From darrena@chem.leeds.ac.uk Thu Mar 26 08:20:17 1998 Received: from chemistry.leeds.ac.uk for darrena@chem.leeds.ac.uk by www.ccl.net (8.8.3/950822.1) id HAA03691; Thu, 26 Mar 1998 07:41:25 -0500 (EST) Received: from [129.11.12.138] (chmmac37.leeds.ac.uk [129.11.12.138]) by chemistry.leeds.ac.uk (8.8.8/8.8.8) with ESMTP id MAA03141 for ; Thu, 26 Mar 1998 12:40:24 GMT Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 26 Mar 1998 12:33:26 +0000 To: chemistry@www.ccl.net From: Darren Andrews Subject: SPECSIM Does anybody know where to get hold of the rotational contour analysis package SPECSIM, which I believe was written by Terry Miller? Darren Andrews. PostGraduate Student, School of Chemistry, University of Leeds, Leeds. LS2 9JT. England. Darrena@chem.leeds.ac.uk Tel: 0113 233 6594. Fax: 0113 233 6565. From mathieu@ripault.cea.fr Thu Mar 26 11:20:19 1998 Received: from nenuphar.saclay.cea.fr for mathieu@ripault.cea.fr by www.ccl.net (8.8.3/950822.1) id KAA04884; Thu, 26 Mar 1998 10:40:47 -0500 (EST) Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.8.8/CEAnet-relay-4.1.1) with ESMTP id QAA10497 for ; Thu, 26 Mar 1998 16:40:22 +0100 (MET) Received: from cerbere.limeil.cea.fr (cerbere.bruyeres.cea.fr [132.165.76.1]) by muguet.saclay.cea.fr (8.8.8/CEAnet-relay-4.1.1) with SMTP id QAA13678 for ; Thu, 26 Mar 1998 16:40:21 +0100 (MET) Received: by cerbere.limeil.cea.fr (CEANET-1.1+) id AA28545; Thu, 26 Mar 1998 16:38:31 +0100 Received: from indre.ripault.cea.fr(132.165.32.1) by cerbere via smap id sma028543; Thu Mar 26 16:38:14 1998 Received: from ripault.cea.fr (cher.ripault.cea.fr [132.165.32.3]) by ripault.cea.fr. (8.8.5/8.7.3) with ESMTP id QAA06687 for ; Thu, 26 Mar 1998 16:38:49 +0100 Received: from cher.ripault.cea.fr (localhost [127.0.0.1]) by ripault.cea.fr (8.8.7/8.8.7) with SMTP id QAA02482 for ; Thu, 26 Mar 1998 16:39:38 +0100 Sender: mathieu@ripault.cea.fr Message-Id: <351A76B9.5E20EBE0@ripault.cea.fr> Date: Thu, 26 Mar 1998 15:39:37 +0000 From: Didier MATHIEU Organization: CEA - Le Ripault X-Mailer: Mozilla 3.01 (X11; I; Linux 2.0.32 i586) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: MOLDY error message Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, We are beginning some molecular dynamics simulations of organic liquids with the MOLDY program. Unfortunately, an error is frequently encountered : > Too many sites (14) for neighbour list arrays (13 slots). > Increase NMULT in "force.c". We get this message with NMULT=3, while attempting preliminary simulations with small numbers of molecules (10-64). Therefore the system may not be inhomogeneous ? Apparently, changing the size of subcells does not help. In fact, according to me, there could be an static array (size 26 ?) of pointers, each pointer being the root of the linked list of neighbour in each of the 26 neighbouring subcells. I suppose the linked list is allocated dynamically. In that case, I really cannot understand what happens... What are the 13 slots mentionned in the error message ? Best regards -- Didier MATHIEU CEA - Le Ripault, BP 16 37260 Monts (France) Tel. 33(0)2.47.34.41.85 From qibvigap@lg.ehu.es Thu Mar 26 14:20:20 1998 Received: from lgsx01.lg.ehu.es for qibvigap@lg.ehu.es by www.ccl.net (8.8.3/950822.1) id NAA06135; Thu, 26 Mar 1998 13:58:39 -0500 (EST) Received: from lgdx04.lg.ehu.es by lgsx01.lg.ehu.es (4.1/4.7 ) id AA22276; Thu, 26 Mar 98 19:32:04 GMT Date: Thu, 26 Mar 1998 19:32:52 +0100 (GMT+0100) From: Pablo Vitoria Garcia To: ccl Subject: Information about MEH-MACC program Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I would like to get some information about the MEH-MACC program. All I know is that it makes charge-consistent Extended-Huckel calculations for molecules and crystals, and several analysis of the electronic density. Does anybody know what computers it runs on and how to get it? Thanks a lot Pablo -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lg.ehu.es Phone: +34 4 4647700 Ext. 2450 -------------------------------------------------------------------------------- From mn1@helix.nih.gov Thu Mar 26 19:20:22 1998 Received: from helix.nih.gov for mn1@helix.nih.gov by www.ccl.net (8.8.3/950822.1) id SAA07637; Thu, 26 Mar 1998 18:34:10 -0500 (EST) Received: (from mn1@localhost) by helix.nih.gov (8.8.5/8.8.5) id SAA00250; Thu, 26 Mar 1998 18:34:10 -0500 (EST) Date: Thu, 26 Mar 1998 18:34:10 -0500 (EST) From: "M. Nicklaus" Message-Id: <199803262334.SAA00250@helix.nih.gov> To: CHEMISTRY@www.ccl.net Subject: G: DFT Resource Usage Cc: mn1@helix.nih.gov Hi, I need information (or pointers thereto) about the resource usage of DFT calculations in G94, specifically the B3LYP method. (I couldn't find too much on detailed resource usage specific for DFT in the Gaussian books.) 1. What are the CPU times spent for the HF two-electron integrals on the one hand vs. the functional integrals on the other hand? 2. Is any--and be it indirect--information about this ratio written in the G94 output? 3. How is the decision made about in-core vs. direct calculation depending on the memory available? Are the same criteria applied for the HF part as for the functional part of the calculation? Again, is any information about this contained in the G94 output? I'll summarize useful answers to the CCL. Thanks in advance for any response. Marc ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 37, Rm 5B29 Phone: (301) 402-3111 37 Convent Dr, MSC 4255 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm Laboratory of Medicinal Chemistry, National Cancer Institute, & Center for Molecular Modeling, Div. of Computer Research and Technology ------------------------------------------------------------------------ From takanori.kanazawa@pharma.Novartis.com Thu Mar 26 21:20:24 1998 Received: from i3se0101.is.chbs.ciba.com for takanori.kanazawa@pharma.Novartis.com by www.ccl.net (8.8.3/950822.1) id UAA08237; Thu, 26 Mar 1998 20:34:05 -0500 (EST) From: Received: from mailhub by i3se0101.is.chbs.ciba.com; (5.65v3.2/1.1.8.2/12Mar96-0208PM) id AA09852; Fri, 27 Mar 1998 02:33:34 +0100 Received: from nts1.novartis.com ([192.168.50.131]) by mta3.is.chbs (8.8.5/8.8.5) with SMTP id CAA07714 for ; Fri, 27 Mar 1998 02:34:04 +0100 (MET) Received: by nts1.novartis.com(Lotus SMTP MTA SMTP MTA v1.1.04 (495.1 10-24-1997)) id 412565D4.00088F2A ; Fri, 27 Mar 1998 02:33:29 +0100 X-Lotus-Fromdomain: PH@N1 To: CHEMISTRY@www.ccl.net Message-Id: <492565D4.000713FC.00@nts1.novartis.com> Date: Fri, 27 Mar 1998 10:32:58 +0900 Subject: Summary - hydration energy : phosphonate anion Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear all, A few days ago, I posted a question about hydration energy of phosphonate(and/or phosphate) anion. Several people have reposned to this question and I'm grateful to them all. My question was >> Does anybody have information about experimental hydration(solvation) energy >> of phosphonate anion or phosphate anion? >> I calculated the solvation energy of CH3PO3(2-) by GB/SA solvation model implemented >> in BatchMin6.0 and it gives c.a. -1200 kJ/mol (= -300 kcal/mol). >>It's quite large compared with a monomeric anion(e.g. experimetal energy for >>acetate ion is -80 kcal/mol). >>M.E.Colvin et al. gives some theoretical results for some phosphorus containing molecules: >> PO4(3-) :-629.2kcal/mol(AM1-SM2), -570.9(PM3-SM3) >> HPO4(2-):-299.9kcal/mol(AM1-SM2), -266.2(PM3-SM3) >> (JACS Vol.117,No.15,4357-4362,(1995)) >> I don't have any further information. 1. Cory (cory@acs.ucalgary.ca) One would expect that the solvation energy would scale as the square of the charge, from Born's equation, so roughly speaking, anions of charge -2 should be stabilized roughly 4 times that of an anion of charge -1. One of the problems of obtaining hydration energies of these kinds of ions are that they can often act as strong bases to give other species as HPO42-. To prevent this one must use very alkaline solutions, but then ionic strength will increase and thus the activity coefficients may deviate significantly from unity. 2. Lars Hemmingsen (lasse@lhe.dina.kvl.dk) The book "Ion solvation" by Y. Marcus (John Wiley and Sons Limited, 1985) contains a lot of references and data, for example for solvation of PO4(3-): -260.5 kcal/mol. 3. Christopher J. Cramer (cramer@pollux.chem.umn.edu) You should recall that the free energy of solvation of an ion goes as the square of the charge (cf. Born formula for charged sphere, delta-G(solv) = (1 - 1/epsilon) * q^2/alpha, where epsilon is the dielectric constant, q is the charge, and alpha is the sphere's radius). So, doubly charged ions should have solvation free energies roughly 4 times those of singly charged analogs. Experimental data are, as far as we are aware, unavailable for ions like those you describe, although "reasonable" estimates can be arrived at by making certain assumptions about entropies, etc., in free energy cycles designed to predict the data. The Colvin paper you cite does as good a job of this as any I've seen. With best regards, Takanori *************************************************************** Takanori Kanazawa, Ph.D. E-mail : takanori.kanazawa@pharma.novartis.com Phone : +81-797-74-2597 FAX : +81-797-74-2598 Drug Discovery Group / CAMM Takarazuka Research Institute Novartis Pharma K.K. 10-66 Miyuki-cho, Takarazuka, Hyogo 665 JAPAN *************************************************************** From iguana@one.net Thu Mar 26 23:20:24 1998 Received: from mail1.one.net for iguana@one.net by www.ccl.net (8.8.3/950822.1) id XAA08689; Thu, 26 Mar 1998 23:01:30 -0500 (EST) Received: from port-31-32.access.one.net ([206.112.210.190] HELO default ident: IDENT-NOT-QUERIED [port 47621]) by mail.one.net with SMTP id <26568-17322>; Thu, 26 Mar 1998 23:01:31 -0500 From: "Ray Crawford" To: chemistry@www.ccl.net Date: Thu, 26 Mar 1998 23:02:00 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Summary: Cool Demos for kids!!! Reply-to: iguana@one.net Priority: normal In-reply-to: <4784381@isis.reed.edu> Message-Id: <19980327040131Z26568-17322+750@mail.one.net> First off, I would like to thank all of you that replied!! I got some really great ideas... They are as follows: //// We have some neat molecular dynamics simulations you can show directly from your web browser at our group's web page: http://www.chem.ucalgary.ca/groups/ziegler >From there go to the CHIME animations or Quicktime animations. The CHIME animations allow you to move and rotate the molecules during the animation (ie. interactive) directly from your web browser with the CHIME plug-in. Tom Woo: tkwoo@zinc.chem.ucalgary.ca ///// My first thought would be to use an example on designing peptide mimetics. Specifically, HIV protease inhibitors have been extensively studied by computational methods. This would be a good example to show models of a peptide, small molecules, and how computational models can be used to optimize drug design. A summary of some of this work (and other peptide mimetics) is in "Reviews in Computational Chemistry" Volume 9, pp 1-80, Lipkowitz and Boyd, Eds. Might give you some ideas for things to look into. Thanks, Ken Lind lind@chet.medc.umn.edu ///// We did some demos for kids aged 8-13 which involved taking different odours and comparing them to the structures of the molecules associated with those smells. We then let a kid build one or two with modelling kits and finally showed how computers could be used to model the more complex ones. It seemed to go down pretty well as we chose common scents like garlic and grapefruit etc and handed them all samples around to smell. btw... I also have some simple animations showing molecular mechanics, conformational analysis and molecular dynamics without any nasty chemistry/maths. If you are interested in these I could mail them to you Steve Todd S.M.Todd@chem.hull.ac.uk ///// We have started to use HyperChem Lite for some "lab demos" for Pharmacy studens. The two activities that I like the best are 1. Determination of the perfered convormation of hexesterol (all three isomers). 2. constructing d-ala-d-ala and comparing the conformation to penicillin. Neither of these oare very hard but the penn one makes them drad a compound with the correct sterochemistry and to view it in a way that most have not done. The hexestero lis good as the meos iosmer is active as an estrogen but the other isomers are nearly inactive. The act is due to the 11-12 anstrom distance between the phenols in mesohexesterol, a conformation not likely in the other compounds. jlb ////// I would calculate a reaction an show the reaction with a movie, which you can make with the MOLDEN program package. You can do the calculations with the G94 (semiempirical) and then read in the output into MOLDEN. Another nice thing is to show the vibrational motions of molecules. Again the same way, use G94 to calculate the harmonic frequencies (you have to make this calculation alone not together with the geometry optimization because MOLDEN has a bug!), read in the output and then show simply the vibrational motions. In my opinion this looks quite nice. bernd engels bernd@rs5.thch.uni-bonn.de ///// There are some neat molecules to view; HIV protease has an interesting alpha-carbon trace, and i happen to thing cyclodextrins look cool also. Other neat protein motifs include "beta barrels" and alpha helices. Then there's DNA of course. With quanta/charmm, you could run MD on a small molecule and view the conformations on-screen. Michael K. Gilson gilson@indigo14.carb.nist.gov ////// I've found most college students (including chemistry majors) are impressed with high resolution graphics no matter what they show. Some of the things I've done in the past are: 3-D model of sucrose; models of structures with similar physical properties (tastes are good) complete with "samples" for munching, and a lot of good graphics on the web. You're welcome to look at links I used for my comp chem class this quarter (Chem 500 link from my home page) particularly weeks 6 and 10. There's also a like to some wonderful graphics from (Cornell?) super computing center. Hope this helps Kimberley Cousins kcousins@wiley.csusb.edu ////// Thanks again, Ray Crawford Research Associate The Procter & Gamble Company crawford.ra@pg.com Ray Crawford Iguana's Dynamic Links List http://w3.one.net/~iguana/Dynamic_Links_List/links.html iguana@one.net