From fdeprof@vub.ac.be Thu Jul 28 05:57:07 1994 Received: from rc1.vub.ac.be for fdeprof@vub.ac.be by www.ccl.net (8.6.9/930601.1506) id FAA09178; Thu, 28 Jul 1994 05:12:18 -0400 Received: from is1e.vub.ac.be by rc1.vub.ac.be (8.6.8.1/2.23.ap) id LAA15153; Thu, 28 Jul 1994 11:14:09 +0200 Received: by is1e.vub.ac.be (5.61/BFUCC-920211) id AA12294; Thu, 28 Jul 94 11:13:13 +0200 From: fdeprof@vub.ac.be (De Proft Frank) Message-Id: <9407280913.AA12294@is1e.vub.ac.be> Subject: Integrating electron densities To: chemistry@ccl.net Date: Thu, 28 Jul 1994 11:13:11 +0200 (DST) X-Mailer: ELM [version 2.4 PL23c] Content-Type: text Content-Length: 165 Hello, Does anyone know of any programs integrating atomic electron densities numerically starting from a grid of points ? Thanks From mealli@cacao.issecc.fi.cnr.it Thu Jul 28 06:57:07 1994 Received: from cacao.issecc.fi.cnr.it for mealli@cacao.issecc.fi.cnr.it by www.ccl.net (8.6.9/930601.1506) id GAA09411; Thu, 28 Jul 1994 06:03:29 -0400 From: Received: by cacao.issecc.fi.cnr.it (5.57/Ultrix3.0-C) id AA13960; Thu, 28 Jul 94 12:01:05 GMT Message-Id: <9407281201.AA13960@cacao.issecc.fi.cnr.it> To: chemistry@ccl.net Subject: CACAO40: missing file for printing! Date: Tue Jul 26 12:00:29 1994 To those who retrieved cacao40 from the FTP site 149.139.10.2 (this address) during the past week: due to a mistake, the ascii file "pl.bat", which launches the printing of the drawings, was not included in the selfextracting file (CACAO40.EXE). Now, you can retrieve the small file "pl.bat", separately (to be added in the directory MOAN). Otherwise, the whole refreshed cacao40.exe can be retrieved. Sorry fo the inconvenience. Carlo Mealli. Dr. Carlo Mealli ISSECC, CNR Via J.NARDI 39, 50132 Firenze, ITALY e-mail: mealli@cacao.issecc.fi.cnr.it Tel. 0039-55-2346653 (243990) - Fax 2478366 - Home 4492709 From ALHINAI@FRCU.EUN.EG Thu Jul 28 07:57:10 1994 Received: from FRCU.EUN.EG for ALHINAI@FRCU.EUN.EG by www.ccl.net (8.6.9/930601.1506) id HAA10053; Thu, 28 Jul 1994 07:22:22 -0400 From: Received: from FRCU.EUN.EG by FRCU.EUN.EG (PMDF V4.2-11 #3805) id <01HF8QOMFN8W002WSE@FRCU.EUN.EG>; Thu, 28 Jul 1994 14:23:42 O Date: Thu, 28 Jul 1994 14:23:42 +0000 (O) Subject: Mulliken matrix in GAMESS..... To: chemistry@ccl.net Message-id: <01HF8QOMGG6A002WSE@FRCU.EUN.EG> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hello netters , Is it possible to obtain a Mulliken matrix from gamess simillar to the one given from gaussian 9x ? Gamess only gives the density matrix , followed by the atomic overlaps and populations . If gamess does not give Mulliken matrix , could it give us the overlap matrix, and we could do the rest . Ashraf From HODGKINE@prince.mm.wyeth.com Thu Jul 28 10:57:11 1994 Received: from mail1 for HODGKINE@prince.mm.wyeth.com by www.ccl.net (8.6.9/930601.1506) id KAA12228; Thu, 28 Jul 1994 10:32:27 -0400 Received: from mr.wyeth.com by mail1.wyeth.com (PMDF V4.2-14 #5660) id <01HF8J8M1328000LVC@mail1.wyeth.com>; Thu, 28 Jul 1994 10:36:45 EST Received: with PMDF-MR; Thu, 28 Jul 1994 10:33:15 EST MR-Received: by mta PRIN1; Relayed; Thu, 28 Jul 1994 10:33:15 -0500 MR-Received: by mta MAIL1; Relayed; Thu, 28 Jul 1994 10:32:31 -0500 Disclose-recipients: prohibited Date: Thu, 28 Jul 1994 15:38:18 -0500 (EST) From: "Hodgkin, Ed" Subject: Modelling Transition States To: "chemistry@ccl.net" Message-id: <01HF8J8MYB1Y000LVC@mr.wyeth.com> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT UA-content-id: Modelling Transition States X400-MTS-identifier: [;51330182704991/169632@PRINCE] A1-type: MAIL Hop-count: 1 From: Hodgkin, Ed Date: Thu, Jul 28, 1994 3:38 PM Subject: Modelling Transition States To: chemistry@ccl.net Dear All I am hoping to model a reaction mechanism using either MOPAC or Gaussian80 and need some help with constructing transition states or following the reaction coordinate. I understand it is possible to do this in both packages. My reaction shows unusual selectivity between two products. Each of the products is formed by a concerted intramolecular mechanism, which I imagine is the most straightforward case to model. Furthermore reactants and products are conformationally constrained so there is no problem with flexibility. I would be very grateful for any hints you can offer. Regards, Edward Hodgkin (hodgkine@prince.mm.wyeth.com) Wyeth Research (UK) From popugurj@sc.ehu.es Thu Jul 28 11:57:11 1994 Received: from scsx01.sc.ehu.es for popugurj@sc.ehu.es by www.ccl.net (8.6.9/930601.1506) id LAA13190; Thu, 28 Jul 1994 11:42:16 -0400 Received: from scdx01.sc.ehu.es by scsx01.sc.ehu.es (4.1/4.7 ) id AA16742; Thu, 28 Jul 94 17:18:22 +0200 Received: by scdx01.sc.ehu.es (5.65/4.7) id AA14054; Thu, 28 Jul 1994 17:02:43 GMT Date: Thu, 28 Jul 1994 17:02:39 +0000 (WET) From: Jesus Ugalde Uribe-Etxeberria Subject: Public Domain MOPAC-93 To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Netter, Could anyone tell if there is any ftp site for the MOPAC-93 or its public domain version Jesus M. Ugalde The University of the Basque Country From popugurj@sc.ehu.es Thu Jul 28 12:00:28 1994 Received: from scsx01.sc.ehu.es for popugurj@sc.ehu.es by www.ccl.net (8.6.9/930601.1506) id LAA13196; Thu, 28 Jul 1994 11:42:48 -0400 Received: from scdx01.sc.ehu.es by scsx01.sc.ehu.es (4.1/4.7 ) id AA16748; Thu, 28 Jul 94 17:20:14 +0200 Received: by scdx01.sc.ehu.es (5.65/4.7) id AA18062; Thu, 28 Jul 1994 17:04:37 GMT Date: Thu, 28 Jul 1994 17:04:36 +0000 (WET) From: Jesus Ugalde Uribe-Etxeberria Subject: Public domain emulator To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi netters, Does anyone know about any ftp-able XWindows emulator for PC's Windows Thanks in advance Jesus M. Ugalde The University of the Basque Country From dickson@zinc.chem.ucalgary.ca Thu Jul 28 12:03:12 1994 Received: from zinc.chem.ucalgary.ca for dickson@zinc.chem.ucalgary.ca by www.ccl.net (8.6.9/930601.1506) id LAA13272; Thu, 28 Jul 1994 11:52:20 -0400 Received: by zinc.chem.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA11921; Thu, 28 Jul 1994 09:58:20 -0600 Date: Thu, 28 Jul 1994 09:58:20 -0600 From: dickson@zinc.chem.ucalgary.ca (Ross M. Dickson) Message-Id: <9407281558.AA11921@zinc.chem.ucalgary.ca> To: chemistry@ccl.net, fdeprof@vub.ac.be Subject: Re: CCL:Integrating electron densities Frank De Proft (fdeprof@vub.ac.be) asked, >Does anyone know of any programs integrating atomic electron densities >numerically starting from a grid of points ? I note that this is the second time he's asked this, so I thought someone should reply. I'm sorry I don't have any software available to so this instantly. My impression is that this is an old and thoroughly solved problem, but I don't have references handy on exactly who solved it how and when. For spherical atoms all you need is a one-dimensional numerical integration, which is well-covered in standard references such as "Numerical Recipes" by Press, Flannery, Teukolsky and Vetterling. I don't think nonspherical atoms are that much more complicated, but then polyatomic molecules are my thing. If you want an example of a general 3-D integration scheme that would be suitable for atomic densities among other things, see A.D. Becke, J.Chem.Phys. 88(4) 2547 (1988). While conciseness is generally a Good Thing in posting to mailing lists such as this one, it is worth mentioning that it is possible to be too concise. Since this is a group of interested individuals and not of servicepeople waiting to solve every problem that comes by, it is often good to provide a little background about your question, if for no other reason than to get your reader and potential helper interested. Good things to mention are why you need a thing and where you have already looked for it, for example. Without this information, it's very easy for the reader to think "Oh, he can solve that problem just by going down to the library and looking in Chem. Abs.," or "Oh, she can solve that problem just by doing a little basic math," in which case no reply will be generated since the readers are busy with more interesting (to them) things. Cheers, Ross M. Dickson (dickson@zinc.chem.ucalgary.ca) From dickson@zinc.chem.ucalgary.ca Thu Jul 28 16:12:19 1994 Received: from zinc.chem.ucalgary.ca for dickson@zinc.chem.ucalgary.ca by www.ccl.net (8.6.9/930601.1506) id LAA13272; Thu, 28 Jul 1994 11:52:20 -0400 Received: by zinc.chem.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA11921; Thu, 28 Jul 1994 09:58:20 -0600 Date: Thu, 28 Jul 1994 09:58:20 -0600 From: dickson@zinc.chem.ucalgary.ca (Ross M. Dickson) Message-Id: <9407281558.AA11921@zinc.chem.ucalgary.ca> To: chemistry@ccl.net, fdeprof@vub.ac.be Subject: Re: CCL:Integrating electron densities Frank De Proft (fdeprof@vub.ac.be) asked, >Does anyone know of any programs integrating atomic electron densities >numerically starting from a grid of points ? I note that this is the second time he's asked this, so I thought someone should reply. I'm sorry I don't have any software available to so this instantly. My impression is that this is an old and thoroughly solved problem, but I don't have references handy on exactly who solved it how and when. For spherical atoms all you need is a one-dimensional numerical integration, which is well-covered in standard references such as "Numerical Recipes" by Press, Flannery, Teukolsky and Vetterling. I don't think nonspherical atoms are that much more complicated, but then polyatomic molecules are my thing. If you want an example of a general 3-D integration scheme that would be suitable for atomic densities among other things, see A.D. Becke, J.Chem.Phys. 88(4) 2547 (1988). While conciseness is generally a Good Thing in posting to mailing lists such as this one, it is worth mentioning that it is possible to be too concise. Since this is a group of interested individuals and not of servicepeople waiting to solve every problem that comes by, it is often good to provide a little background about your question, if for no other reason than to get your reader and potential helper interested. Good things to mention are why you need a thing and where you have already looked for it, for example. Without this information, it's very easy for the reader to think "Oh, he can solve that problem just by going down to the library and looking in Chem. Abs.," or "Oh, she can solve that problem just by doing a little basic math," in which case no reply will be generated since the readers are busy with more interesting (to them) things. Cheers, Ross M. Dickson (dickson@zinc.chem.ucalgary.ca) From UNDERHILLR%MECH_STAFF%ELEC@BANEE.rmc.ca Thu Jul 28 17:12:08 1994 Received: from BANEE.rmc.ca for UNDERHILLR%MECH_STAFF%ELEC@BANEE.rmc.ca by infomeister (8.6.9/930601.1506) id QAA00360; Thu, 28 Jul 1994 16:28:11 GMT From: Message-Id: <199407281628.QAA00360@infomeister> Received: by BANEE.rmc.ca with VINES ; Thu, 28 Jul 94 12:38:29 EDT Date: Tue, 26 Jul 94 13:15:34 EDT Subject: MM2 or AMBER Force Field Parameters for Phosphonates To: chemistry@ccl.net Forwarded to: smtp[chemistry@ccl.net] cc: Comments by: UNDERHILLR@MECH_STAFF@ELEC -------------------------- [Original Message] ------------------------- I'm looking for parameters for an MM2 or AMBER force field calculation on a series of methyl phosphonates [(RO)2MePO]. I would appreciate it if anyone could forward some appropriate data or references to me. From cletner@remcure.bmb.wright.edu Thu Jul 28 17:14:04 1994 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by infomeister (8.6.9/930601.1506) id QAA00335; Thu, 28 Jul 1994 16:24:22 GMT Received: by remcure.bmb.wright.edu (931110.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA03021; Thu, 28 Jul 94 12:19:27 -0700 Date: Thu, 28 Jul 1994 12:05:18 -0700 (PDT) From: Charles Letner Subject: Image translation program To: Computational Chemistry List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, I am having a little problem that is REALLY starting to annoy me. I am trying to output images to a printer. My printer is capable of 600 dpi postscript output. I also have access to a color postscript printer. I can save my images in any number of formats including postscript (only 91 dpi). However, 91 dpi is not publication quality. I'd like to know if there is a file conversion program that will take my image files (TIFF would be good, though as I said I can output other formats) and output 600 dpi postscript files? I would like this to be a unix program (I'm using a SG Indigo II) and viewing capabilities isn't essential for this utility. As I expect I'm not the first to have this little problem I will send a summary of the responses. Your help will be appreciated. Thank you, Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 e-mail: cletner@remcure.bmb.wright.edu From raman@bioc01.uthscsa.edu Thu Jul 28 19:12:11 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by infomeister (8.6.9/930601.1506) id SAA04412; Thu, 28 Jul 1994 18:54:51 GMT Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Thu, 28 Jul 1994 14:03:17 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA25679; Thu, 28 Jul 94 14:00:45 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9407281900.AA25679@bioc01.uthscsa.edu> Subject: Re: CCL:Image translation program To: cletner@remcure.bmb.wright.edu (Charles Letner) Date: Thu, 28 Jul 1994 14:00:44 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: from "Charles Letner" at Jul 28, 94 12:05:18 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1633 Chuck: > 91 dpi). However, 91 dpi is not publication quality. I'd like to know if > there is a file conversion program that will take my image files (TIFF > would be good, though as I said I can output other formats) and output 600 > dpi postscript files? I would like this to be a unix program (I'm using a > SG Indigo II) and viewing capabilities isn't essential for this utility. > As I expect I'm not the first to have this little problem I will send a What you want is the PBM translation suite. It comes in three different flavors: PBM PBMPLUS NETPBM You can find these at many anon. FTP sites (using ARCHIE). PBM is capable of converting images from one format to numerous others and is extremely useful. Alternatively, you could also try John Christy's ImageMagik available at various anon. FTP sites. You may have to search for some of the utilities that go with it to accomplish your task. Cheers -raman -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From vvk@itsa.ucsf.EDU Thu Jul 28 20:12:15 1994 Received: from itsa.ucsf.EDU for vvk@itsa.ucsf.EDU by infomeister (8.6.9/930601.1506) id TAA05328; Thu, 28 Jul 1994 19:35:31 GMT Received: by itsa.ucsf.EDU (AIX 3.2/UCB 5.64/GSC4.22) id AA66100; Thu, 28 Jul 1994 12:42:28 -0700 Date: Thu, 28 Jul 1994 12:42:28 -0700 From: vvk@itsa.ucsf.EDU (Jaeho Kim) Message-Id: <9407281942.AA66100@itsa.ucsf.EDU> To: chemistry@ccl.net Subject: Looking for e-mail address Hello, Can anyone out there supply the Email address for J.J. Regan, in San Diego, or supply information on how we can obtain his PATHWAYS II, version 2 program for calculating pathways for electron transfer in enzymes. Also, any information on running platforms, interfacing to graphics programs, input file formats would be appreciated. We are also interested in any procedures, algorithms, references, programs, etc. for locating inorganic cation binding sites in proteins. Many thanks in advance for any help. Bill McIntire & Vlad Kuusk VA Medical Center and University of California San Francisco, CA Email - vvk@itsa.ucsf.edu From JMOSCOSO@uop.com Thu Jul 28 21:12:12 1994 Received: from uop.com for JMOSCOSO@uop.com by infomeister (8.6.9/930601.1506) id VAA06506; Thu, 28 Jul 1994 21:11:43 GMT Received: from disney.dp.uop-net.com ([138.90.72.74]) by uop.com (4.1/3.1.090690-UOP) id AA05300; Thu, 28 Jul 94 16:23:36 CDT Received: from mktserv.uop-net.com by disney.dp.uop-net.com (4.1/SMI-4.1) id AA20916; Thu, 28 Jul 94 16:17:34 CDT Message-Id: <9407282117.AA20916@disney.dp.uop-net.com> From: JMOSCOSO@uop.com (JMOSCOSO) Date: Thu, 28 Jul 94 16:06 To: chemistry@ccl.net Subject: QUADRUPOLE MOMENTS Return-Receipt-To: JMOSCOSO@uop.com Hello Netters: Does anyone know how to get quadrupole moments for: N2 O2 or organics etc?. I need the quadrople moments in order to calculate absorptions of gases in zeolites using GCMC. The only software that I have is Biosym Catalysis with the all the modules. Thank you for your reply. Jaime Moscoso JMOSCOSO@uop.com FAX: 708-391-3727 Phone 708-391-3769 UOP Des Plaines IL From Omar.Stradella@sgibos.boston.sgi.com Thu Jul 28 21:15:21 1994 Received: from sgigate.sgi.com for Omar.Stradella@sgibos.boston.sgi.com by infomeister (8.6.9/930601.1506) id UAA06034; Thu, 28 Jul 1994 20:31:53 GMT Received: from relay.sgi.com (relay.sgi.com [192.26.51.36]) by sgigate.sgi.com (940519.SGI.8.6.9/8.6.4) with SMTP id NAA06617; Thu, 28 Jul 1994 13:37:05 -0700 Received: from sgibos.boston.sgi.com by relay.sgi.com via SMTP (920330.SGI/920502.SGI) for @sgigate.sgi.com:cletner@remcure.bmb.wright.edu id AA12936; Thu, 28 Jul 94 13:37:01 -0700 Received: from arkham.boston.sgi.com by sgibos.boston.sgi.com via SMTP (931110.SGI/911001.SGI) for @relay.sgi.com,@FORWARDHOST.BAR.FOO.COM:chemistry@ccl.net id AA21406; Thu, 28 Jul 94 16:36:42 -0400 Received: by arkham.boston.sgi.com (931110.SGI/930416.SGI) for @FORWARDHOST.BAR.FOO.COM:cletner@remcure.bmb.wright.edu id AA06490; Thu, 28 Jul 94 16:34:02 -0400 From: "Omar Stradella" Message-Id: <9407281634.ZM6488@arkham.boston.sgi.com> Date: Thu, 28 Jul 1994 16:34:01 -0400 In-Reply-To: Charles Letner "CCL:Image translation program" (Jul 28, 12:05pm) References: Organization: Silicon Graphics, Inc. Reply-To: Omar.Stradella@sgibos.boston.sgi.com X-Mailer: Z-Mail (3.0B.0 25aug93 MediaMail) To: chemistry@ccl.net Subject: Re: CCL:Image translation program Cc: cletner@remcure.bmb.wright.edu Content-Type: text/plain; charset=iso-8859-1 Mime-Version: 1.0 On Jul 28, 12:05pm, Charles Letner wrote: > Subject: CCL:Image translation program > Hello all, > I am having a little problem that is REALLY starting to annoy me. > I am trying to output images to a printer. My printer is capable of 600 > dpi postscript output. I also have access to a color postscript printer. > I can save my images in any number of formats including postscript (only > 91 dpi). However, 91 dpi is not publication quality. I'd like to know if > there is a file conversion program that will take my image files (TIFF > would be good, though as I said I can output other formats) and output 600 > dpi postscript files? I would like this to be a unix program (I'm using a > SG Indigo II) and viewing capabilities isn't essential for this utility. > As I expect I'm not the first to have this little problem I will send a > summary of the responses. > Your help will be appreciated. > > Thank you, > Chuck > Depends on what you mean by 91 dpi, that probably really means cells/inch instead of pixels/inch, since your PostScript printer will print at whatever dpi was built or configured for. Let's use as an example your B/W 600 dpi printer, each dot can be only white or black. If you are printing a B/W image (that means no grays at all) such as a molecule represented with circles (balls) and straight lines (sticks) then you can get the full 600 dpi resolution. If you want to print an image with gray levels, the conversion program has to "halftone" the image, halftoning is the process by which continuous-tone colors are approximated by a pattern of pixels that can achieve only a limited number of discrete colors. So now the "points" that form the image are not longer pixels but groups of black and white pixels that combined produce the correct level of gray. So, if your image is 91 cells/inch that is 600/91 = 6 pixels per side or 36 pixels per cell, then 37 levels of gray are possible. Your image looks grainy but you can appreciate the differences of "color". If you convert a rasterized image (like a TIFF file) to PostScript, you'll always have to halftone the image, if you want a finer grain you'll get a smaller range of gray tones. If you want 600 dpi you will get only black and white, no grays at all. In that case I would prefer an image created with PostScript primitives (lines and circles) instead of a rasterized image. Publication quality rasterized images can only be obtained with "publication quality printers", that is 1500 dpi or more, since 1500/6 = 250 cells/inch or 250 gray dots/inch which should look good enough. The same principles apply to color printers. -- **************************************************************************** * Dr. Omar G. Stradella "Ph-nglui mglw'nafh Cthulhu * * R'lyeh wgah'nagl fhtagn" * * Silicon Graphics * * * * E-mail: omar@boston.sgi.com Snail-mail: One Cabot Road * * Hudson, MA 01749 * * Phone: +1-(508) 562-4800x358 U.S.A. * * FAX: +1-(508) 562-4755 Lat/Long: 42.24 N / 71.34 W * **************************************************************************** From rgab@trpntech.com Thu Jul 28 23:12:12 1994 Received: from netcomsv.netcom.com for rgab@trpntech.com by infomeister (8.6.9/930601.1506) id WAA08108; Thu, 28 Jul 1994 22:43:36 GMT Received: from trpntech.com by netcomsv.netcom.com with UUCP (8.6.4/SMI-4.1) id PAA25817; Thu, 28 Jul 1994 15:47:50 -0700 Message-Id: <199407282247.PAA25817@netcomsv.netcom.com> Date: 28 Jul 1994 15:33:39 -0800 From: "Richard Bone" Subject: Atomic Integrations To: "CCL" Subject: Atomic Integrations I am not sure that this exactly answers the recent request but the AIMPAC suite of programs from Richard Bader's group at McMaster Univ. in Hamilton, Ontario Canada, contains a couple of devices for numerical integration of atomic densities. The prerequisite is a ".wfn" file from a prior ab initio calculation. The methods of integration are rather complicated because of the way in which the atomic boundaries are defined. All the theory behind the methods can be found in the "Theory of Atoms in Molecules". The programs yield other useful information such as atomic charges and other integrated properties. The programs can be obtained free from Prof. Bader E-mail: bader@mcmail.cis.mcmaster.ca The same theory has also been implemented in program-form by Prof. Cioslowski at Florida State, but I do not know if his programs are immediately available. I have heard that his contributions will soon be included in the Gaussian program suite. Richard Bone __________________________________________________________ Richard G. A. Bone, PhD. Computational Chemist Terrapin Technologies, Inc. South San Francisco USA E-mail rgab@trpntech.com From sliu@mastermodel.ps.uci.edu Fri Jul 29 00:12:13 1994 Received: from mastermodel.ps.uci.edu for sliu@mastermodel.ps.uci.edu by infomeister (8.6.9/930601.1506) id XAA08434; Thu, 28 Jul 1994 23:45:23 GMT Received: from localhost.ps.uci.edu by mastermodel.ps.uci.edu (920330.SGI/5.17) id AA11602; Thu, 28 Jul 94 16:50:50 -0700 Message-Id: <9407282350.AA11602@mastermodel.ps.uci.edu> To: chemistry@ccl.net Subject: Organic Compound on Ge/Se Date: Thu, 28 Jul 94 16:50:48 -0800 From: Song Liu Dear Everyone : I am trying to model the organic compound substrate on Ge(Se) surface, is there any parameters comparable to L-J potential for the Ge or Se? I will summarize all responses! Thanks in advance! Song Liu Chemistry, UC Irvine From raman@bioc01.uthscsa.edu Fri Jul 29 00:17:01 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by infomeister (8.6.9/930601.1506) id XAA08257; Thu, 28 Jul 1994 23:12:13 GMT Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Thu, 28 Jul 1994 18:20:39 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA26334; Thu, 28 Jul 94 18:18:08 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9407282318.AA26334@bioc01.uthscsa.edu> Subject: Re: CCL:Looking for e-mail address To: vvk@itsa.ucsf.EDU (Jaeho Kim) Date: Thu, 28 Jul 1994 18:18:07 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <9407281942.AA66100@itsa.ucsf.EDU> from "Jaeho Kim" at Jul 28, 94 12:42:28 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 3055 Vlad and Bill: > Can anyone out there supply the Email address for J.J. Regan, in > San Diego, or supply information on how we can obtain his > PATHWAYS II, version 2 program for calculating pathways for > electron transfer in enzymes. Also, any information on running Jeff Regan can be reached at: jeffr@tucano.ucsd.edu An alternate approach would be contact David Beratan at U. Pitt or Jose' Onucic at UCSD. > We are also interested in any procedures, algorithms, > references, programs, etc. for locating inorganic cation binding > sites in proteins. Try the program "ion" used for identifying metal binding sites in proteins. When I checked last, it was present on one of the anon. FTP sites at UCLA (mbi.molbio.ucla.edu?). You can contact Dave Eisenberg's group to find additional details. Cheers -raman -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** > platforms, interfacing to graphics programs, input file formats > would be appreciated. > We are also interested in any procedures, algorithms, > references, programs, etc. for locating inorganic cation binding > sites in proteins. > Many thanks in advance for any help. > > > Bill McIntire & Vlad Kuusk > VA Medical Center and University of California > San Francisco, CA > > Email - vvk@itsa.ucsf.edu > > ---Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator > MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 > Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search > http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV > -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From PHTH1@cc.newcastle.edu.au Fri Jul 29 01:12:13 1994 Received: from BROLGA.NEWCASTLE.EDU.AU for PHTH1@cc.newcastle.edu.au by infomeister (8.6.9/930601.1506) id AAA08774; Fri, 29 Jul 1994 00:51:04 GMT Received: from cc.newcastle.edu.au by cc.newcastle.edu.au (PMDF V4.3-8 #6545) id <01HF9XVCBQU89AQ2J9@cc.newcastle.edu.au>; Fri, 29 Jul 1994 10:56:14 +1000 Date: Fri, 29 Jul 1994 10:47:07 +1000 From: Tony Dyson Subject: CCL: More on CAMP-ATAMI manual translation To: chemistry@ccl.net Message-id: <01HF9Y84OF9G9AQ2J9@cc.newcastle.edu.au> MIME-version: 1.0 Content-transfer-encoding: 7BIT In my original message about the translation of chapters 3 & 4 from the CAMP-ATAMI manual, I omitted some important information! Chapters 3 & 4 of the manual were kindly translated by Ms. Emi Ikeda on behalf of Dr. Xiaoming Zheng, School of Chemistry, University of Sydney, Australia. They reserve the right to make corrections in the future as they see fit. The manual translation is not to be sold for profit. My role has been to attempt to coordinate a complete translation of the CAMP-ATAMI manual. So far, I have obtained Ch. 3 & 4 from Emi and Xiaoming, and there is another party working on chapter 5. If you feel that you have benefited from obtaining chapters 3 & 4, and are in a position to assist with one of the other chapters, I would love to hear from you. All who have written requesting copies of chapters 3 & 4 should receive those sometime today. (Sorry for the delay.) Tony --------------------------------------------------------------------- Anthony J. Dyson Surface Theory Group Dept. of Physics, University of Newcastle Australia phth1@cc.newcastle.edu.au ---------------------------------------------------------------------