chem.,1992,96,7316;J.Phys.Chem.,1992,96,9801;JACS,1993,115,11202 Best regards, Martin Kaupp ------------------------------------------------------------------------- | Dr. Martin Kaupp | | | Departement de chimie | | | Universite de Montreal | Fax (514) 343-2468 | | C.P. 6128, Succ. A | Tel. (514) 343-6111x3991 | | Montreal, Quebec H3C 3J7 | | | Canada | e-mail: | | | kauppm@chims1.chimcn.umontreal.ca | ------------------------------------------------------------------------- That's all folks ! From makula@bisance.citi2.fr Wed Sep 28 05:10:47 1994 Received: from FRMOP11.CNUSC.FR for makula@bisance.citi2.fr by www.ccl.net (8.6.9/930601.1506) id EAA27060; Wed, 28 Sep 1994 04:22:13 -0400 Received: from galaad.citi2.fr by FRMOP11.CNUSC.FR (IBM VM SMTP V2R2) with TCP; Wed, 28 Sep 94 09:21:15 EST Received: from bisance.citi2.fr by galaad.citi2.fr; (5.65/1.1.8.2/20Jun94-0455PM) id AA01699; Wed, 28 Sep 1994 09:12:57 +0100 Received: by bisance.citi2.fr (5.0/SMI-SVR4) id AA05377; Wed, 28 Sep 1994 09:21:57 --100 From: makula@bisance.citi2.fr (makula-bisance) Message-Id: <9409280821.AA05377@bisance.citi2.fr> Subject: Sparkles in Mopac : summary To: chemistry@ccl.net Date: Wed, 28 Sep 1994 09:21:56 +0100 (MET) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Content-Length: 7381 Dear Netters, here is a summary of the messages I received after my original posting about the use of sparkles in Mopac. --------------------------------------------------- Original posting : Dear Netters, I would like to calculate with MOPAC the geometry of an organic anion. I am not sure that the calculation of an ion alone in the gas-phase would be very realistic (mainly because of intramolecular electrostatic repulsion), so I tried to use the so-called "sparkles" which are defined in the MOPAC manual as "pure ionic charges" or more precisely as an "integer charge at the center of a repulsion sphere of form exp(-alpha*r)". The manual explains further that the sparkles can be used as counterions. Unfortunately, my MOPAC calculation with a positive sparkle "+" ended up with the positive charge almost superimposed on the atom of my anion bearing most of the negative charge. Have I missed something in the keyword specification ? does anybody have experienced this MOPAC feature with some success ? (some refs would be welcome ). --------------------------------------------------- I managed to fix my problem when I realized that I was starting the geometry optmization with a too short distance between the sparkle and the anion. This caused the sparkle to nearly overlap the molecule in the end. Starting with a distance longer than the supposed radius of the sparkle allowed convergence to a geometry where the sparkle stays at a reasonable distance from the anion. Thanks to all who replied to me. Remi Le Goas Computer Aided Molecular Design Rhone-Poulenc Agrochimie LYON - France e-mail: remi.le-goas@rp.fr *************************************************** from jstewart@fujitsuI.fujitsu.com : Please check that your copy of MOPAC has the following bug-fixes: 17 June 1993 ++++ In MOLDAT, after CALL CALPAR add DO 91 I=1,107 91 IF(AM(I).LT.1.D-4)AM(I)=1.D0 Reason: Sparkles were not being handled correctly 8 January 1994 ++++ In block.f, after DATA VS(104) /10.0D0/ insert DATA ALPAM1(104) / 1.5D0/ Reason: The AM1 sparkle `+' was not correctly specified. James J. P. Stewart ****************************************************************** Dear Dr. Le Goas, Sparkles are not really quantum mechanical objects, but are simply acting as "polarizers". They have no electrons and is the geometry is optimized with one being used, it will simply move toward the negative charge as you noted. If you want to try computing the geometry of an organic anion as if it were in solution, I would use one of the semi- empirical continuum models. In modern versions of MOPAC I think that this is COSMO. In our AMPAC proogram, it is AMSOL. I will be happy to send you info on that program if you would like. This is not perfect, but should be better that a "bare" anion. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry ** Internet Addr: aholder@vax1.umkc.edu Univ. of Missouri - Kansas City ** Phone Number: (816) 235-2293 Spencer Chemistry, Room 315 ** FAX Number: (816) 235-5502 Kansas City, Missouri 64110 ** =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= *********************************************************************** Dear Dr Goas, It seems that the program worked correctly. Most probably you have asked the program to optimize the distance between the sparkle and the anion (or the atom concerned). Try to fix the distance (to see the effect of the potential created by the sparkle (or sparkles). But, as it is written in the Mopac Manual, you have to be very careful when using them. You could alternatively use COSMO within MOPAC if you do not wish to handle isolated anion species. I had problems getting rezonable results using sparkles when I tried to mimic iron atom within ferrocenophanes (J.Phys. Org. Chem. 1989,2,602-610) and then decided to develop my own molecular mechanics force field for this species (J.Phys.Org. Chem. 1992,5,382-394). You could also ask for help to MOPAC Forum that was opened for a while at no cost. Then you should get help from Dr Stewart directly. Wishes, Jerzy Rudzinski Dr Jerzy M Rudzinski Fujitsu Kyushu System Fukuoka, Japan jerzy@fqs.fujitsu.co.jp ********************************************************************* Remi, Here is a sparkles job that i've run. It is not an acid counter ion but coordinates to the carbonyl of acrylic acid. The results of the four isomers of acrylic acid coordinated with the potassium sparkle mimic the corresponding results of ab initio calculations coordinated with Li+. This case should give you an idea of the use of the sparkle and can help you to determine if there are problems with your code. rick rjl@lilly.com internet address AM1 GNORM=0.001 SCFCRT=1.D-16 T=9999M HESS=1 EF CHARGE=1 acrylic acid cis,syn conformation coordinated with K+ FINAL HEAT OF FORMATION = -62.04709 KCAL C 0.000000 0 0.000000 0 0.000000 0 0 0 0 -0.0565 C 1.329716 1 0.000000 0 0.000000 0 1 0 0 -0.2014 H 1.087972 1 123.151621 1 0.000000 0 1 2 0 0.0986 H 1.086237 1 122.310316 1 180.000000 0 1 2 3 0.0746 C 1.482676 1 121.909848 1 0.000000 0 2 1 3 0.2569 H 1.097405 1 120.693802 1 180.000000 0 2 1 3 0.1048 O 1.228531 1 125.734878 1 0.000000 0 5 2 1 -0.3987 O 1.396593 1 117.806960 1 180.000000 0 5 2 1 -0.0089 H 0.989783 1 120.953680 1 180.000000 0 8 5 2 0.0557 K 2.989783 1 120.953680 1 180.000000 0 7 5 8 0.0557 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 ********************************************************************* Dear Dr. Remi, Please take a look at our paper entitled: "Sparkle Model for the Quantum Chemical Calculation of Lanthanide Complexes" Chem. Phys. Lett. 227 (1994) 349-353. There you will find a description of how to optimize the sparkle parameters. It may be of help to you. I guess that you may have to reparametrize them to suit your needs. Sincerely, ************************************************************************ * * * Alfredo Mayall Simas e-mail: AMS@npd1.ufpe.br * * Departamento de Quimica Fundamental Fax: (081) 271-8442 * * Universidade Federal de Pernambuco Office: (081) 271-8440 x 37 * * 50.739-000 Recife, PE CCEN: (081) 271-8400 * * Brasil * * * ************************************************************************ From grfamini@cbdcom.apgea.army.mil Wed Sep 28 07:10:47 1994 Received: from cbdcom.apgea.army.mil for grfamini@cbdcom.apgea.army.mil by www.ccl.net (8.6.9/930601.1506) id GAA27831; Wed, 28 Sep 1994 06:26:02 -0400 Date: Wed, 28 Sep 94 6:20:30 EDT From: George R Famini To: chemistry@ccl.net Subject: COMP Division Schedule for Anaheim Message-ID: <9409280620.aa04688@cbdcom.apgea.army.mil> I have enclosed the tentative (tentatively final?) schedule of symposia and sessions for the Division of Computers in Chemistry at the Spring 1994 American Chemical Society Meeting in Anaheim (2-7 April 1995). There may still be minor tweeks and changes, but should not change drastically. This is also a good opportunity to point out abstracts for presentations (oral and poster) are due to the respective symposium chair by 28 October (on official ACS abstract form). If you wish to participate in one of the symposia and don't know who the organizer is, please contact me. George Famini COMP Program Chair 209th ACS National Meeting, Anaheim Division of Computers In Chemistry G. Famini, US Army SUNDAY, APRIL 2 - AM . Conformational Analysis . Combinatorial Synthesis SUNDAY, APRIL 2 - PM . Application of Parallel Computing to Computational Chemistry . Conformational Analysis MONDAY, APRIL 3 - AM . Application of Density Functional Theory to Problems in Chemistry . Combinatorial Synthesis . Conformational Analysis MONDAY, APRIL 3 - PM . Conformational Analysis . Application of Parallel Computing to Computational Chemistry . Molecular Modeling for the Bench Chemist MONDAY, APRIL 3 - EVE . Sci-Mix 8:00 PM TUESDAY, APRIL 4 - AM . Computers in Chemistry Award Symposium . Application of Density Functional Theory to Problems in Chemistry . Molecular Modeling for the Bench Chemist TUESDAY, APRIL 4 - PM . Genetic Algorithms in Chemistry . Molecular Modeling for the Bench Chemist TUESDAY, APRIL 4 - EVE . General Poster Session 7:00 PM WEDNESDAY, APRIL 5 - AM . Artifical Intelligence in Chemistry . Molecular Modeling for the Bench Chemist . Application of Density Functional Theory to Problems in Chemistry WEDNESDAY, APRIL 5 - PM . Genetic Algorithms in Chemistry . General Oral THURSDAY, APRIL 6 - AM . Data-Flow Programming and Molecular Visualization . Artifical Intelligence in Chemistry THURSDAY, APRIL 6 - PM . General Oral . Data-Flow Programming and Molecular Visualization . Artifical Intelligence in Chemistry From pvarnai@lamar.ColoState.EDU Wed Sep 28 10:13:20 1994 Received: from lamar.ColoState.EDU for pvarnai@lamar.ColoState.EDU by www.ccl.net (8.6.9/930601.1506) id JAA02845; Wed, 28 Sep 1994 09:51:56 -0400 Received: by lamar.ColoState.EDU (AIX 3.2/UCB 5.64/4.03) id AA157159; Wed, 28 Sep 1994 07:51:54 -0600 From: pvarnai@lamar.ColoState.EDU (Peter Varnai) Message-Id: <9409281351.AA157159@lamar.ColoState.EDU> Subject: Re:IRC with G92 To: chemistry@ccl.net Date: Wed, 28 Sep 1994 07:51:54 -0600 (MDT) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 456 Dear Antonio, Unfortunately qftramos@usc.es didn't work out so my answer is: If you have G92 user's guide can find interesting points on page 32. If not: opt=ef will follow the lowest eigenvector for a structure regardless if it is TS or not. You can also define opt=(ef,calcfc) in order to calculate force constants analitically (I can advise). If you need something else feel free to write: pvarnai@lamar.colostate.edu Best to You Peter Varnai From cmartin@rainbow.uchicago.edu Wed Sep 28 11:10:59 1994 Received: from midway.uchicago.edu for cmartin@rainbow.uchicago.edu by www.ccl.net (8.6.9/930601.1506) id KAA04535; Wed, 28 Sep 1994 10:18:46 -0400 Received: from rainbow.uchicago.edu by midway.uchicago.edu for chemistry@ccl.net Wed, 28 Sep 94 09:18:43 CDT Received: by rainbow.uchicago.edu (920330.SGI/920502.SGI) for @midway.uchicago.edu:chemistry@ccl.net id AA06075; Wed, 28 Sep 94 09:36:54 -0500 From: cmartin@rainbow.uchicago.edu (Charles Martin) Message-Id: <9409281436.AA06075@rainbow.uchicago.edu> Subject: questions about charges To: chemistry@ccl.net Date: Wed, 28 Sep 1994 09:36:53 -0600 (CDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1780 Continung the discussion about charges After reading several posts here and some of the papers suggested, I have some questions for the experts (1) Consider the RESP charge model. First, is the following assement correct? This model seems to reliably reproduce electrostatic charges of a single nuclear configuration, however, in order to reproduce binding energetics, model is refit over an average of nuclear configurations. Second, if so, then how well does this (and related models) perform in MD simulations designed to reproduce dynamical properties? (2) How well do point charge models perfom in dynamical simulations as well? Can this even be assesed with the current stages of technology? (3) In molecule-protien interactions, are there situations where the binding molecule greatly alters the electrstatics of the protien? For example, imagine a high polar molecule inside a protein. Won't the molecule polarize the surrounding medium? Additionally, classical polarization dies of as (1/r^3), so I would expect this effect to be fairly long ranged? Have there been any studies which address this (e.g. large semi-empirical calculations of a molecule inside a protein, where the protein is also polarizable?) What kind of models are used to represent the polarizable protein? A polarization tensor centerd at each atom? ================================================================== Charles H. Martin email: chm6@quads.uchicago.edu US Mail: c/o Freed Group The James Franck Institute and The Department of Chemistry The University of Chicago 5640 South Ellis Avenue Chicago, Illinois 60637 Work: (312) 702-3457 Fax: (312) 702-5863 ================================================================== From rickr@scripps.edu Wed Sep 28 11:12:53 1994 Received: from scripps.edu for rickr@scripps.edu by www.ccl.net (8.6.9/930601.1506) id LAA06375; Wed, 28 Sep 1994 11:05:09 -0400 Received: from ppg.scripps.edu by scripps.edu (5.61/1.34) id AA08573; Wed, 28 Sep 94 08:05:05 -0700 Received: by ppg.Scripps.EDU (4.1/SMI-4.1) id AA16081; Wed, 28 Sep 94 07:48:05 PDT Date: Wed, 28 Sep 94 07:48:05 PDT From: rickr@scripps.edu (Rick Ross) Message-Id: <9409281448.AA16081@ppg.Scripps.EDU> To: chemistry@ccl.net Subject: virus_summary Folks, Greetings here is a summary of responses to: On Tue, 20 Sep 1994, Rick Ross wrote: > Folks, > Greetings. I know this is not a direct computational chemistry question but > I think it is a concern to all. I was wondering if folks would be willing to > share how they protect themselves from viruses that could be imported via > anonomous FTP to their: UNIX workstations; Personal Computers; or Macintosh > Computers. > I would be very glad to summarize for the net if their is interest. To > avoid swamping the net, perhaps folks could send answers to me directly > first. > Thanks a bunch. > Rick Ross > rickr@ppg.scripps.edu > PPG Industries > P.O. Box 9 > Allison Park, PA 15101 > Thanks a bunch to all folks who replied. In addition to the very useful info on how folks at individual sites take virus precautions is the message that points out a virus maillist, a usenet conference, and a FAQ document on this topic. THanks again to all who responded! regards, Rick Ross P.S. Some folks requested copies of this summary which I did not send because I have sent the summary to the list and didn't want to clutter mail boxes. Thanks again to respondants! ****** Please post a summary when you get it. We scan our PC's & Macs every boot. ************* Dear Rick, When I download software from any site to my Mac, I run Disinfectant (John Norstad, Northwestern University) on it just to be safe. We have a policy @ IAF of not downloading pre-compiled UNIX software from anonymous ftp sites. We usually request the source code and compile it ourselves, unless it is from a reliable company or academic resource. We also keep regular backups of the whole system to minimize any possible loss. ********* Disinfectant is pretty much the standard for Macs. It is freely available at major archives, and is updated as soon as a new virus appears. I have had good success with it. Other virus utilities for Mac, commercial or not, basically have different bells and whistles (faster checking perhaps, checking of archived material). Gatekeeper specifically is more agressive (veto-ing things at the first hint of trouble), and requires more configuration to allow legit programs to do what they should do. ********** I am good with Macs. There are two excellent anti-virus software, both free, for Macs, thanks to John Nosted of Northwestern U. and Chris Johnson of U. Texas. You can find them from the famous Sumex, UMich, and UT sites and their mirror sites. Nosted's Disinfectant can scan disks and eradicate viruses, and install an init to prevent invation of any known virus. The Johnson's GateKeeper monitors application activities and veto any virus-like actions, which has been the major weapon against any unknown virus for the Mac world. A few new viruses were actually detected by GateKeeper by users of non-expert on virus. Are there such softwares for PC's and Unix? I am not sure. Please send me a copy of your summary. Thanks! ********* I can only speak about the Mac: I have used Disinfectant for probably 5 years now and it has served me well. It is just as effective as commercially available programs and less obtrusive than most of those. Disinfectant's author looks into every virus report sent to him and there is a team of people that immediately react when a new virus appears. Highly recommended. Of course I don't represent my company's point of view as they want everybody to use SAM something or other, which I threw off any machine I worked on first thing. ******** My feeling is that viruses are not realy an issue with Unix machines. I am not up-to-date on the miriad of viruses and anti-virus software on PC clones. But, I can tell you that, for Macintoshes, Disinfectant is all you will ever need. It is free, and extremely effective. It does not interrupt your work to scan floppies or any such nonsense. It discovers and protects against *every* known Macintosh virus, and when new ones are discovered, an update is usually available within hours or days of the discovery. Since Mac viruses are much harder to write than PC viruses, and since Disinfectant has managed to eliminate new viruses so quickly and effectively, Mac viruses are nearly extinct. Disinfectant's author, John Norstad, is certainly the Jonas Salk of Macintosh Viruses. Disinfectant can be obtained via anonymous ftp from ftp.acns.nwu.edu [129.105.16.53] in pub/disinfectant. ******** We protect our Macs using Gatekeeper and Disinfectant. Together, they provide enough protection that we've never had a problem For unix stations, the file protection system is one of your best protections. As such, the most important thing is to never run anything as root where you arent pretty darn sure of its security. Read scripts and makefiles; look through source when possible. Try to only install packages that are well known and get it froma well known source. Oh, we also run the security program tripwire, which allows you to check for alteration to a wide number of files, using secure, non-spoofable message digest functions to generate a checksum for each file. ******** Rick, Hello. Recently there was a cross posting to a list (this one I think) about a program called CD-IT. The authors claim it is a CDROM program by a real company - a false claim. It is a virus in disguise and can be downloaded via a file transfer. When it is used it reportedly causes catastrophic damage to hard disks. Our department has a warning on our internet gateway about this program. Hope this is of some help even though this doesn't answer your question. A single gateway to a department or company is one way I believe that helps to protect the attached systems. Regards ****** Hi Rick, since other people did the job for you, you won't need to summarize (unless you want more concise informations). You may be familiar with Usenet conferences. There is one called comp.virus, and there is a mailing list (similar to DIBUG) called VIRUS-L. These two have a common FAQ document (Frequently Asked Questions). This is an extensive survey of viruses, what they are, how to protect yourself on different systems, etc. This FAQ document is available from simtel20 servers, or directly through ftp >from cert.org (192.88.209.5) in the file pub/virus-l/FAQ.virus-l (the best way to ftp is to use 'Mosaic ftp://cert.org/pub/virus-l/FAQ.virus-l', if you have Mosaic installed. If someone is unable to ftp, please tell me; I'll be happy to send you a copy. The file is some 84 kilobytes, so I'll refrain from posting it to DIBUG :-) It was last updated on 18 November 1992, so the virus list is not up-to-date, but infos about how to protect your system still apply. A full list of current viruses can be downloaded with packages such as ScanV (currently version 117, for MS-DOS, look for scanv117.zip on simtel20, e.g. 'Mosaic ftp://ftp.switch.ch/software/msdos/simtel20/virus/scanv117.zip' (in Switzerland)). Most important is to worry about viruses before you have them. Some are hard to detect or fix once they infected your system. Checking files you downloaded with a _current_ version of scanv or another virus checker _before_ you ever start them up is a good idea. I hope this helps. Best regards, ****** Rick, >From a Unix perspective the first rule is to never run programs off the net as super user. This in effect quarantines the program. Also if possible get the program from the writers own system which may me more secure than some public systems. ******* Hi Rick, on the Macintosh the definitive programs are: Disinfectant - contains code to detect all known Mac viruses and to eliminate them. Updated by John Norstad within days (hours) of when new viruses are discovered. ftp://ftp.acns.nwu.edu//pub/disinfectant/disinfectant35.sea.hqx Gatekeeper - looks for suspicious activity (e.g., modification of system files) and reports and/or blocks it. ftp://microlib.cc.utexas.edu//microlib/mac/virus/gatekeeper-13.hqx Both have execellent documentation included and are free. ****************** Hi, For the Mac the basic virus-protection you need is Disinfectant, freeware >from John Norstad, Northwestern University and Gatekeeper, freeware from Chris Johnson. Both available from sumex-aim.stanford.edu on the info-mac/vir directory. This software is updated for each new virus, almost immediately after discovery. More protection (scanning of archives, and much, much more) is obtained by applying SAM (Symantec). Hope to be of help (I'm sure I am the zillionth to give you this info) *************** Hi! Simple. My access is through a Mac that runs Virex. The Mac is connected to an INDIGO R4000 SGI. Hence, everything goes through the Mac first. Cumbersome, but I have yet to experience a virus problem! ************ I would not recommend anyone import binary executables from the Internet. I use lots of public domain stuff under UNIX. I always have the source, and build from source. This will not prevent introduction of a virus, but if it happens, I should then be able to work back to the origin of the problem. For new things, I sometimes test under a special account, but that won't catch things that are set to go on certain dates, etc... So far, I have had no problems. Ian From bear@ellington.pharm.arizona.edu Wed Sep 28 13:10:52 1994 Received: from ellington.pharm.arizona.edu for bear@ellington.pharm.arizona.edu by www.ccl.net (8.6.9/930601.1506) id NAA08663; Wed, 28 Sep 1994 13:02:58 -0400 Received: by ellington.pharm.arizona.edu (931110.SGI/920502.SGI) for chemistry@ccl.net id AA13317; Wed, 28 Sep 94 09:57:22 -0700 Date: Wed, 28 Sep 94 09:57:22 -0700 From: bear@ellington.pharm.arizona.edu (Soaring Bear) Message-Id: <9409281657.AA13317@ellington.pharm.arizona.edu> To: chemistry@ccl.net Subject: CCL:BS/MS Computational Chemists? Hello: Mailing to Bill Laidig bounced so I hope he'll see this here. As a computational chemist with just a BS I found your posting quite interesting. When I got my degree I was able to continue work with the professor who trained me but I considered that the scarcity of publicized jobs in this newly developing field to be part of my impetus to go on to PhD (where of course, I'll also become a better computational chemist). I suspect part of the rationale for a higher degree requirement is that the average recent BS graduate hasn't really had the time to learn BOTH chemistry & computers. As kids learn computers in grade school and calculus spreads more in high schools (assuming a greater national interest in funding education) then comp chem will also trickle down to lower levels. It also helps when enlightened organizations join yours in lowering the barriers, making up deficiencies by OJT, and emphasizing employee retention to keep valued people. Until there are many positions, I doubt anyone will be bothered by your rare notice to the several comp chem groups of a position opening. bear * UU UU SOARING BEAR * * UU UU Computer Aided Drug Design * * UU UU A University of Arizona, New Pharmacy 404 * * UUUU AAA Tucson, AZ 85721 602-626-6133 * * AA AA where the sun shines * * AAAAAAA * * AA AA e-mail:bear@ellington.pharm.arizona.edu * From bishop@lisboa.ks.uiuc.edu Wed Sep 28 14:10:53 1994 Received: from lisboa.ks.uiuc.edu for bishop@lisboa.ks.uiuc.edu by www.ccl.net (8.6.9/930601.1506) id OAA09767; Wed, 28 Sep 1994 14:04:55 -0400 Received: from helsinki by lisboa.ks.uiuc.edu (NX5.67d/NX3.0M) id AA05911; Wed, 28 Sep 94 13:06:08 -0500 From: Tom Connor Bishop Message-Id: <9409281806.AA05911@lisboa.ks.uiuc.edu> Received: by helsinki.ks.uiuc.edu (NX5.67d/NX3.0X) id AA01373; Wed, 28 Sep 94 13:06:07 -0500 Date: Wed, 28 Sep 94 13:06:07 -0500 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: chemistry@ccl.net Subject: molec surfaces. Reply-To: bishop@lisboa.ks.uiuc.edu Dear netters, i'm looking for references to algorithms (not programs) which are used to calculate molecular surfaces, (vdW,elect...etc). We wish to include this as a feature in our own molecular graphics package. Please send any refs that you have to me and i will summarize a list to the net. thanks in advance. tom --- Thomas Connor Bishop +------------------------------------------------- |doctoral candidate |Theoretical Biophysics bishop@ks.uiuc.edu |Beckman Institute Tel: (217)-244-1851 |University of Illinois fax: (217)-244-6078 |405 N Mathews, Urbana, IL61801 NeXTmail Ok | | I don't suffer from insanity; I'm enjoying | every minute of it. +-------------------------------------------------- From shepard@dirac.tcg.anl.gov Wed Sep 28 14:15:11 1994 Received: from dirac.tcg.anl.gov for shepard@dirac.tcg.anl.gov by www.ccl.net (8.6.9/930601.1506) id NAA09149; Wed, 28 Sep 1994 13:31:46 -0400 Received: by dirac.tcg.anl.gov (4.1/SMI-4.1) id AA24684; Wed, 28 Sep 94 12:31:44 CDT Date: Wed, 28 Sep 94 12:31:44 CDT From: shepard@dirac.tcg.anl.gov (Ron Shepard) Message-Id: <9409281731.AA24684@dirac.tcg.anl.gov> To: chemistry@ccl.net Subject: RE: CCL:IRC with GAUSSIAN92 Cc: shepard@tcg.anl.gov qftramos@usc.es (Antonio F. Ramos) wrote: >Dear netters: > I've been trying IRC calculations with G92. There is no problem >from TS to reactives or products, but I'd like to be able to follow the >lowest frequency normal mode from reactives or products to the opposite >side where the TS is. Although this was originally a G92 question, there are a couple of points that might be of general interest to the maillist. First, the IRC is everywhere parallel to the gradient (in mass-weighted cartesians, etc., you know what I mean :-). However, there are an infinite number of paths that are parallel to the gradient that lead to a minimum on a surface, all of which (ignoring spatial symmetry and other special situations), are parallel to the lowest frequency normal mode at the minimum point, and only one of which happens to pass through the TS. Therefore, it is relatively difficult to try to construct the IRC in reverse, that is, >from a minimum to a TS. It is probably more efficient to search for the TS using some stable method, then determine the reaction path from the TS to the connecting minima in the downhill direction, although this is an active research topic. Secondly, the gradient is in general parallel to a normal mode only at a stationary point, not everywhere along the IRC path. The normal mode to which the gradient is parallel at one stationary point (e.g. the minimum) is not necessarily the same normal mode at a different stationary point (e.g. the TS). Therefore, it is not always possible to follow a normal mode from a minimum to a stationary point. Even if a normal mode does connect the minimum to the TS, the path it takes is not necessarily anything like a reaction path (IRC, least motion, or otherwise). K. Ruedenberg and coworkers have recently published some nice examples of how screwy these paths can be on some model surfaces. $.02 -Ron Shepard From rull@RUUCI19.chem.ruu.nl Wed Sep 28 14:15:52 1994 Received: from ruucv1.chem.ruu.nl for rull@RUUCI19.chem.ruu.nl by www.ccl.net (8.6.9/930601.1506) id NAA08893; Wed, 28 Sep 1994 13:14:17 -0400 Received: from ruuci19.chem.ruu.nl by ruucv1.chem.ruu.nl (5.65b/4.13) with SMTP id AA09801; Wed, 28 Sep 94 18:13:26 +0100 Received: by RUUCI19 (931110.SGI/930416.SGI.AUTO) for @RUUCV1.chem.ruu.nl:CHEMISTRY@ccl.net id AA21987; Wed, 28 Sep 94 18:12:02 +0100 From: rull@RUUCI19.chem.ruu.nl (Ton Rullmann) Message-Id: <9409281712.AA21987@RUUCI19> Subject: Re: CCL:charges To: CHEMISTRY@ccl.net Date: Wed, 28 Sep 1994 18:11:59 +0100 (WDT) Reply-To: rull@ruuci9.chem.ruu.nl In-Reply-To: <199409280244.TAA15350@socrates.ucsf.EDU> from "Wendy Cornell" at Sep 27, 94 07:44:21 pm X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 4881 Thanks to Wendy Cornell for the instructive mails about the ESP and RESP models for deriving atomic charges! I would like to comment on the last paragraph of the second mail: > useful for modelling biomolecular systems. The alternatives > usually involve either (1) models such as Mulliken charges > which do not necessarily reproduce the molecular electrostatic > potential or (2) empirically derived charges such as those > fit to reproduce interaction energies and distances (CHARMM) > or liquid properties (OPLS). Because electrostatic potential and remark that other alternatives exist, based on reproducing not the electrostatic potential but the electric multipole moments of a quantum mechanical calculation. Some references are: - Sokalski & Sawaryn, "Correlated molecular and cumulative atomic multipole moments", J.Chem.Phys. 87, 526 (1987). - Stone & Alderton, "Distributed multipole analysis", Mol. Phys. 56, 1047 (1985). - Faerman & Price, "A transferable distributed multipole model for the electrostatic interactions of peptides and amides", JACS 112, 4915 (1990). - Thole & van Duijnen, "A general population analysis preserving the dipole moment", Theor. Chim. Acta 63, 209 (1983). (applied in: Bellido & Rullmann, "Atomic charge models for polypeptides derived from ab initio calculations", J. Comput. Chem. 10, 479 (1989).) What these methods have in common is that they try to reproduce the quantum mechanical charge density by a series of local multipoles, using the expectation values of the one- and two-center contributions to the electric multipole moments as a starting point. Simplifying, these methods can be seen as an extension of the Mulliken method, which only preserves the lowest multipole (total charge). It would be interesting to compare the results of these multipole based methods to those of electrostatic potential fitting. An advantage of the former methods is that one does not fit to function values at a series of judiciously chosen points i.e. one does not have to worry about a "proper" choice of grid points, weighting functions etc. Finally I would like to comment on the desirability of having charges that result in dipole moments larger than in the gas phase, as mentioned in one of the posts. From a practical point of view this makes sense, of course, if you want to compensate for electronic polarization effects that are neglected in standard force fields. On the other hand it means that energy contributions that are rigourously separable on the theoretical level become inextricably mixed. E.g. the electric potential calculated with these charges is not the true molecular potential, and it is virtually impossible to retrieve the latter from an "energy fitted" charge set because the distance and orientation dependence of energy and potential are not the same. One may also encounter problems with the transferability of charges: surely the "effective polarization compensation" must be different for cases involving neutral, singly ionized, doubly ionized and charge-separated (transition states!) species. By these remarks I don't mean to attack the work described by Wendy Cornell, but I do want to draw attention to a problem that in my opinion is sometimes overlooked in discussions of force fields, which is that in almost all cases the parameters represent "effective", not "true" interactions; the parameters are not independent of one another and may not be transferable to other molecules or other systems. If one decides to use ab initio theory wouldn't it make sense to start from the perturbation theoretical approach to intermolecular interactions, describing interactions in terms of true unimolecular properties such as multipoles and polarizabilities? And if one chooses to stick with pair-additive two-body potentials - for solid practical reasons such as limits of computer time, if not (wo)man power needed to redesign a force field - would it be feasible to discriminate between "true charge distributions" derived for isolated molecules, and the "charge corrections" needed to get a good fit to inter- molecular energies in cases of interest? Does anyone care to venture opinions on the issue of using perturbation theory vs. fitting, and on the use of ab initio data? (The case for perturbation theory was argued in: Rullmann & van Duijnen, Reports in Molecular Theory 1, 1 (1990). This was a rewrite of a chapter of my PhD thesis. After that I have worked on other things, but I'm very interested to hear opinions on the current state of affairs). -- | Ton Rullmann NMR Spectroscopy | | Bijvoet Center for Biomolecular Research | Tel. : int+31.30.533641 | | Utrecht University, Padualaan 8, | Fax : int+31.30.537623 | | 3584 CH Utrecht, The Netherlands | Email: rull@nmr.chem.ruu.nl | From CHEM8@vax.york.ac.uk Wed Sep 28 16:10:54 1994 Received: from leeman.york.ac.uk for CHEM8@vax.york.ac.uk by www.ccl.net (8.6.9/930601.1506) id PAA12246; Wed, 28 Sep 1994 15:36:25 -0400 Via: uk.ac.york.vax; Wed, 28 Sep 1994 20:22:56 +0100 Date: Wed, 28 Sep 94 20:32 BST From: "John Waite, Tel 1-7238958, N.H.R.F., Vas. Konstantinou 48, Athens 116-35" To: CHEMISTRY Subject: Summary: Molecular Volume Calculation Message-ID: <"leeman.yor.837:28.08.94.19.23.14"@york.ac.uk> I posted the following question and below this is a summary of the replies. Thank you all. John Dear netters, Does anyone have a code that can calculate molecular volumes, given the atomic coordinates (polar or cartesian), in particular for organo-metallics? Or is there a public domain code available for this, in which case, where? Hopefully, John Waite (CHEM8@VAX.YORK.AC.UK) **************************************************************** Bob Pearlman of Concord fame wrote a program SAVOL, available from QCPE. I think it is SAVOL2, the second version. You can add radii if the program doesn't know them. It is very fast. Can calculate areas & volumes of parts of the molecules as well. @@@@@@@@@@@ Yvonne Martin, Senior Project Leader @ Computer Assisted Molecular Design Project @@@@@@@@ @ D-47E, AP9A-LL @ @ Abbott Laboratories @ @ One Abbott Park Road @@@@@@@@@@ Abbott Park, IL 60064 Phone: 708 937-5362 FAX: 708 937-2625 ****************************************************************** Prof. Doros Theodorou and I developed a fast analytic algorithm that does this. It is written in Fortran. If you're interested let me know and I will e-mail it to you. -- Larry dodd@roebling.poly.edu (718) 260-3029 ****************************************************************** MOLSV is a Fortran program for the PC distributed by QCPE. It takes Cartesian coordinates and allows you to easily edit the radii used. This will be the problem for you because, although many modeling programs will do this calculation, it is not entirely settled on what radii to use. They are really parameters in molecular mechanics force fields. Since most of the volume of a complex is due to the ligands, and the metal is often well buried, this problem is not what it might be. We did some of this in trying to correlate molar volumes and molecular volumes (Inorganic Chemistry 31, 2460 (1992)). Please let me know what else you learn. Scot Wherland Dept. of Chemistry Washington State University Pullman, WA 99164-4630 wherland@wsuvm1.wsu.csc.edu ***************************************************************** Someone mentioned a similar posting in July, so I searched and came up with the below three, including a summary. (I missed these as while I was on holiday my directory became full so I couldn't receive mail). ***************************************************************** Heather: > Is there a program which does both, or a way to have Midas > give me volumes and/or Sybyl give me surface area? There is a "connolly" > routine in Sybyl for solvent accessable surface area, but this results in > a third set of Sybyl vdw radii. > I just want surface area & volume calculated the same way with > the same parameters. Is there a way to do this? > What you need are the programs ACCESS (for calculating solvent accessible surface areas) and VOLUME from Fred Richards at Yale. I suggest that you contact Art Perlo (perlo@hhvms8.csb.yale.edu) to obtain an academic license (free for academia!). Since you are in New Haven there should be no problem. ACCESS will let you define any probe radius and is pretty straight-forward to use. Yet another package called MSP (Molecular Surface Package) is available >from Mike Connolly (Connolly@netcom.com) for detailed dissection of surfaces. Finally, GRASP (from Tony Nichols, Columbia U.) also has various features to manipulate surfaces. Hope this helps Cheers -raman -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** Hi, You may like to rtry QUANTA from MSOI and voiVOID from QCPE to for your calculatonion. Chris chen!@agiyourom.cn.com -- San Diego, the finest city in the Sattetates ***************************************************************** I was asked to post a summary of the responses I received about finding molecular surface areas and volumes. I would like to thank everyone who responded, especially those who offered copies of their own programs! We've decided to use Fred Richards programs (thanks C. S. Raman) since they're a standard & he's across the science courtyard!! Heather Carlson heather@ramana.chem.yale.edu SUMMARY: ------------------------------------------------------------------------- From: jle@world.std.com (Joe M Leonard) I'm not sure whether Yale ever got Spartan, but if it has, we calculate the area and volume using the same radii. There are other codes floating about in the PD or at QCPE, which you can probably recompile with changed radii... Joe Leonard jle@world.std.com ------------------------------------------------------------------------- From: RAVANTTI@msvax.mssm.edu The program GRASP from Anthony Nicholls, nicholls@cuhhca.hhmi.columbia.edu should have an answer to your problem. Liisa Laakkonen ------------------------------------------------------------------------- From: maxv@iserver.pdl.com (Max Vasquez) Take a look at a program by Frank Eisenhaber; information below. Good luck. Thank you very much for your interest in the paper "Improved Strategy in Analytic Surface Calculation for Molecular Systems: Handling of Singularities and Computational Efficiency" published in Journal of Computational Chemistry, v. 14, N11, (1993), pp.1272-1280 by Frank Eisenhaber and Patrick Argos and the associated program ASC. The program text in standard C for UNIX systems can be obtained from the author in the following way (for academic use): (1) ftp 192.54.41.168, the ftp-server is falcon.EMBL-Heidelberg.DE; (2) login: ftp, during login give your E-mail address as password; (3) change to the directory /pub/asc; (4) move all files of this directory to your site, do not name your local directory asc (better ASC or something else to avoid interference with the executable asc !!); (5) execute asc.call (calls make to make executable "asc") and (6) use manual.int as introduction and manual.lib as command reference; Since the time of the publication, a few improvements have been introduced. As a result, the CPU-consumption was further reduced. The three time thresholds for the analytical surface calculation in Tables I and II can be corrected to the following values: (1) 1PPT: 0.24, 1.74, 1.97 (2) 4PTI: 0.71, 3.66, 4.02 (3) 2PCY: 1.97, 7.38, 8.14 (4) 2RHE: 2.00, 7.72, 8.80 (5) 3FXN: 3.54, 11.43, 13.13 (6) 2UTG: 3.44, 11.29, 12.86 and (7) 1CRN: 0.39, 2.46, 2.71. The time consumption had been measured for an R3000 processor in a SGI-workstation. The overall time dropped by about 40\% compared with the data in the article, e.g. the cpu-time for 1CRN decreased from 4.27 seconds to 2.71 seconds.a >From time to time I may change a few files at the ftp site because some of the users or I myself find some strange behaviour. As long as the changes are minor and, especially, do not touch the surface calculation section, the version number will not be changed. It might be useful to update your local version from time to time. The program had been tested for ULTRIX on DEC-stations and for IRIX on SGI-computers. It runs also under SunOS 4.1.3 if compiled with gcc ! Please, contact me by E-mail, if you have suggestions, problems or questions. Sincerely, Frank Eisenhaber E-mail : IN%"EISENHABER@EMBL-Heidelberg.DE" ------------------------------------------------------------------------- From: dirk@rulglj.LeidenUniv.nl (Dirk Huckriede) I posted a similar request like yours say half a year ago and got quite a number of responses. One of the (Fortran) programs I obtained is able to calculate surfaces and volumes in one run without altering the input etc. I think it is best suited for your purposes. I left it at our anonymous ftp server for you to collect: ftp rulglj.leidenuniv.nl anonymous your mail-adres cd pub/heather binary get volume1.tar If you are not able to use ftp, please mail be, I can send you the file uuencoded (the system manager won't like it though). Bye ! ------------------------------------------------------------------------- From: schaefer@tammy.harvard.edu (Michael Schaefer) I can't give you advice how to use Sybyl for your task, but I have a program that calculates the solvent inaccessible volume of a molecule AND the solvent accessible surface. Volume and surface are calculated for each atom (output format: pdb, volume and surface in the 4th and 5th data column). If you are interested, let me know. Michael Schaefer ------------------------------------------------------------------------- From: David White I am interested in getting into the derivation and coding of analytical algorithms to calculate molecular surface areas and volumes. The data you ask for could be vital in my determining the effecacy of such an algorithm. Please summarize the repsonses! Thanks Dave ------------------------------------------------------------------------- From: raman@bioc01.uthscsa.edu (C.S.RAMAN) What you need are the programs ACCESS (for calculating solvent accessible surface areas) and VOLUME from Fred Richards at Yale. I suggest that you contact Art Perlo (perlo@hhvms8.csb.yale.edu) to obtain an academic license (free for academia!). Since you are in New Haven there should be no problem. ACCESS will let you define any probe radius and is pretty straight-forward to use. Yet another package called MSP (Molecular Surface Package) is available >from Mike Connolly (Connolly@netcom.com) for detailed dissection of surfaces. Finally, GRASP (from Tony Nichols, Columbia U.) also has various features to manipulate surfaces. Hope this helps Cheers -raman ------------------------------------------------------------------------- From: Volkhard Helms I have used the program GRASP of Anthony Nicholls from Barry Honig's group a few times (I'm no expert with it though) and it is very easy to calculate both molecular surfaces and volumes with it and also to display them. It uses a certain set of vdW parameters for both cases, and one can also modify this set. Hope this helps. Volkhard Helms ------------------------------------------------------------------------- From: hurst@hyper.hyper.com (Graham Hurst) The ChemPlus set of extensions to HyperChem includes a QSAR Properties module that can calculate surface area and volume using the same radii. The radii are kept in a text file that you can edit if you want to use different values. You can also drive the calculation from a Windows spreadsheet program (such as Excel) to collect volumes and surface areas for a set of molecules into a spreadsheet. It can also calculate hydration energy, Log P, refractivity, polarizability, mass and partial atomic charges using published empirical methods. For more information send email to info@hyper.com. Cheers, Graham ------------------------------------------------------------------------- From: chen@agouron.com (Chris Chen) Hi, You may like to try QUANTA from MSI and VOID from QCPE for your calculation. Chris chen@agouron.com ------------------------------------------------------------------------- From: HUTCHINS%CMDA Another program to try is SAVOL by Robert Perlman at the University of Texas at Austin. I believe this is readily available from him. Charles Hutchins Abbott Laboratories ------------------------------------------------------------------------- From: "J. Eric Slone" Please take a look at a product which I market, a demo of which is in ccl.net, /pub/chemistry/software/MS-DOS/MOLGEN-demo. It can handle what you are looking for, plus a lot more. And it will read your Sybyl files! Let me know if you are interested (academic pricing is $290). Eric *************************END OF SUMMARY********************************** From szeinfel@snfma1.if.usp.br Wed Sep 28 17:10:59 1994 Received: from snfma1.if.usp.br for szeinfel@snfma1.if.usp.br by www.ccl.net (8.6.9/930601.1506) id QAA14796; Wed, 28 Sep 1994 16:31:11 -0400 Received: (szeinfel@localhost) by snfma1.if.usp.br (8.6.8/8.6.4) id RAA23275; Wed, 28 Sep 1994 17:28:00 -0300 Date: Wed, 28 Sep 1994 17:28:00 -0300 (EST) From: Rafael Iosef Najmanovich Szeinfeld {S To: computational biology cc: biophysics , protein analysis , computational chemistry , "WSN:Water Science Network" Subject: hidrophobic/Van der Walls interactions energy... Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi All, I'm developing a montecarlo model for protein folding and I would like to discuss with you the ratio of the energies of an Hydrophobic interaction and a Van der Wall (or hydrogen bridge) interaction. I know that that's an open question because it deppends on the species participating in the interaction and the enviroment but it may be possible to find an average value. You don't need to send messages asking me to send a summary because I'll post a summary with all the replies. Thank's for Discussing. Rafael. *-----------------------------------------------------------------------------* * Rafael Iosef Najmanovich Szeinfeld |SMAIL: Depto. de Bioquimica - B10 INF.* * Dept. Biochemistry -Chemistry Inst. | Universidade de Sao Paulo * * Dept. Math. Physics -Physics Inst. | Av. Prof. Lineu Prestes 748 * * University of Sao Paulo | CEP 05508-900 * * E-MAIL : szeinfel@snfma1.if.usp.br | Sao Paulo - SP - Brazil * *-----------------------------------------------------------------------------* From KUS%SUEARN2.BITNET@mps.ohio-state.edu Wed Sep 28 17:16:03 1994 Received: from ohstpw.mps.ohio-state.edu for KUS%SUEARN2.BITNET@mps.ohio-state.edu by www.ccl.net (8.6.9/930601.1506) id QAA13900; Wed, 28 Sep 1994 16:12:19 -0400 Received: from SUEARN2.BITNET (MAILER@SUEARN2) by MPS.OHIO-STATE.EDU (PMDF V4.2-14 #5888) id <01HHNH11LJR48WXTRD@MPS.OHIO-STATE.EDU>; Wed, 28 Sep 1994 16:12:17 EDT Date: Wed, 28 Sep 94 23:11 MSK From: Mikhail Kuzminsky -135-6388 (095) Subject: Re: 'raw speed' To: CHEMISTRY@ccl.net Message-id: <01HHNH11LJR68WXTRD@MPS.OHIO-STATE.EDU> Content-transfer-encoding: 7BIT Some additional remarks to benchmarks data and discussion what is the difference between workstation and mainframe: 1) I may add the data for well known test 178 for Gaussian 92 (direct SCF, 300 basis orbitals) for SGI Power Challenge based on TFP processors: Nproc Time (min) 1 14.93 2 9.03 4 5.80 You may compare this data with data for another computers,I take only Cray C90 8/256 data- 4.25 min . As you may see, the results are close to that received for Amber runs: 4-CPU Power Challenge is close to C90 processor. 2) Therefore the question what when workstations will be supercompu- ters is interesting :-) In addition to SGI Power Challenge , it's necessary take into account CONVEX SPP1000 multiprocessor system. Both systems may be upgraded up to very big configurations. Taking into account Cray T3D and Hitachi project (MPP on RISC processors also) it look that like systems will be competitors of usual vector supercomputers. In any considerations it's necessary take into account the price/ performance ratio, what may be better for MPP. Mikhail Kuzminsky, N.D.Zelinsky Institute of Organic Chemistry, Moscow From hurst@hyper.hyper.com Wed Sep 28 17:17:40 1994 Received: from seraph.uunet.ca for hurst@hyper.hyper.com by www.ccl.net (8.6.9/930601.1506) id RAA16388; Wed, 28 Sep 1994 17:09:44 -0400 Received: from hyper by mail.uunet.ca with UUCP id <101934-5>; Wed, 28 Sep 1994 17:09:53 -0400 Received: by hyper.hyper.com.hyper.com (931110.SGI/890607.SGI) (for ruuci9.chem.ruu.nl!rull) id AA21780; Wed, 28 Sep 94 16:51:28 -0400 Date: Wed, 28 Sep 1994 16:51:28 -0400 From: hurst@hyper.hyper.com (Graham Hurst) Message-Id: <9409282051.AA21780@hyper.hyper.com.hyper.com> To: rull@ruuci9.chem.ruu.nl Subject: Re: CCL:charges Cc: chemistry@ccl.net rull@nmr.chem.ruu.nl (Ton Rullmann) writes: > If one decides to use ab initio theory wouldn't it make sense to start from the > perturbation theoretical approach to intermolecular interactions, describing > interactions in terms of true unimolecular properties such as multipoles and > polarizabilities? And if one chooses to stick with pair-additive two-body > potentials - for solid practical reasons such as limits of computer time, if > not (wo)man power needed to redesign a force field - would it be feasible > to discriminate between "true charge distributions" derived for isolated > molecules, and the "charge corrections" needed to get a good fit to inter- > molecular energies in cases of interest? Does anyone care to venture opinions > on the issue of using perturbation theory vs. fitting, and on the use of > ab initio data? > (The case for perturbation theory was argued in: Rullmann & van Duijnen, > Reports in Molecular Theory 1, 1 (1990). This was a rewrite of a chapter of > my PhD thesis. After that I have worked on other things, but I'm very > interested to hear opinions on the current state of affairs). I vote for perturbation theory! 8-) Like Ton, I also did my Ph.D. studying intermolecular forces by perturbation theory (and have also since moved on to other things). We found that atom based multipoles gave remarkably good results compared to more rigorous perturbation theory [Hurst, Fowler, Stone & Buckingham, Int. J. Quantum Chem. 29:1223-1239 (1986)]. Cheers, Graham ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 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