From zhy@pchsgi25.IPC.PKU.EDU.CN Mon Apr 3 01:56:10 1995 Received: from pchsgi25.IPC.PKU.EDU.CN for zhy@pchsgi25.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/930601.1506) id BAA08688; Mon, 3 Apr 1995 01:44:00 -0400 Received: by pchsgi25.IPC.PKU.EDU.CN (911016.SGI/911001.SGI) for CHEMISTRY@ccl.net id AA04760; Mon, 3 Apr 95 13:46:25 +0800 Date: Mon, 3 Apr 95 13:46:25 +0800 From: zhy@pchsgi25.IPC.PKU.EDU.CN (Zhang Hongyu) Message-Id: <9504030546.AA04760@pchsgi25.IPC.PKU.EDU.CN> To: CHEMISTRY@ccl.net Subject: Summary on "Request of 3d graph softwares" Dear netters, Please let me express my pleasant thanks to all of those who repspond to my post of "Request of 3d graph softwares". To those with the same interest, I'd like to recommand the gnuplot, which is refered by most responses. First, it's free and easily got from many gnu ftp site, such as ftp://prep.ai.mit.edu/pub/gnu, and also it's portable in many machines. I've tried it, it's ok. Cheers Henry H. Zhang ---------------------------------------------------------------------- Henry Hongyu Zhang, Ph.D. student | email: zhy@pchsgi25.ipc.pku.edu.cn Molecular Design Laboratory | Tel: 861-2501490 Institute of Physical Chemistry | Fax: 861-2501725 Peking University | Peking 100871 , China | ----------- Too stiff, easily broken Too soft, easily crashed ------------ old Chinese Saying From h9290218@hkusub.hku.hk Mon Apr 3 02:41:13 1995 Received: from hkusub.hku.hk for h9290218@hkusub.hku.hk by www.ccl.net (8.6.10/930601.1506) id CAA09154; Mon, 3 Apr 1995 02:33:08 -0400 Received: from hkusua.hku.hk by hkusub.hku.hk (4.1/SMI-4.1) id AA01535; Mon, 3 Apr 95 14:35:45 HKT Received: by hkusua.hku.hk (5.0/SMI-SVR4) id AA16436; Mon, 3 Apr 1995 14:31:27 +0800 From: h9290218@hkusub.hku.hk (Danny Yau) Message-Id: <9504030631.AA16436@hkusua.hku.hk> Subject: translational order parameter To: chemistry@ccl.net Date: Mon, 3 Apr 1995 14:31:26 +0800 (HKT) Cc: h9290218@hkusub.hku.hk (Danny Yau) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 1094 Dear Netters: I am doing the Monte-Carlo simulation of simple fluid. I would like to calculate the translational order parameter(melting factor) of the fluid which is started from fcc lattice. According to the text book Allen, it shown the parameter is equal to : 1/N * Sum of cos(k*r) where N is no. of particle, k is a reciprocal lattice vector of the initial lattice = ((2N)sup(1/3)*pi/L) r is the position vector of the molecule. The book also metion the parameter should be unity in a lattice. However, I cannot get unity from my starting configuration even it is a fcc lattice. Would anyone know how to calculate the order parameter and reciprocal lattice vector k and how to get the unity from lattice? Best wishes, -- Danny Yau email: h9290218@hkuxa.hku.hk Department of chemistry, or h9290218@hkusub.hku.hk The university of Hong Kong. -- Danny Yau email: h9290218@hkuxa.hku.hk Department of chemistry, or h9290218@hkusub.hku.hk The university of Hong Kong. From praa2@cluster1.urz.uni-halle.de Mon Apr 3 03:11:12 1995 Received: from mlucom.urz.uni-halle.de for praa2@cluster1.urz.uni-halle.de by www.ccl.net (8.6.10/930601.1506) id CAA09411; Mon, 3 Apr 1995 02:56:03 -0400 From: Received: from cluster1.urz.Uni-Halle.DE by mlucom.urz.uni-halle.de with SMTP (1.36.108.7/15.6) id AA24678; Mon, 3 Apr 1995 08:54:18 +0200 Posted-Date: Mon, 3 Apr 1995 08:53:24 +0200 (MESZ) Received-Date: Mon, 3 Apr 1995 08:54:18 +0200 Received: by cluster1.urz.uni-halle.de (AIX 3.2/UCB 5.64/4.03) id AA57137; Mon, 3 Apr 1995 08:53:24 +0200 Message-Id: <9504030653.AA57137@cluster1.urz.uni-halle.de> Subject: summary: 'low cost' methods available ? To: chemistry@ccl.net Date: Mon, 3 Apr 1995 08:53:24 +0200 (MESZ) X-Mailer: ELM [version 2.4 PL22] Content-Type: text Content-Length: 8084 Dear colleguages, now there is the summary of my recent inquiry about 'low-cost' methods. My pleasant thank to all the people who answered me. My original posting: Dear colleagues, I'm trying to model the key steps of catalytic reactions involving one or several transition metal atoms (for the present only 1st row TM atoms are involved). Because of the largeness of the systems ab-initio techniques (HF-, post-HF or DFT) can only be applied to distict pre-evaluted key structures (or simplfied models) wich are previously examined by any lower cost methods. Such methods are the common semiempirical approaches (CNDO, ZINDO, NDDO-type methods, ...) or maybe force field methods, but they should yield reliable enough results. Our experiences with ZINDO are not so encouranging because they not give the desired accuracy of the results. We are mainly interested in describing the interaction of saturated/unsaturated hydrocarbons with nickel. So there is my question. Are there any recommended 'low cost' methods available that can be used side by side with ab-initio techniques in order to get a basic knowledge of the potential energy surface, that can be used in further examinations by ab-initio methods ? Is there a way out to self-contruct an appropriate force field for nickel describing the structural and energetical behaviour of some model systems obtained by ab-initio methods ? Any hints, suggestions or pointers are highly appreciated. Regards Peter ------------------------------------------------------------------------------------- From: jle@world.std.com (Joe M Leonard) Spartan V4.0 has implemented Thiel's MNDO/d formalism for both MNDO and PM3 parameter sets. Ni has been included in the first set of Trans. Metals for PM3(tm)... Have you seen Spartan in the past? Would you like additional information? Joe Leonard jle@world.std.com jle@wavefun.com ------------------------------------------------------------------------------------ From: pavan@daffy.bnpi.com Dear Peter, I saw your note in the CCL for a low-cost semiempirical/MM program for working with 1st row transition metal complexes. Have you ever tried PRDDO (Partial retention of diatomic Differential overlap) program . It is a program well tested for transition metals (especially 1st row) complexes by Dennis Marynick's group at Univ. of Texas at Arlington , Arlington, Texas. If u need further info about Dennis I can pass on the info. pavan ------------------------------------------------------------------------------------------ From: young@slater.cem.msu.edu (Dave Young) Hi, Please post a summary of your replies. I can't give you much hope, however. We do transition metal systems at high levels of theory (multi-reference CI) and have found even simple things like HF to be pretty useless. Occassionally you will find a mechanics calculation where someone has parameterized the metal to behave correctly, but only for that one specific corridination environment. Trying to ask mechanicstic questions in this type of format generally range from very crude to totally useless. Good Luck. Dave Young young@slater.cem.msu.edu ------------------------------------------------------------------------------------------- Subject: Re: CCL:'low cost' methods available ? Dear Peter, There are some ways to do what you want, som hard and some less hard, but it may be difficult to assess the reliability in advance. Starting with the easiest to implement, there have just recently become available some new semi-empirical methods that are especially well suited for transition metals. The first of these, and the bases for other implementations, is Thiel's MNDO-d. I have only experience with PM3(tm) in Spartan, I know it is parameterized for nickel. This is in Spartan 4.0, which was announced today! There, you will also have access to DFT from the same interface. I only made a few quick tests with nickel, but I'm satisfied with the accuracy in palladium calculations, in both PM3 and DFT. As for force field methods, that is definitely possible. If you can't find something that works, you should be able to implement your own force field for a limited range of nickel complexes without too much difficulty. You will be able to calculate you complex immediately with UFF, available in Cerius2 from Molecular Simulation. However, my experiences with this force field are mixed. Some complexes are very well treated, whereas others just give junk. You will just have to try to see if your complex is one where you can get reliable results. The same is true about ESFF in Insight. I know that a few other programs are parameterized for some metals (eg. PCModel), but I have no experience of my own. If you can't find anythin that works without modification, I would suggest that you parameterize a program that can handle the required coordination on the metal. I have best experience with MM2* and MM3* in MacroModel, but also some with MM3 (I'm using Allingers code with the MacMimic package). I have heard Dr. Allinger talk about an MM3 specifically parameterized to reproduce ab initio (6-31G*), not experimental geometries. That may be your best option, but you'll have to contact Dr. Allinger directly for it. MM3 is also one of the few force fields that is able to reproduce nonstationary low-energy points on the energy hypersurface (others are CFF and, I believe, Halgrens MMFF). Regards, Per-Ola Norrby * Per-Ola Norrby * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, peo@compchem.dfh.dk --------------------------------------------------------------------------------------- From: "Dr. Jan Hrusak" (in german) Hallo Peter, wir haben in den letzten drei Jahren an aehnlichen Problemen gearbeitet. (d.h. TM Reaktionen mit liganden) es ist eine sehr hartes Brot wenn man eine gewisse genauigkeit erwartet. Unsere erfahrung zeigt, dass man die semiempirischen Verfahren schlicht vergessen kann. Force field Methoden sind manchmal gute startpunkte aber wie kann man eine dative Bindung und/oder Bindungsbruch beschrieben? Die DFT (oder DFT /HF) methoden (mit RECP) scheinen die ainzige Alternative zu sein. Wir haben fast fuer alle TM metalle 3d, 4d, 5d einschliesslich der Lanthanide Testrechnungen durchgefuehrt und die Uebereinstimmung mit qualitativ hoeheren (CCSDT)) daten ist verbluffend gut. Weiterhin ist die Basisatzkonvergenz der Ergebnisse viel schneller als bei SCF oder gar CI Methoden. D.h. man kann gute Geometrieabschaetzung mit DZ(p) machen und dan auf dieser Geometrie eine single point Rechnung mit einer besseren Basis Durchfuehren. Der Aufwandt ist c. das 1.5 fache einer SCF. Sicher kann man auch hier auf Grenzen hinsichtlich der Groesse stossen , aber wir haben ohne groessere Probleme eine vollstaendige (C1 Symmetrie ) Optimierung fuer Systeme Fe+(C10Hn) n=10, 12, 14 oder Au+ (Buten, Benzen) durchstehen koennen. die ergebnisse sind bedeutend besser, als sie mit einer anderen Methode sein koennen. Gruesse Jan ---------------------------------------------------------------------------- Dr. Jan Hrusak ############################### J. Heyrovsky Institute of Physical Chemistry ## MEMOR ESTO CONGREGATIONIS ## Academy of Sciences of the Czech Republic ## TVAE QVAM POSSEDISTI ## Dolejskova 3, CZ-182 23 Prague 8 ## AB INITIO ## Czech Republic ############################### ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Phone: (0042 2) 66 05 3436 FAX: (0042 2) 858 2307 E-Mail: hrusak@jh-inst.cas.cz ---------------------------------------------------------------------------- Once again, many thankx to all people who responded. Regards Peter From KSK@tifrvax.tifr.res.in Mon Apr 3 08:26:15 1995 Received: from tifrvax.tifr.res.in for KSK@tifrvax.tifr.res.in by www.ccl.net (8.6.10/930601.1506) id IAA11689; Mon, 3 Apr 1995 08:25:23 -0400 From: Received: from tifrvax.tifr.res.in by tifrvax.tifr.res.in (PMDF #12198) id <01HOUVABEDKW002VNG@tifrvax.tifr.res.in>; Sun, 2 Apr 1995 08:35 +0530 Date: Sun, 2 Apr 1995 08:35 +0530 Subject: Jobs in Molecular Biology TIFR Bombay To: chemistry@ccl.net Message-id: <01HOUVABEDKW002VNG@tifrvax.tifr.res.in> X-VMS-To: IN%"chemistry@ccl.net" Molecular Bology Unit, Tata Institute of Fundamental Research is seeking to expand in the following broad areas: Cell Biology, Genetics Neurobiology and Development. Currently there are active groups in Neural Deevelopment in Drosophila, Cell Biology of Synapse, Regulation of yeast glycolysis,plant development and differentiation and mechanisms of homologous recombination in plants. Young persons with between three and five years of post doctoral experience and with a flair for Molecular Cell Biological and Genetic appraoches to study of Deevelopment and function of the nervous system, Cell Biology and genetic regulation in yeast and development and Differentiation in plants will find this a condusive place to develop a viable research program. Those interested may contact The chairman, Molecular Biology Unit, Tata Institute Of Fundamental Research, Homi Bhabha Road, Colaba, Bombay 400 005. India FAX 215 2110/2181 E mail MOLBIO@TIFRVAX. If you need clarifications you might write to me at my mail address Krishnan: KSK@TIFRVAX From KSK@tifrvax.tifr.res.in Mon Apr 3 08:41:16 1995 Received: from tifrvax.tifr.res.in for KSK@tifrvax.tifr.res.in by www.ccl.net (8.6.10/930601.1506) id IAA11818; Mon, 3 Apr 1995 08:33:27 -0400 From: Received: from tifrvax.tifr.res.in by tifrvax.tifr.res.in (PMDF #12198) id <01HOVC4YOXN8003ZV7@tifrvax.tifr.res.in>; Sun, 2 Apr 1995 16:37 +0530 Date: Sun, 2 Apr 1995 16:37 +0530 Subject: jobs in Molecular Biology TIFR To: chemistry@ccl.net Message-id: <01HOVC4YOXN8003ZV7@tifrvax.tifr.res.in> X-VMS-To: IN%"chemistry@ccl.net" Molecular Bology Unit, Tata Institute of Fundamental Research is seeking to expand in the following broad areas: Cell Biology, Genetics Neurobiology and Development. Currently there are active groups in Neural Deevelopment in Drosophila, Cell Biology of Synapse, Regulation of yeast glycolysis,plant development and differentiation and mechanisms of homologous recombination in plants. Young persons with between three and five years of post doctoral experience and with a flair for Molecular Cell Biological and Genetic appraoches to study of Deevelopment and function of the nervous system, Cell Biology and genetic regulation in yeast and development and Differentiation in plants will find this a condusive place to develop a viable research program. Those interested may contact The chairman, Molecular Biology Unit, Tata Institute Of Fundamental Research, Homi Bhabha Road, Colaba, Bombay 400 005. India FAX 215 2110/2181 E mail MOLBIO@TIFRVAX. If you need clarifications you might write to me at my mail address Krishnan: KSK@TIFRVAX From KSK@tifrvax.tifr.res.in Mon Apr 3 08:46:42 1995 Received: from tifrvax.tifr.res.in for KSK@tifrvax.tifr.res.in by www.ccl.net (8.6.10/930601.1506) id IAA11815; Mon, 3 Apr 1995 08:33:17 -0400 From: Received: from tifrvax.tifr.res.in by tifrvax.tifr.res.in (PMDF #12198) id <01HOVC2WQWB4003ZV7@tifrvax.tifr.res.in>; Sun, 2 Apr 1995 16:36 +0530 Date: Sun, 2 Apr 1995 16:36 +0530 Subject: Jobs In Molecular Biology TIFR To: chemistry@ccl.net Message-id: <01HOVC2WQWB4003ZV7@tifrvax.tifr.res.in> X-VMS-To: IN%"chemistry@ccl.net" Molecular Bology Unit, Tata Institute of Fundamental Research is seeking to expand in the following broad areas: Cell Biology, Genetics Neurobiology and Development. Currently there are active groups in Neural Deevelopment in Drosophila, Cell Biology of Synapse, Regulation of yeast glycolysis,plant development and differentiation and mechanisms of homologous recombination in plants. Young persons with between three and five years of post doctoral experience and with a flair for Molecular Cell Biological and Genetic appraoches to study of Deevelopment and function of the nervous system, Cell Biology and genetic regulation in yeast and development and Differentiation in plants will find this a condusive place to develop a viable research program. Those interested may contact The chairman, Molecular Biology Unit, Tata Institute Of Fundamental Research, Homi Bhabha Road, Colaba, Bombay 400 005. India FAX 215 2110/2181 E mail MOLBIO@TIFRVAX. If you need clarifications you might write to me at my mail address Krishnan: KSK@TIFRVAX From mbdtsnm@hpf.ch.man.ac.uk Mon Apr 3 09:11:17 1995 Received: from nessie.mcc.ac.uk for mbdtsnm@hpf.ch.man.ac.uk by www.ccl.net (8.6.10/930601.1506) id JAA12527; Mon, 3 Apr 1995 09:01:41 -0400 Received: from hpf.ch.man.ac.uk (actually mchhpf.ch.man.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Mon, 3 Apr 1995 14:01:13 +0100 From: Nathaniel (noj) Malcolm Message-Id: <6832.9504031300@hpf.ch.man.ac.uk> Subject: SAS summary To: chemistry@ccl.net Date: Mon, 3 Apr 95 14:00:39 BST Mailer: Elm [revision: 70.85] Here is the summary of replies that i recieved concerning the location of a number of points (solvation sights) on the accessable molecular surface (AMS as defined by Richards) my original question was: ............................................................................ >Does anyone have a program that will generate a >set of equally spaced points (in xyz coordinates) >on a surface of over-lapping spheres? > > If so i would be very interested,and will summarise >any replies that i get for respondants. > > thank-you > Noj Malcolm > > Noj.Malcolm@man.ac.uk > ............................................................................ Thanks to all who replied, i had tried implementing a triangulation method for generating the points around the spheres, this is of course the easy bit. Removing points that are too close (on adjacent spheres etc.) , and setting up points to replace is as has benn pointed out the "tricky" bit. This is probably a larger problem than i first imagined and involves more work than i have time for at the moment. ............................................................................ ............................................................................ I would be particularly interested in your summary. I have written a program (GERM) to generate a receptor site model by placing a shell of atoms around one or more active ligands. I first tried a rectangular grid of points for generating the shell. Currently I am generating a shell by (1) centering the ligand(s) in the coordinate system; (2) placing points on a sphere much larger than the ligands; (3) bringing each point in radially toward the origin until it contacts the ligands. It's better than the rectangular grid, but I suspect it is still not ideal. Please let me know what you find. Best regards, Eric Walters D. Eric Walters, Ph.D., Associate Professor, Biological Chemistry Finch University of Health Sciences/The Chicago Medical School 3333 Green Bay Road, North Chicago, IL 60064 ph 708-578-3000, x-498;fax 708-578-3240; email: walterse@mis.finchscms.edu ............................................................................ ............................................................................ It depends what you mean by "equally-spaced": this is not as simple mathematically as you may think. I think that the "gnomonic projection" should interest you - see the papers from P. M. Dean's group (J. Molec. Graph. 5, 97, (1987) and later papers). In addition about 1 year ago there was a similar posting (I think from the group at U. Montreal) on CCL about methods to disperse points on the surface of a sphere. There were quite a number of replies - you should definitely check the archives. Yours, Richard Bone __________________________________________________________ Richard G. A. Bone, PhD. Computational Chemist Terrapin Technologies, Inc. South San Francisco USA E-mail rgab@trpntech.com ............................................................................ ............................................................................ It's not quite clear to me what type of point distribution you're interested in but you should have a look at GEOPOL from QCPE, e-mail qcpe@ucs.indiana.edu. This "vanilla" f77 program generates an regular array of points on the surface of intersecting spheres (polyhedra) such that each point then represents an equal fraction of the spheres surface area. Points within neighboring spheres are eliminated. The equilateral triangles, tesserae, formed by neighboring points give the appearance of a geodesic dome if visualized - a more pleasing appearance than simple dots. GEOPOL is very fast and you, as I have, could easily compute higher dot densities by computing the centers of the tesserae and extrapolating to the sphere's surface. You might also want to check an article by Truhlar, Cramer, et. al., in the most recent J. Comp. Chem. on improved solvation models for AMSOLV, also available from QCPE. They discuss their new/improved method analytical computation of solvent-accessible surface areas. _______________________________________________________________________ / \ | Comments are those of the author and not Unilever Research U. S. | | | | Karl F. Moschner, Ph. D. | | | | Unilever Research U. S. e-mail: Karl.F.Moschner@urlus.sprint.com | | 45 River Road Phone: (201) 943-7100 x2629 | | Edgewater, NJ 07020 FAX: (201) 943-5653 | \_______________________________________________________________________/ ............................................................................ ............................................................................ I was impressed with the optimal distribution of points on the surface of a sphere given by Scott leGrand and Ken Merz in J Comp. Chem. 14, 349-352 (1993) in their paper titled, "Rapid Approximation to molecular surface area via the use of boolean logic and look-up tables". Their implementation minimizes the function: U(x,y) = SUM((180 - B)**2) where B is the arc length on the sphere in degrees between points x and y. -----> richard *********************************************************** Richard D. Macdonald, Ph.D. voice: (619) 546-5527 Lead Scientist fax: (619) 458-0136 Biosym Technologies internet: richard@biosym.com 9685 Scranton Road San Diego, CA 92121-2777 *********************************************************** ............................................................................ ............................................................................ The following article proposes an improved 'marching-cube' method for molecular surface triangulation. -Dongchul Lim, Dept. of Chemistry, Yale Univ. X. Zhexin, S. Yunyu, and X. Yingwu, "Calculating the Electric Potential of Macromolecules: A Simple Method for Molecular Surface Triangulation", J. Comp. Chem. 1995, 16, 512-6. ............................................................................ ............................................................................ > > The following article proposes an improved 'marching-cube' method > for molecular surface triangulation. > -Dongchul Lim, Dept. of Chemistry, Yale Univ. > > X. Zhexin, S. Yunyu, and X. Yingwu, "Calculating the Electric > Potential of Macromolecules: A Simple Method for Molecular > Surface Triangulation", J. Comp. Chem. 1995, 16, 512-6. I belive that the marching cubes algorithm is already implemented in the program GRASP available from Anthony Nicholls (Barry Honig's group). He can be reached at nicholls@cuhhca.hhmi.columbia.EDU. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? "-Albert Einstein" _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ ............................................................................ ............................................................................ From arthur@pchindigo2.IPC.PKU.EDU.CN Mon Apr 3 10:12:33 1995 Received: from pchindigo2.IPC.PKU.EDU.CN for arthur@pchindigo2.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/930601.1506) id KAA13735; Mon, 3 Apr 1995 10:03:18 -0400 Received: by pchindigo2.IPC.PKU.EDU.CN (920330.SGI/911001.SGI) for chemistry@ccl.net id AA01661; Fri, 3 Mar 95 22:04:09 +0800 Date: Fri, 3 Mar 1995 22:04:08 +0800 (SST) From: Wang Arthur To: CCL mailing list Subject: Re: CCL:Q:Free Energy Perturbation In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sun, 2 Apr 1995, Steven Schafer wrote: > > Can anyone recomend any good introductory books or articles on the > topic of Free Energy Perturbation Theory? Hi, Steven! Look at Chem.Rev., 1993, 93:2395-2417. This is a good review with many many cross references. Regards, Arthur +===========================================================+ | | | Arthur Wang Doctoral Candidate | | | | Molecular Design Lab | | Institute of Physical Chemistry, Peking University | | Beijing 100871, P.R.China | | | | E-mail: arthur@pchindigo2.ipc.pku.edu.cn | | Tel: 86-10-2501490 Fax: 86-10-2501725 | | WWW: ftp://162.105.177.1/sys/www/arthur/homepage.html | | http://www.ipc.pku.edu.cn/arthur/homepage.html | | | +===========================================================+ From stoutepf@chemsci1.dmpc.com Mon Apr 3 10:26:19 1995 Received: from gatekeeper.es.dupont.com for stoutepf@chemsci1.dmpc.com by www.ccl.net (8.6.10/930601.1506) id KAA14045; Mon, 3 Apr 1995 10:19:02 -0400 Received: by gatekeeper.es.dupont.com; id AA06997; Mon, 3 Apr 95 10:19:01 -0400 Received: from [158.117.153.76] (esm153076.dmpc.com) by chemsci1.dmpc.com (4.1/SMI-4.1) id AA05793; Mon, 3 Apr 95 10:17:27 EDT Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Organization: The DuPont Merck Pharmaceutical Company X-Mailer: Eudora 1.5.1 for Macintosh Date: Mon, 3 Apr 1995 10:19:41 -0500 To: kamal@univ-orleans.fr (Kamal Azzaoui) From: stoutepf@chemsci1.dmpc.com (Pieter Stouten) Subject: Re: CCL:GROMOS PARAMETERS Cc: chemistry@ccl.net Hi Kamal, >I try to make MD on glucose (beta and alpha conformers) in a water box >using GROMOS force field. >I am looking for angle parameters of O-C-OH where C is the anomeric carbon. >Does any one can help me ? > This is a follow-up to my previous mail. Here are the relevant references: * B.P. van Eijck & J. Kroon, "Molecular Dynamics simulations of -D-ribose and -D-deoxyribose solutions." J. Mol. Struct. 195 (1989) 133. * J. Koehler, W. Saenger & W.F. van Gunsteren, "Molecular Dynamics simulation of crystalline -cyclodextrin at 293K and 120K." Eur. Biophys. J. 15 (1987) 211. I know that van Eijck has done more work on sugars (including glucose), subsequently. Just do a literature search or contact him by e-mail: vaneyck@chem.ruu.nl. Hope this helps, Pieter. -- Pieter Stouten, Senior Research Scientist Computer Aided Drug Design Group The DuPont Merck Pharmaceutical Company P.O. Box 80353, Wilmington, DE 19880-0353 Phone: +1 (302) 695 3515 Fax: +1 (302) 695 2813 Internet: stoutepf@chemsci1.dmpc.com CompuServe: 73172,2004 WWW: http://www.halcyon.com/stouten/stouten.html From ramon@ce.ifisicam.unam.mx Mon Apr 3 11:11:21 1995 Received: from ce.ifisicam.unam.mx.ifisicam.unam.mx for ramon@ce.ifisicam.unam.mx by www.ccl.net (8.6.10/930601.1506) id KAA14858; Mon, 3 Apr 1995 10:56:46 -0400 Message-Id: <199504031456.KAA14858@www.ccl.net> Received: by ce.ifisicam.unam.mx (1.38.193.3/16.2) id AA10272; Mon, 3 Apr 95 09:47:15 -0500 From: Ramon Garduno Subject: Re: CCL:ACS in Anaheim To: chemistry@ccl.net Date: Mon, 3 Apr 95 9:47:15 CDT In-Reply-To: ; from "ch172954" at Mar 31, 95 11:03 pm Mailer: Elm [revision: 70.85] > > Dear Netters, > > > Sometimes ago, I received a message from Dr. Andrew Holder, > through the net, with the subject of " AM1 vs. PM3 " ( the > posting was on Tue, 12 Apr 1994 19:33:55 CST ). I would like > to ask how I can refer to that message in my thesis. Is there > any scientific way for this sort of references. > > Many thanks, > Mansoor > > Hi fellows! I think that this question is easily answered. Just treat it as a personal communication, after all what he got was private mail. Unless he decides to make public the contest of the letter (email) I think there is no need to flame up this issue. Please save band width!! Cheers, Ramon -- ____________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics INSTITUTO DE FISICA | EMAIL: ramon@ce.ifisicam.unam.mx UNIVERSIDAD NAL. AUTONOMA DE MEXICO | rgard@redvax1.dgsca.unam.mx Laboratorio de Cuernavaca | VOICE: (73)175388 Apdo. Postal 139-B | (73)111611 62191 Cuernavaca, Morelos | FAX: (73)111603 MEXICO | (73)173077 ___________________________________ EOF _____________________________________ From mayer@cric.chemres.hu Mon Apr 3 11:41:19 1995 Received: from cric.chemres.hu for mayer@cric.chemres.hu by www.ccl.net (8.6.10/930601.1506) id LAA15541; Mon, 3 Apr 1995 11:27:42 -0400 From: Received: by cric.chemres.hu (AIX 3.2/UCB 5.64/4.03) id AA14729; Mon, 3 Apr 1995 18:27:33 +0200 Date: Mon, 3 Apr 1995 18:27:33 +0200 Message-Id: <9504031627.AA14729@cric.chemres.hu> To: chemistry@ccl.net Subject: Mail was lost Dear Netters, Recently I have posted a message about Ab initio bond orders. Unfortunately, there was a restart at our mashine and any mail you might have sent me was lost. Please repeat your messages. Preferably use this (brand-new) e-mail address. Sorry and thank you. Istvan Mayer Central Research Institute for Chemistry of the Hungarian Academy of Sciences E-mails: mayer@cric.chemres.hu and IB13lVIB@HUEARN.sztaki.hu (or IB13lVIB@HUEARN.bitnet) (Reserve path: H1376May@ella.hu or H1376May@HUELLA.bitnet) From PA13808@UTKVM1.UTK.EDU Mon Apr 3 11:46:15 1995 Received: from phem3 for PA13808@UTKVM1.UTK.EDU by www.ccl.net (8.6.10/930601.1506) id LAA15595; Mon, 3 Apr 1995 11:31:24 -0400 From: Received: from UTKVM1.BITNET (MAILER@UTKVM1) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HOWFOXGIW098R5GZ@phem3.acs.ohio-state.edu>; Mon, 3 Apr 1995 11:31:06 EDT Received: from UTKVM1.UTK.EDU (PA13808) by UTKVM1.BITNET (Mailer R2.10 ptf000) with BSMTP id 3043; Mon, 03 Apr 95 11:16:48 LCL Date: Mon, 03 Apr 95 11:05:01 LCL Subject: SUN install of G92 To: comp chem network Message-id: <01HOWFP0XDHY98R5GZ@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT After almost two years of legal wrangling we managed to get a site licence for G92. However we are now having installation problems and would appreciate advice. In attempting to run on a SUN Solaris ( SUM OS 5.3) with compiler version 3.0 optimisation causes an error message DATA TREE IS CORRUPTED This could be due to our using a later compiler than was used for the progr am. It leads to a great deal of frustration when trying to run many of the test cases. Any ideas on how to get rid of this error. In trying to instal on an IBM MVS machine( dont ask why, please) we try to use the fancy installation pro supplied by IBM and it doesnt work and IBM apparently too busy to offer help at the present time. Any one else tried to d install G92 on an IBM/3090. and how did you do it. PA13808 at UTKVM1.utk.edu( John Bloor, Univ. Tenn.at Knoxville) From rbw@msc.edu Mon Apr 3 15:56:21 1995 Received: from noc.msc.edu for rbw@msc.edu by www.ccl.net (8.6.10/930601.1506) id PAA21825; Mon, 3 Apr 1995 15:49:29 -0400 Received: from uh.msc.edu by noc.msc.edu (5.65/MSC/v3.0.1(920324)) id AA29480; Mon, 3 Apr 95 14:48:51 -0500 From: rbw@msc.edu (Richard Walsh) Received: (rbw@localhost) by uh.msc.edu (8.6.8.1/8.6.6) id OAA22147 for chemistry@ccl.net; Mon, 3 Apr 1995 14:48:49 -0500 Date: Mon, 3 Apr 1995 14:48:49 -0500 Message-Id: <199504031948.OAA22147@uh.msc.edu> To: chemistry@ccl.net Subject: Semi-empirical parameters for Ag ... Hello, There was some discussion of Ni parameters for semi-empirical methods over the last week; what is the current state of development of parameters for Ag. Replies from the authors/vendors of MOPAC, AMPAC, MNDO, SPARTAN, and HYPERCHEM might be expected. Are there references? Sincerely, Richard Walsh Minnesota Supercomputer Center, Inc. From ramon@ce.ifisicam.unam.mx Mon Apr 3 16:26:21 1995 Received: from ce.ifisicam.unam.mx.ifisicam.unam.mx for ramon@ce.ifisicam.unam.mx by www.ccl.net (8.6.10/930601.1506) id QAA22365; Mon, 3 Apr 1995 16:21:30 -0400 Message-Id: <199504032021.QAA22365@www.ccl.net> Received: by ce.ifisicam.unam.mx (1.38.193.3/16.2) id AA10404; Mon, 3 Apr 95 15:11:58 -0500 From: Ramon Garduno Subject: PROCHECK To: chemistry@ccl.net (POST MSG's) Date: Mon, 3 Apr 95 15:11:58 CDT Mailer: Elm [revision: 70.85] Dear Netters: Today I sent an email to Dr. Roman Laskowski author of PROCHECK: a program to check the stereochemical quality of protein structures (J. Appl. Crys. V26:283 (1993)). the email address given in his paper is roman@uk.ac.ucl.bioc.bsm but all I got was 501 ... 550 Host unknown (Name server: uk.ac.ucl.bioc.bsm: host not found) Thus, my question is obvious. Does any one of you know of his whereabouts? It may help if you know that the address given in the paper was Biomolecular Structure and Modelling Unit, Dept. of Biochemistry and Molecular Biology, University College, Gower Street, London, England. Cheers, -- ____________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics INSTITUTO DE FISICA | EMAIL: ramon@ce.ifisicam.unam.mx UNIVERSIDAD NAL. AUTONOMA DE MEXICO | rgard@redvax1.dgsca.unam.mx Laboratorio de Cuernavaca | VOICE: (73)175388 Apdo. Postal 139-B | (73)111611 62191 Cuernavaca, Morelos | FAX: (73)111603 MEXICO | (73)173077 ___________________________________ EOF _____________________________________ From gavin@vangogh.chem.uab.edu Mon Apr 3 18:41:23 1995 Received: from vangogh.chem.uab.edu for gavin@vangogh.chem.uab.edu by www.ccl.net (8.6.10/930601.1506) id SAA24170; Mon, 3 Apr 1995 18:27:32 -0400 From: Received: by vangogh.chem.uab.edu (AIX 3.2/UCB 5.64/4.03) id AA17791; Mon, 3 Apr 1995 17:21:46 -0500 Date: Mon, 3 Apr 1995 17:21:46 -0500 Message-Id: <9504032221.AA17791@vangogh.chem.uab.edu> To: CHEMISTRY@ccl.net Subject: INSTABILITY Cc: GAVIN@vangogh.chem.uab.edu Dear Nettlers, Someone can show me how to do the instability analysis ? ANY INFO will appreciate! Gavin Tsai From raman@bioc01.uthscsa.edu Mon Apr 3 19:11:23 1995 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.10/930601.1506) id TAA24497; Mon, 3 Apr 1995 19:03:47 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Mon, 3 Apr 1995 18:07:19 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA20581; Mon, 3 Apr 95 18:03:35 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9504032303.AA20581@bioc01.uthscsa.edu> Subject: Re: CCL:PROCHECK To: ramon@ce.ifisicam.unam.mx (Ramon Garduno) Date: Mon, 3 Apr 1995 18:03:34 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <199504032021.QAA22365@www.ccl.net> from "Ramon Garduno" at Apr 3, 95 03:11:58 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 3703 Ramon: > Today I sent an email to Dr. Roman Laskowski author of PROCHECK: a program > to check the stereochemical quality of protein structures (J. Appl. Crys. To get PROCHECK you need to complete the license agreement available via the PDB gopher site and return it to them. I am appending the information for acquiring this program: ************************************************************************** We are pleased to announce that the Procheck software package is being made available for electronic distribution from the PDB. Oxford Molecular, Ltd. and the PDB have agreed that, upon receipt of a signed license agreement at the PDB, the source and documentation for Procheck will be made available free of charge. The Procheck software package which was created by J. M. Thornton, M. W. MacArthur, R. A. Laskowski, and D. S. Moss, performs evaluations of the stereochemical quality of protein structures. In order to acquire a copy of Procheck, you must obtain the license agreement, copies of which are available via ftp or gopher from the PDB in the file called procheck-license. You must complete and sign this license agreement, returning it to the PDB. Once we have your signed agreement, we will either e-mail the source to you or place it on the machine of your choice via ftp. Your signed license agreement will be forwarded to Oxford Molecular who will keep you up to date about further developments. All queries concerning the software should be directed to Steve Gardner at Oxford Molecular at the address below. Dr. Steve Gardner Macromolecular Product Mananger Oxford Molecular, Ltd. The Magdalen Centre Oxford Science Park Sanford-on-Thames Oxford, England OX4 4GA (Tel: +44-865-784600) ************************************************************************* > V26:283 (1993)). the email address given in his paper is > roman@uk.ac.ucl.bioc.bsm but all I got was > 501 ... > 550 Host unknown (Name server: uk.ac.ucl.bioc.bsm: host not found) > just do a 180 degree flip of everything after the @ symbol and it should work fine. Cheers -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? "-Albert Einstein" _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From jeremy@med.su.oz.au Mon Apr 3 21:56:25 1995 Received: from blackburn.med.su.oz.au for jeremy@med.su.oz.au by www.ccl.net (8.6.10/930601.1506) id VAA26132; Mon, 3 Apr 1995 21:53:30 -0400 Received: (jeremy@localhost) by blackburn.med.su.oz.au (8.6.10/8.6.4) id LAA26649 for chemistry@ccl.net Tue, 4 Apr 1995 11:51:45 +1000 From: Jeremy R Greenwood Message-Id: <199504040151.LAA26649@blackburn.med.su.oz.au> Subject: nmr & point charges / free-radical visualisation To: chemistry@ccl.net Date: Tue, 4 Apr 1995 11:51:44 +1000 (EST) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1454 Dear CCL, Two unrelated queries: -------------------------------------------------------------------------- Firstly, it occurs to me, that since the chemical shift of a proton or carbon 13 nucleus depends on electronic shielding (in an nmr experiment), there should be some (at least loose and qualitative) correlation between point charges calculated by one or other theoretical method, and chemical shift (not withstanding solvent effects). I am attempting to identify the correct structures of some isomeric heterocycles from their 1H and 13C spectra. Would you expect changes in point charges to reflect changes in shift between equivalent centres of the isomers? If so, calculated by which method? I'm using semi-empirical (AM1, PM3), and HF calculations. My intuition is that ESP-derived charges are more likely to reflect trends in chemical shift. -------------------------------------------------------------------------- Secondly, I am interested in visualising localisation of free radicals calculated by MOPAC or G92. Some kind of map of spin density would seem to be an appropriate method. Can anyone suggest software (preferably cheap or free!) which can extract and produce this kind of output? I believe that Spartan has this capability, but is outside our price-range. -------------------------------------------------------------------------- Jeremy Greenwood Department of Pharmacology University of Sydney NSW 2006 Australia From ch172954@student.uq.edu.au Mon Apr 3 22:56:26 1995 Received: from student.uq.edu.au for ch172954@student.uq.edu.au by www.ccl.net (8.6.10/930601.1506) id WAA26556; Mon, 3 Apr 1995 22:47:31 -0400 Received: from student.uq.edu.au (ch172954@localhost [127.0.0.1]) by student.uq.edu.au (8.6.10/8.6.9) with SMTP id MAA19404; Tue, 4 Apr 1995 12:46:59 +1000 Date: Tue, 4 Apr 1995 12:46:53 +1000 (GMT+1000) From: ch172954 To: Ramon Garduno cc: chemistry@ccl.net Subject: Citation In-Reply-To: <199504031456.KAA14858@www.ccl.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 3 Apr 1995, Ramon Garduno wrote: > > I think that this question is easily answered. Just treat it as a > personal communication, after all what he got was private mail. Unless > he decides to make public the contest of the letter (email) > Hello there, I would like to add that the message was not a private communication as far as you consider " chemistry@ccl.net" a public mail server; besides, many responses have been delivered during the time. Now, I would like to ask if there is an archive for these articles and whether or not they are available by anonymous-ftp. Finally, those who have been interested in the original article I will send them by snail post, since I have just access to the hard copy at the moment, or perhaps Dr. Andrew Holder can help me to send it again to the net, if he has access to the article. Best Regards, Mansoor