From arthur@csb0.IPC.PKU.EDU.CN Fri Dec 1 02:54:34 1995 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/950822.1) id CAA19680; Fri, 1 Dec 1995 02:42:47 -0500 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA09340; Fri, 1 Dec 95 14:37:40 -0800 Date: Fri, 1 Dec 1995 14:37:39 -0800 (PST) From: Arthur Wang To: CCL mailing list Subject: Summary of 3D to 2D conversion Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, CCLers, Last week I put forward the question "How to convert 3D to 2D". From then, I have received many responses. It seems an exactly same question was asked before, Paul Soper's summary proves much help. A few of new comments are added to the summary below, may it be useful. ------------------------------------------------------------------------------ My original question is: Are there any softwares whcih can convert 3D structures of small organic compounds from, say, MOL2 or PDB format to comfortable 2D topological structures? ------------------------------------------------------------------------------ From: J.A.C. Rullmann, rull@nmr.chem.ruu.nl Maybe the program LIGPLOT, developed at UCL, could help you. LIGPLOT is advertised as a tool for automatically generating schematic diagrams of protein-ligand interactions for a given PDB file, byt maybe it will work for your type of problem too. See the WWW page: http://www.biochem.ucl.ac.uk/~roman/ligplot/ligplot.html Example outputs are included. ------------------------------------------------------------------------------ From: soperpd@nylon.es.dupont.com (Paul D. Soper) I recently asked for programs which could convert 3D structures to 2D drawings. The replies, which follow, included these programs: Cambridge Crystal Structure Database System CAMEO Catalyst - MSI ChemDraw & Chem3D - Cambridge Scientific Chemeleon - Exographics Chemistry 4D-Draw - ChemInnovation Depict, Daylight Programmers Toolkit - Daylight Simon Kilvington provided the following reference: D.Weininger; "Smiles 3. Depict. Graphical depiction of chemical structures." J. Chemical Information and Computer Sciences, 30 (1990) pp237-243. Layout - MDL Sybyl, Unity, dbtranslate - TRIPOS Bob Zinn suggested the transform xp(i)=y(i)-x(i) yp(i)=(x(i)+y(i)-2*z(i))/2 which he has implemented in MathCAD ------------------------------------------------------------------------ From: dough@mdli.com If you have access to MACCS, with 3D module, at your site, you can do MEDIT GET FILE - some 3D MDL molfile MEDIT FLATTEN - this generates bond hash and wedge marks - optional... MEDIT CLEAN - this does what the CLEAN command in MACCS Draw menu does It may take a couple of cycles of MEDIT CLEAN to get an acceptable structure. There is also a LAYOUT program which does a lot more in the way of orienting and layout. Other vendors have similar capability - e.g., Daylight's DEPICT, and any of the programs which input SMILES. The Exographics Chemeleon program has some 2D modeling capability, too. ------------------------------------------------------------------------ From: Harold Helson The program CAMEO (Computer-Assisted Mechanistic Evaluation of Organic Reactions) can read PDB files and redraw them in two-dimensions. There might be a Mac version of this program available now. If you are interested, you can contact Professor William L. Jorgensen: bill@adrik.chem.yale.edu ------------------------------------------------------------------------ From: bob.zinn@chemgate.chem.lsu.edu (bob zinn) in a program I wrote a few years ago, to display molecules from x,y,z coordinates as stereo pairs, I plotted xp(i)=y(i)-x(i) and yp(i)=(x(i)+y(i)-2*z(i))/2 as one of the pictures. the other one had the coordinates transformed by a small rotation around the center. If you have mathcad available, I can send a copy of the program. It kind of worked ok for the proteins a professor was working with. The rotation was kinda slow, when I was trying to see how things lined up in the molecule. I think the 3d-2d transformation shown above came from one of mathcad's examples. ------------------------------------------------------------------------ From: wallyr@netcom.com (Walter E. Reiher III) I am aware of two such systems: software distributed by Daylight Chemical Information Systems and by Tripos Inc. I have not personally used the Daylight software, so I'm not 100% certain they can take a 3D structure + connection table and create such a depiction, but I'm pretty sure then can: they can certainly create a depiction from a connection table specified as a SMILES string. I have used the Tripos software in the Unity database package and the Molecular Spreadsheet. I would advise you that the depictions from the Tripos software are generally dismal; they seldom look anything like what a chemist would draw using a chemical drafting program. What I've seen of the Daylight depictions aren't great but better than Tripos'. Cambridge Scientific, the ChemDraw people, may be able to do this since Chem3D and ChemDraw seem to work together; it's worth a call to them. ------------------------------------------------------------------------ From: ellen@nautilus.ariad.com (Ellen R. Laird) If your site maintains a Sybyl license, the following may be of interest: I have seen a brief demonstration of a new SPL script that I am told is integrated into the newest version of Sybyl (6.1). For the cases to which I saw it applied, the results were very pleasing. ------------------------------------------------------------------------ From: nxb96@acs.org (Nanette Butterworth) Hello, There is a product by ExoGraphics called Consystant/Chemeleon which does exactly that. The 3-D formats it supports are: AlchemyIII, Mol MDL's Mol Beilstein's ROSDAL Tripos' SYBYL, Mol2 Tripos' SYBYL Line Notation BioSym BioCad HyperChem, Hin The 2-D formats is supports are: ISISDraw Molecular Presentation Graphics ChemPrint (near future) ChemWindows/ChemIntosh The price of this product for ACS members is $159. On December 1 the price may be reduced even lower. To order this product call ACS at1-800-227-5558 and select 9, 1, 1 on the voice menu. Good luck! NB ------------------------------------------------------------------------ From: MARTIN%cmda@randb.abbott.com The pictures are ok, not great, by using the Daylight software Depict. Also Sybyl will do this. Both give postscript output. ------------------------------------------------------------------------ From: "A.Masunov" Try the software accompanying Cambridge Crystal Structure Database. I've seen the output of the last version. It contains nice structural formulas even for cage molecules. ------------------------------------------------------------------------ From: Mike Wang Here is a program which may indirectly help you if you know the IUPAC names of the structures: Chemistry 4D-Draw (tm) is an advanced drawing program with an intelligent module, NamExpert, that understands IUPAC organic nomenclature rules. The program interprets chemical names and automatically creates high quality structures. It provides intelligent drawing tools for creating publication-quality graphics. It allows you to create structure templates with user-defined trivial names. ------------------------------------------------------------------------ From: Leif Norskov Catalyst from MSI and Unity from Tripos will both do that. Catalyst does it very nicely, too. But in both cases it is a bit like using a Ferrari instead of a bicycle to go a few blocks across town. ------------------------------------------------------------------------ From: Dave Cosgrove This one cropped up a few months ago, but I don't think a summary was posted. Perhaps you could post a summary when you've got some answers, just for the archive! My own solutions to this problem are two-fold : There is a Depict toolkit from Daylight (try yosi@daylight.com) that will take a SMILES string and produce a set of 2D structures. We have some quibbles about the pictures produced ( straight chain alkanes come out as a straight line, for instance ), but the toolkit is cheap(ish) for what it does. I think you would probably need to buy the SMILES toolkit as well, but I don't think the two together come to more than 5000 pounds sterling ( I don't have a dollar price). With the SMILES toolkit you are no longer restricted to SMILES strings, since you can read any file and build the molecule into a SMILES string before calling Depict to produce the coordinates. These are toolkits, however, you need to build them into a program, in any of C, C++, FORTRAN or even, I believe, Ada and Pascal. If you have Sybyl, you can persuade it to produce fairly dodgy 2D pictures, from a SMILES string, using the following commands: SMILESTOMOL M1 TRUE MOL OUT M1 Again, this uses a SMILES string as input. In principle you can get Sybyl to create a SMILES string for you, from a file you have read in, but in my experience this is frequently unsuccessful. ------------------------------------------------------------------------ From: Simon Kilvington the Daylight programmers toolkit will do what you want - sorry I don't have an address, but I do have a reference to a description of how the connection table to 2D representation works if you want to write your own version. D.Weininger; "Smiles 3. Depict. Graphical depiction of chemical structures." J. Chemical Information and Computer Sciences, 30 (1990) pp237-243. ------------------------------------------------------------------------ From: Tom Moock x1301 In response to your question about 3D -> 2D conversion: I don't know of a program that takes 3d coordinates and returns a "2D" representation of it. It brings to mind some sort of 2D optimization, or flattening, of the structure, that still retains some of the original relative atom positions. However, there are programs that take a connection table, with NO coordinate info, and generates a 2D picture. Here at MDL we have a program called LAYOUT, although the demand for it has been light in the last several years. Daylight also has a program DEPICT that runs on smiles codes, and does a similar thing. There are a few other database products (Questel Darc) that do not store coordinates in their databases, but generate them upon retrieval. ------------------------------------------------------------------------ From: Brian Karlak I've found that dbtranslate, in Tripos' suite of Unity products, can perform the 3D -> 2D coordinate translation by translating the 3D structure into SMILES or SLN (which contain only connectivity info, thus stripping the coordinate info) and then translating that file into a sybmol, sybmol2 or maccs file. The double translation can be performed with a single Unix command and is very fast. ------------------------------------------------------------------------ From: Matt Stahl The best answer to your question can be found by searching the comp. chem. archives. The last time the question was asked there were numerous responses. The short of it is (if i recall correctly) that there are programs to do what you want - but nothing particularly cheap. ----------------------------------------------------------------------- From: Andreas Goeller In principal you can read it in Hyperchem and cut and paste it in C-Design/ Chem structure. I think this works also with other Windows programs also. --------------------------------------------------------------- From: Paul Soper I asked the same question a while back. Here is the summary I posted: (SEE ABOVE) ----------------------------------------------------------------- From: "tamasgunda@tigris.klte.hu" I think the problem is the same as in the case of another quite often heard question: is there any program to convert a SMILES string back to graphical structure? Generally, how to draw/restore the structure >from pure connectivity information, and in turn, the result should please the eyes of organic chemists. There are some programs, but as a whole, I am quite pessimistic. It can be done easily in the case of aniline or dodecylbromide, but how about a complicated natural product like taxol or strychnine or a cyclopeptide or a macrolid antibiotics? It is nearly impossible to create an algorithm which could figure out what kind of projection is the "desired" one. Maybe a program with an immense structural library could solve the majority of the cases. ----------------------------------------------------------------------------- From: Eric Martin Daylight makes utility programs to convert MDL or PDB files to SMILES, which can then be depicted with their prado program. Good luck. ---------------------------THE END------------------------------------------- From info@anny.psgvb.com Fri Dec 1 04:09:35 1995 Received: from anny.psgvb.com for info@anny.psgvb.com by www.ccl.net (8.6.10/950822.1) id DAA20521; Fri, 1 Dec 1995 03:56:26 -0500 Received: by anny.psgvb.com (931110.SGI/920502.SGI.AUTO) for chemistry@www.ccl.net id AA21429; Fri, 1 Dec 95 00:56:24 -0800 Date: Fri, 1 Dec 95 00:56:24 -0800 From: info@anny.psgvb.com (Info at Schrodinger Inc.) Message-Id: <9512010856.AA21429@anny.psgvb.com> To: chemistry@www.ccl.net Subject: PS-GVB version 2.2 release Dear CCLers, Version 2.2 of Schrodinger, Inc.'s electronic structure software, PS-GVB, has just been released. This version's new features include transition state optimization, geometry optimization in solution, IR intensities, and thermochemical properties. PS-GVB contains the fastest set of electronic structure algorithms available, with extremely efficient scaling with basis set size. Other features include o Hartree-Fock, MP2, and density functional theory (DFT) wavefunctions o extremely rapid local MP2 (LMP2) algorithms, including "local local" MP2 o robust, efficient generalized valence bond (GVB) and GVB-RCI algorithms o ab initio molecular structure optimizations in gas phase or in solution o frequencies, hyperpolarizabilities, charge fitting, and other properties Please check out our Web page, http://www.psgvb.com/, if you would like more information, or contact us by email at info@psgvb.com with any questions you have. Thanks for your attention. -- Schrodinger, Inc. / info@psgvb.com / (800) 20-PSGVB / 818-568-9778 (fax) 80 S. Lake Avenue, Suite 735, Pasadena, CA 91101 / http://www.psgvb.com/ From owner-chemistry@ccl.net Fri Dec 1 05:24:36 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id FAA21360; Fri, 1 Dec 1995 05:16:25 -0500 Received: from pchindigo2.IPC.PKU.EDU.CN for zhy@pchindigo2.IPC.PKU.EDU.CN by bedrock.ccl.net (8.7.1/950822.1) id FAA11940; Fri, 1 Dec 1995 05:16:15 -0500 (EST) Received: by pchindigo2.IPC.PKU.EDU.CN (920330.SGI/911001.SGI) for chemistry@ccl.net id AA02550; Fri, 10 Nov 95 17:10:09 +0800 Date: Fri, 10 Nov 1995 17:10:08 +0800 (SST) From: Zhang Hongyu To: COMP_CHEM_LIST Subject: Grade of Journals. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers, As I have a paper on protein loop modeling waiting to be submitted to international journals, I'd like to know how most of you consider the accademic grade and/or level of popular computational chemistry and structural biology journals (Of course, except Nature & Science :-) ). Since this probably is a sensitive topic ( perhaps for those publishers and editors :-( ), please email directly to me if you are kind to introduce it or have same interest. Henry ---------------------------------------------------------------------- Henry Hongyu Zhang, Ph.D. student | email: zhy@ipc.pku.edu.cn Molecular Design Laboratory | zhy@pschnetware.pku.edu.cn Institute of Physical Chemistry | Tel: 8610-2501490 Peking University | Fax: 8610-2501725 Peking 100871 , China | URL: http://www.ipc.pku.edu.cn/moldsgn/ | zhy/hom.htm Too hard, to be broken Too soft, to be worthless * Old Chinese Saying * --------------------------------------------------------------------- From rull@rhino.chem.ruu.nl Fri Dec 1 05:54:36 1995 Received: from chemail.chem.ruu.nl for rull@rhino.chem.ruu.nl by www.ccl.net (8.6.10/950822.1) id FAA21611; Fri, 1 Dec 1995 05:40:07 -0500 Received: from rhino (rhino.chem.ruu.nl) by chemail.chem.ruu.nl with SMTP id AA19786 (5.67b/IDA-1.5 for <@chemail.chem.ruu.nl:chemistry@www.ccl.net>); Fri, 1 Dec 1995 11:41:03 +0100 Received: by rhino (940816.SGI.8.6.9/940406.SGI.AUTO) id LAA07708; Fri, 1 Dec 1995 11:40:36 GMT From: "Ton Rullmann" Message-Id: <9512011140.ZM7706@rhino.chem.ruu.nl> Date: Fri, 1 Dec 1995 11:40:33 +0000 Reply-To: rull@ruuci9.chem.ruu.nl X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: X-Windows for Mac Cc: boelens@rhino.chem.ruu.nl Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Last week I posted a summary about MachTen software (Unix for Macintosh), in which I also included some info about X-window emulation on Mac. The X-server programs I mentioned in my previous posting were: MachTen, MacX and Xoftware. I won't repeat the info about the first two here. Ray Fort (rcfort@maine.maine.edu) supplied some additional info on Xoftware (one crucial line was missing from the text included previously): >From an ad in BYTE, I had learned of XoftWare for Windows, from AGE >Logic, Inc. (sales@age.com). Katie Breen was particularly helpful >in faxing me a copy of the sales brochure. Xoftware comes in >versions for both PC and Mac; Craig Martens (cmartens@uci.edu) has a >positive experience with the Mac version. I also learned that an X-server program called eXodus exists, which comes both in Windows and Macintosh versions. Demo info can be obtained from http://www.wpine.com/demofront.html. Ton. -- J.A.C. Rullmann http://www-nmr.chem.ruu.nl/users/rull/rull.html Bijvoet Center for Biomolecular Research E-mail : rull@nmr.chem.ruu.nl Utrecht University, Padualaan 8, Phone : int+31.30.2533641 3584 CH Utrecht, the Netherlands Fax : int+31.30.2537623 ^ NOTE: phone numbers have changed - insert a 2 From owner-chemistry@ccl.net Fri Dec 1 07:09:38 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id GAA22421; Fri, 1 Dec 1995 06:55:37 -0500 Received: from mailb.surrey.ac.uk for D.Durran@surrey.ac.uk by bedrock.ccl.net (8.7.1/950822.1) id GAA12163; Fri, 1 Dec 1995 06:55:34 -0500 (EST) Received: from central.surrey.ac.uk by mailb.surrey.ac.uk with SMTP (PP); Fri, 1 Dec 1995 11:55:09 +0000 Received: from chemmdpc.chem.surrey.ac.uk by central.surrey.ac.uk with SMTP (1.37.109.8/16.2) id AA18070; Fri, 1 Dec 1995 11:55:06 GMT Message-Id: <9512011155.AA18070@central.surrey.ac.uk> X-Sender: chp1dd@central.surrey.ac.uk X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 01 Dec 1995 12:55:27 +0000 To: chemistry@ccl.net From: D.Durran@surrey.ac.uk (Mike Durran) Subject: Gaussian94 reference The Gaussian94 manual cites the following reference : J.R.Cheeseman et al, "A comparison of models for calculating nuclear magnetic resonance shielding tensors" in prep. (1995) Does anybody know whether it has been published yet ? Thanks for any info. Mike Durran ********************* Mike Durran Dept. Chemistry University of Surrey Guildford. Tel: 01483 259591 ********************* From owner-chemistry@ccl.net Fri Dec 1 07:39:38 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id HAA22774; Fri, 1 Dec 1995 07:34:04 -0500 Received: from gatekeeper.eastman.com for bewilson@eastman.com by bedrock.ccl.net (8.7.1/950822.1) id HAA12258; Fri, 1 Dec 1995 07:34:02 -0500 (EST) Received: by gatekeeper.eastman.com; id HAA07774; Fri, 1 Dec 1995 07:50:11 -0500 Received: from emngw1.eastman.com(164.89.254.2) by gatekeeper.eastman.com via smap (g3.0.1) id xma007766; Fri, 1 Dec 95 07:49:48 -0500 Received: by eastman.com id AA26455 (5.67b/IDA-1.5 for chemistry@ccl.net); Fri, 1 Dec 1995 07:26:48 -0500 Received: from stc150.kpt.emn.com by eastman.com with SMTP id AA30804 (5.67b/SMI-4.1 for ); Fri, 1 Dec 1995 07:26:47 -0500 Date: Fri, 1 Dec 1995 07:26:47 -0500 Message-Id: <199512011226.AA30804@eastman.com> Received: from prla26 by stc150.kpt.emn.com (MX V4.1 VAX) with SMTP; Fri, 01 Dec 1995 07:33:10 EDT X-Sender: u859723@stc150 X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: Bruce Wilson Subject: NMR Coupling constants Does anyone have good leads on ab initio calculations of coupling constants. A colleague is looking at a molecule (2,5-dihydrofuran) where the coupling between the protons on C2 and C3 are much smaller than would be expected based on the Karpluss equation. The RHF 6-31G* geometry shows a dihedral of ~60 deg, which is not near any of the Karpluss equation zeros. I figure I'm going to have to do some learning on this one, but I need some starting points. Bruce E. Wilson (bewilson@eastman.com) Information Technology Division Eastman Chemical Company Voice: (423) 229-8886 FAX: (423) 229-4558 From owner-chemistry@ccl.net Fri Dec 1 09:54:39 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id JAA24827; Fri, 1 Dec 1995 09:53:23 -0500 Received: from CHEMNA.DICHI.UNINA.IT for ENZO@CHEMNA.DICHI.UNINA.IT by bedrock.ccl.net (8.7.1/950822.1) id JAA13185; Fri, 1 Dec 1995 09:50:28 -0500 (EST) From: Received: from CHEMNA.DICHI.UNINA.IT by CHEMNA.DICHI.UNINA.IT (PMDF V5.0-4 #3559) id <01HYAKT9TIV40002I0@CHEMNA.DICHI.UNINA.IT> for CHEMISTRY@ccl.net; Fri, 01 Dec 1995 12:45:19 +0100 (CET) Date: Fri, 01 Dec 1995 12:45:19 +0100 (CET) Subject: RE:DZP' basis set To: CHEMISTRY@ccl.net Message-id: <01HYAKT9WGYQ0002I0@CHEMNA.DICHI.UNINA.IT> X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear net-ters, answering to the question of Dr. Ellson: the DZP' basis set (now called EPT-II) is not exactly the Chip1 one, since the contraction coefficients are determined by B3LYP atomic computations. Furthermore the polarization functions are from the CC basis sets of Dunning. The whole basis set is given in my chapter on Recent Advances in Density Functional Methods, ed.D.P.Chong, World Scientific Publishing Co., in press. In the meantime I enclose the whole basis set. Sincerely Vincenzo Barone Professor of Physical Chemistry ------------------------------------------------------------------------------- prof. Vincenzo Barone | tel. +39-81-5476503 Dipartimento di Chimica | fax +39-81-5527771 via Mezzocannone 4 | e-mail ENZO@CHEMNA.DICHI.UNINA.IT I-80134 Napoli | Italy | ________________________________________________________________________________ ---------------------------------------------------------------------------- EPR-II basis set ---------------------------------------------------------------------------- -H S 3 1.00 0.1279497600D+03 0.1073600000D-01 0.1924060000D+02 0.1195440000D+00 0.2899200000D+01 0.9264160000D+00 S 1 1.00 0.6534000000D+00 0.1000000000D+01 S 1 1.00 0.1776000000D+00 0.1000000000D+01 P 1 1.00 0.7270000000D+00 0.1000000000D+01 **** -B S 5 1.00 0.2788410000D+04 0.2122000000D-02 0.4190390000D+03 0.1671000000D-01 0.9646830000D+02 0.7835600000D-01 0.2806940000D+02 0.2632500000D+00 0.9376000000D+01 0.5967290000D+00 S 1 1.00 0.1305700000D+01 0.1000000000D+01 S 1 1.00 0.3406200000D+01 0.1000000000D+01 S 1 1.00 0.3245000000D+00 0.1000000000D+01 S 1 1.00 0.1022000000D+00 0.1000000000D+01 P 4 1.00 0.1134130000D+02 0.1798700000D-01 0.2436000000D+01 0.1103390000D+00 0.6836000000D+00 0.3831110000D+00 0.2134000000D+00 0.6478600000D+00 P 1 1.00 0.7010000000D-01 0.1000000000D+01 D 1 1.00 0.3430000000D+00 0.1000000000D+01 **** -C S 5 1.00 0.4232610000D+04 0.2029000000D-02 0.6348820000D+03 0.1553500000D-01 0.1460970000D+03 0.7541100000D-01 0.4249740000D+02 0.2571210000D+00 0.1418920000D+02 0.5965550000D+00 S 1 1.00 0.1966600000D+01 0.1000000000D+01 S 1 1.00 0.5147700000D+01 0.1000000000D+01 S 1 1.00 0.4962000000D+00 0.1000000000D+01 S 1 1.00 0.1533000000D+00 0.1000000000D+01 P 4 1.00 0.1815570000D+02 0.1853400000D-01 0.3986400000D+01 0.1154420000D+00 0.1142900000D+01 0.3862060000D+00 0.3594000000D+00 0.6400890000D+00 P 1 1.00 0.1146000000D+00 0.1000000000D+01 D 1 1.00 0.5500000000D+00 0.1000000000D+01 **** -N S 5 1.00 0.5909440000D+04 0.2004000000D-02 0.8874510000D+03 0.1531000000D-01 0.2047900000D+03 0.7429300000D-01 0.5983760000D+02 0.2533640000D+00 0.1999810000D+02 0.6005760000D+00 S 1 1.00 0.2686000000D+01 0.1000000000D+01 S 1 1.00 0.7192700000D+01 0.1000000000D+01 S 1 1.00 0.7000000000D+00 0.1000000000D+01 S 1 1.00 0.2133000000D+00 0.1000000000D+01 P 4 1.00 0.2678600000D+02 0.1825700000D-01 0.5956400000D+01 0.1164070000D+00 0.1707400000D+01 0.3901110000D+00 0.5314000000D+00 0.6372210000D+00 P 1 1.00 0.1654000000D+00 0.1000000000D+01 D 1 1.00 0.8170000000D+00 0.1000000000D+01 **** -O S 5 1.00 0.7816540000D+04 0.2031000000D-02 0.1175820000D+04 0.1543600000D-01 0.2731880000D+03 0.7377100000D-01 0.8116960000D+02 0.2476060000D+00 0.2718360000D+02 0.6118320000D+00 S 1 1.00 0.3413600000D+01 0.1000000000D+01 S 1 1.00 0.9532200000D+01 0.1000000000D+01 S 1 1.00 0.9398000000D+00 0.1000000000D+01 S 1 1.00 0.2846000000D+00 0.1000000000D+01 P 4 1.00 0.3518320000D+02 0.1958000000D-01 0.7904000000D+01 0.1241890000D+00 0.2305100000D+01 0.3947270000D+00 0.7171000000D+00 0.6273750000D+00 P 1 1.00 0.2137000000D+00 0.1000000000D+01 D 1 1.00 0.1185000000D+01 0.1000000000D+01 **** -F S 5 1.00 0.9994790000D+04 0.2017000000D-02 0.1506030000D+04 0.1529500000D-01 0.3502690000D+03 0.7311000000D-01 0.1040530000D+03 0.2464200000D+00 0.3484320000D+02 0.6125930000D+00 S 1 1.00 0.4368800000D+01 0.1000000000D+00 S 1 1.00 0.1221640000D+02 0.1000000000D+01 S 1 1.00 0.1207800000D+01 0.1000000000D+01 S 1 1.00 0.3634000000D+00 0.1000000000D+01 S 1 1.00 0.1101000000D+00 0.1000000000D+01 P 4 1.00 0.4435550000D+02 0.2086800000D-01 0.1008200000D+02 0.1300920000D+00 0.2995900000D+01 0.3962190000D+00 0.9383000000D+00 0.6203680000D+00 P 1 1.00 0.2733000000D+00 0.1000000000D+01 P 1 1.00 0.8280000000D-01 0.1000000000D+01 D 1 1.00 0.1640000000D+01 0.1000000000D+01 **** From owner-chemistry@ccl.net Fri Dec 1 11:39:41 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA27712; Fri, 1 Dec 1995 11:29:49 -0500 Received: from uni-paderborn.de for GF@chemie.uni-paderborn.de by bedrock.ccl.net (8.7.1/950822.1) id LAA14574; Fri, 1 Dec 1995 11:29:44 -0500 (EST) Received: from physik.uni-paderborn.de (physik.uni-paderborn.de [131.234.242.11]) by uni-paderborn.de (8.7.1/8.7.1) with SMTP id RAA07087 for ; Fri, 1 Dec 1995 17:29:06 +0100 (MET) Received: From FB6/WORKQ1 by physik.uni-paderborn.de via Charon-4.0A-VROOM with IPX id 100.951201172731.480; 01 Dec 95 17:29:22 +0100 Message-ID: From: "Gregor Fels" Organization: Universitaet-GH Paderborn FB13 To: chemistry@ccl.net Date: Fri, 1 Dec 1995 17:27:25 GST Subject: viewing of stereoimages X-Confirm-Reading-To: "Gregor Fels" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.0-WB3) With respect to the evaluation of different techniques of viewing stereoimages of molecules we are very interested in a publication by J. Hsu, Z. Pizlo, C.F. Babbs, D.M. Chelberg and E.J. Delp on the topic "Is stereo viewing really better" in the Proceedings of the SPIE - The International Society for Optical Engineering, Vol. 2177, p.211-222, 1994. We have trouble to get this paper in Germany and I would appreciate very much assistance in retrieving the publication (which has at least some connections to the subject of this reading list). Many thanks Gregor Dr. Gregor Fels Universitaet-GH-Paderborn FB 13-Org. Chemie Warburgerstr. 100 D-33098 Paderborn, Germany Tel. 0049-5251-602181/Fax -603245 EMail GF@chemie.uni-paderborn.de From owner-chemistry@ccl.net Fri Dec 1 12:54:43 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA29151; Fri, 1 Dec 1995 12:51:18 -0500 Received: from owl.ewu.edu for emcgoran@ewu.edu by bedrock.ccl.net (8.7.1/950822.1) id MAA15597; Fri, 1 Dec 1995 12:51:08 -0500 (EST) Received: from [146.187.64.155] (ewu61589.ewu.edu) by ewu.edu (PMDF V5.0-5 #9372) id <01HYAERDMMM8HTWCI6@ewu.edu> for Chemistry@ccl.net; Fri, 01 Dec 1995 09:51:46 -0800 (PST) Date: Fri, 01 Dec 1995 10:03:34 -0800 From: emcgoran@ewu.edu (Ernie McGoran) Subject: Chemical Drawing Programs for IBM UNIX? X-Sender: emcgoran@eagle.ewu.edu To: Chemistry@ccl.net Message-id: X-Envelope-to: Chemistry@ccl.net MIME-version: 1.0 Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Does anyone know of a IBM UNIX program that can be used to draw 2D chemical structures for importing into text documents on IBM workstations? The only program that I know of for the UNIX system is ChemDraw, but it does not run with the AIX operating system. Has anyone tried to use an OS emulator with either a Mac or DOS chemical drawing program on a AIX system? Is this a viable option? Thanks. Ernie McGoran, Ph. D. | Phone: (509) 359-7931 Dept. of Chem./Biochem. MS 74 | FAX: (509) 359-6937 Eastern Washington University | email: emcgoran@ewu.edu Cheney, WA 99004 From wrigjz@postman.essex.ac.uk Fri Dec 1 14:09:43 1995 Received: from postman.essex.ac.uk for wrigjz@postman.essex.ac.uk by www.ccl.net (8.6.10/950822.1) id OAA00542; Fri, 1 Dec 1995 14:00:17 -0500 Received: from postman.essex.ac.uk by postman.essex.ac.uk with SMTP (PP) id <03995-0@postman.essex.ac.uk>; Fri, 1 Dec 1995 17:34:21 +0000 From: "Jon.Essex-Chemistry" Date: Fri, 1 Dec 95 16:40:48 GMT Message-Id: <19873.9512011640@solb1.essex.ac.uk> PP-warning: Illegal Received field on preceding line To: CHEMISTRY Subject: Charmm and hydrogens Hi, I'me trying to use Charmm on some some peptide chains. I'm using the Whatif graphics package to create the peptides and then read those into Charmm. However I'm having errors thrown up by Charmm regarding missing hydrogens and also for my terminal HIS residue missing oxygens. Can someone tell me how to get Charmm to automatically create these hydrogens (and oxygens) and place them in `reasonable' positions. Also how do I set Charmm to minimise in a water continuum (ie an external dielectric of 78.4). Thanks Jon wrigjz@essex.ac.uk From gerardo@houston.cray.com Fri Dec 1 14:39:43 1995 Received: from timbuk.cray.com for gerardo@houston.cray.com by www.ccl.net (8.6.10/950822.1) id OAA01447; Fri, 1 Dec 1995 14:33:55 -0500 Received: from houston.cray.com (gerardo@houston.cray.com [128.162.61.112]) by timbuk.cray.com (8.6.12/CRI-gate-8-2.11) with ESMTP id NAA09572 for ; Fri, 1 Dec 1995 13:33:55 -0600 Received: by houston.cray.com (SMI-8.6/CRI-5.13) id NAA01535; Fri, 1 Dec 1995 13:33:53 -0600 From: gerardo@houston.cray.com (Gerardo Cisneros) Message-Id: <199512011933.NAA01535@houston.cray.com> Subject: 3rd UNAM-Cray Supercomputing Conference To: CHEMISTRY@www.ccl.net Date: Fri, 1 Dec 1995 13:33:53 -0600 (CST) X-Mailer: ELM [version 2.4 PL24-CRI-c] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit +---------------------------------------------------------------+ | | | ----THIRD UNAM-CRAY SUPERCOMPUTING CONFERENCE---- | | ----------------------------------------- | | | | | | C O M P U T A T I O N A L C H E M I S T R Y | | | | | | A symposium to be held in Mexico City | | from August 13th through the 16th, 1996 | | | | First Announcement (Please post and circulate) | | Abstract deadline: 4 February 1996 | +---------------------------------------------------------------+ SCIENTIFIC COMITTEE/INVITED SPEAKERS: Dr. Ren\'e Ba\~nares-Alc\'antara, University of Edinburgh, UK Dr. Ludger Br\"ull, Bayer AG, Germany Dr. Carlos Bunge, Instituto de F\'{\i}sica, UNAM, M\'exico Dr. Michel Dupuis, Pacific Northwest Laboratory, USA Dr. Roger Elliott, Oxford University, UK Dr. Charlotte Froese Fischer, Vanderbilt University, USA Dr. Per-Olov L\"owdin, Uppsala University, Sweden, and U. of Florida, USA Dr. Matti Manninen, University of Jyv\"askyl\"a, Finland Dr. Octavio Novaro, Instituto de F\'{\i}sica, UNAM, M\'exico Dr. Dennis R. Salahub, University of Montreal, Canada Dr. Mark A. Stadtherr, University of Illinois at Urbana-Champaign, USA Dr. Michael D. Zerner, University of Florida, USA ORGANIZING COMITTEE: Dr. Alberto Alonso, Direcci\'on General de Servicios de C\'omputo Acad\'emico (DGSCA), UNAM Dr. Enrique R. Baz\'ua, Facultad de Qu\'{\i}mica, UNAM Dr. Miguel Castro, Facultad de Qu\'{\i}mica, UNAM Dr. Juan Antonio Cogordan, Instituto de Qu\'{\i}mica, UNAM Dr. Gerardo Cisneros S., Cray Research de M\'exico, S.A. de C.V. Dr. Alejandro Pisanty, Comit\'e Asesor de C\'omputo, UNAM Dr. Chumin Wang Chen, Instituto de Materiales, UNAM ----------------------------------------------------------- The goal of the supercomputing conference on Computational Chemistry is to address the state-of-the-art in computational methodologies in chemistry and chemical engineering. Emphasis will be made on the problems that arise when the studied systems are large or when chemically accurate calculations are desired, and when attempts are made to include in the calculations most of the effects (solvent, electric fields, etc.) that surround a molecule or system in a real situation. We hope that this event will offer an opportunity for a critical review of the most recent advances in quantum chemistry and process modelling methodologies as well as help to provide orientation in the search for guidelines and future trends in the field. TOPICS I. Ab initio, DFT, semiempirical, and other methods for the calculation of the electronic structure and properties of atoms, molecules and solids. II. Simulations of molecules and solids by molecular dynamics and MonteCarlo methods. III. Catalysis -- ligand activation in homogenous and heterogeneous systems. IV. Chemical Engineering process modelling. ----------------------------------------------------------- REGISTRATION The conference registration fee is US$300.00 which includes a copy of the proceedings and a ticket for the closing dinner. A limited number of grants for partial support of attendance and/or travel expenses will be available. Please indicate if you need financial assistance before May 3, 1996. Please fill in the following form and return by e-mail to: simposio@servidor.unam.mx +---------------------------------------------------------------+ | REGISTRATION FORM | | | | ----THIRD UNAM-CRAY SUPERCOMPUTING CONFERENCE---- | | ----------------------------------------- | | | | | | C O M P U T A T I O N A L C H E M I S T R Y | | | | | | A symposium to be held in Mexico City | | from August 13th through the 16th, 1996 | | | +---------------------------------------------------------------+ Name (last, first): E-mail address: Institution: Address: Phone: Fax: Do you intend to present a contribution? Yes ____ No ____ Title of contribution: DEADLINE FOR ABSTRACT SUBMISSION: 4 February 1996 (E-MAIL SUBMISSION PREFERRED). DEADLINE FOR FULL PAPERS: 13 August 1996 ---------------------------------------------------------------------- Contact Address: 3rd UNAM-CRAY Supercomputing Conference DGSCA/UNAM Apdo. Postal 20-059 01000 Mexico, D.F. MEXICO Electronic Mail: simposio@servidor.unam.mx Fax: (+52+5) 622-8043 ----------------------------------------------------------------------- Announcement submitted by -- Dr. Gerardo Cisneros |Cray Research de M'exico, S.A. de C.V. Technical Services Mgr. |Tuxpan 10-403, Col. Roma Sur gerardo@cray.com |06760 M'exico, D.F. (+52+5)622-8584 |MEXICO From owner-chemistry@ccl.net Fri Dec 1 15:24:44 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id PAA02359; Fri, 1 Dec 1995 15:24:10 -0500 Received: from oregon.uoregon.edu for campos@OREGON.UOREGON.EDU by bedrock.ccl.net (8.7.1/950822.1) id PAA17630; Fri, 1 Dec 1995 15:23:58 -0500 (EST) Received: from gerardo.uoregon.edu (gerardo.uoregon.edu) by OREGON.UOREGON.EDU (PMDF V5.0-5 #13764) id <01HYAK2WP7C091W465@OREGON.UOREGON.EDU> for chemistry@ccl.net; Fri, 01 Dec 1995 12:23:47 -0800 (PST) Date: Fri, 01 Dec 1995 12:25:06 -0300 From: campos@OREGON.UOREGON.EDU (Gerardo Soto-Campos) Subject: WASP X-Sender: campos@oregon.uoregon.edu To: chemistry@ccl.net Message-id: <01HYAK2WRI7M91W465@OREGON.UOREGON.EDU> MIME-version: 1.0 X-Mailer: Content-type: text/plain; charset="us-ascii" Content-transfer-encoding: 7BIT Can somebody give me an "explanation for pedestrians" of what WASP does (good and bad), and whether it's possible to get it as free software? If not, who sells it, what sorts of things should I look for? What kind of computers can run it, is there good documentation written about it? What's the best book about it? Etc... Since this is a very informative question, I'll post only if somebody request it. I would sincerely appreciate your comments, Gerardo Soto-Campos Chemistry Dept. University of Oregon Eugene OR, 97403 From setlik@acsu.Buffalo.edu Fri Dec 1 18:24:45 1995 Received: from autarch.acsu.buffalo.edu for setlik@acsu.Buffalo.edu by www.ccl.net (8.6.10/950822.1) id SAA04816; Fri, 1 Dec 1995 18:17:44 -0500 Received: (from setlik@localhost) by autarch.acsu.buffalo.edu (8.6.10/8.6.12) id SAA29653 for CHEMISTRY@www.ccl.net; Fri, 1 Dec 1995 18:17:43 -0500 From: "Robert F. Setlik" Message-Id: <199512012317.SAA29653@autarch.acsu.buffalo.edu> Subject: dielectric constant in SYBYL To: CHEMISTRY@www.ccl.net Date: Fri, 1 Dec 1995 18:17:43 -0500 (EST) X-Mailer: ELM [version 2.4 PL22] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 735 Hi netters, I am using SYBYL with Kollman all-atom parameters to energy minimize a nucleic acid model. Do any of you have any ideas on the dielectric constant to use if there are no explicit waters or counterions present. I would appreciate any suggestions. Cheers, Rob Setlik _______________________________________________________________ Robert F. Setlik Biophysics Department, Roswell Park Cancer Institute, Buffalo, NY 14263 CCC 218 Phone (716) 845-3048 (Lab) Fax: (716) 845-8906 Email: setlik@acsu.buffalo.edu Member of "Buffalo's inability to ever win a world championship in any major sport due to our incessent infatuation with mediocraty task force" _______________________________________________________________