From cklein@uic.edu Fri Oct 3 09:28:17 1997 Received: from tigger.cc.uic.edu for cklein@uic.edu by www.ccl.net (8.8.3/950822.1) id JAA08934; Fri, 3 Oct 1997 09:27:38 -0400 (EDT) Received: from draco (MMAD1.PMMP.UIC.EDU [128.248.78.171]) by tigger.cc.uic.edu (8.8.5/8.8.5) with SMTP id IAA197658 for ; Fri, 3 Oct 1997 08:27:48 -0500 Sender: klein@tigger.cc.uic.edu Message-ID: <3434F34B.167E@uic.edu> Date: Fri, 03 Oct 1997 08:29:47 -0500 From: Christian Klein Organization: Lab. Molecular Modeling & Design, UIC X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: CCL Subject: Summary: Fortran for Irix 6.x Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Thanks to all who responded! Here is the outcome: SGI does provide Fortran compilers for the latest Irix versions. Both f77 and f90/95 compilers can be bought as part of a package (MIPSpro Compilers package), which also includes C and C++. Some responders acknowledged the good performance of these compilers. From a conversation with an SGI sales representative, however, I concluded that the cheapest solution for our lab will cost at least $1500, and probably twice as much. Free, or cheaper, compilers do not seem to be available. Konrad Hinsen wrote that he used to work with f2c and did not experience any trouble, although the generated code is somewhat slower than the one from "genuine" Fortran compilers. The problem with our source is, that it is quite large and we hope that a recompilation with a genuine Fortran compiler works smoother than the f2c, so we can get along with fewer changes. Chris From MMENDEZ@DELTA.IS.TCU.EDU Fri Oct 3 11:28:19 1997 Received: from DELTA.IS.TCU.EDU for MMENDEZ@DELTA.IS.TCU.EDU by www.ccl.net (8.8.3/950822.1) id LAA09673; Fri, 3 Oct 1997 11:13:52 -0400 (EDT) Received: from DELTA.IS.TCU.EDU by DELTA.IS.TCU.EDU (PMDF V5.1-7 #20456) id <01IOD7CQXZN20091L9@DELTA.IS.TCU.EDU> for chemistry@www.ccl.net; Fri, 3 Oct 1997 10:13:43 CDT Date: Fri, 03 Oct 1997 10:13:42 -0500 (CDT) From: "Miguel A. Mendez Rojas" Subject: Re: CCL:thermodynamical data request. In-reply-to: <199709261603.SAA03764@pegase.total.fr> To: "clemendot au CERT/TRD tel: +33 (0)2.35551482" Cc: chemistry@www.ccl.net, francois.hutschka@total.com Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII The actual issue of ALEPHZERO Journal of Science Divulgation & Education is located in: http://www.udlap.mx/~aleph/alephzero11/alephzero11.html Thanks. /////////////////////////////////////////////////////////////////////////// Miguel Angel Mendez Rojas, Editor & Director of the Chemistry Ph.D. Journal ALEPHZERO, of Sciences Texas Christian University Divulgation. Fort Worth, TX 76120 http://www.udlap.mx/~aleph/ http://delta.is.tcu.edu/~mmendez/ aleph@udlapvms.pue.udlap.mx e-mail: mmendez@delta.is.tcu.edu \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ From shenkin@still3.chem.columbia.edu Fri Oct 3 12:12:39 1997 Received: from mailrelay1.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id LAA09629; Fri, 3 Oct 1997 11:07:55 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id LAA01038; Fri, 3 Oct 1997 11:07:52 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) id LAA22141; Fri, 3 Oct 1997 11:07:51 -0400 From: "Peter Shenkin" Message-Id: <9710031107.ZM22139@still3.chem.columbia.edu> Date: Fri, 3 Oct 1997 11:07:51 -0400 In-Reply-To: Christian Klein "CCL:Summary: Fortran for Irix 6.x" (Oct 3, 8:29am) References: <3434F34B.167E@uic.edu> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: Christian Klein , CCL Subject: Re: CCL:Summary: Fortran for Irix 6.x Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Oct 3, 8:29am, Christian Klein wrote: > Subject: CCL:Summary: Fortran for Irix 6.x > Thanks to all who responded! > > Here is the outcome: > > SGI does provide Fortran compilers for the latest Irix versions. Both > f77 and f90/95 compilers can be bought as part of a package (MIPSpro > Compilers package), which also includes C and C++. Some responders > acknowledged the good performance of these compilers. > > >From a conversation with an SGI sales representative, however, I > concluded that the cheapest solution for our lab will cost at least > $1500, and probably twice as much. If your institution joins the SGI Varsity program, you can get the compilers and more for much, much less. I forget the exact numbers.... -P. -- ******************* Jimmy Witherspoon, 1923 - 1997, RIP ******************* * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From mhb@unx.berkeley.edu Fri Sep 26 19:09 EDT 1997 Received: from unx.berkeley.edu for mhb@unx.berkeley.edu by bedrock.ccl.net (8.8.6/950822.1) id TAA13126; Fri, 26 Sep 1997 19:09:12 -0400 (EDT) Received: from unex-Message_Server by unx.berkeley.edu with Novell_GroupWise; Fri, 26 Sep 1997 16:13:00 -0800 Message-Id: X-Mailer: Novell GroupWise 4.1 Date: Fri, 26 Sep 1997 15:52:05 -0800 From: Meg Bryant To: jkl@ccl.net Subject: 97.11.17 Course: Comp. Chem. for Biomed. Appl. Meg Bryant Senior Publications Coordinator UC Berkeley Extension mhb@unx.berkeley.edu >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> THE IMPACT OF COMPUTATIONAL MOLECULAR AND CHEMICAL MODELING ON THE BIOMEDICAL FIELD UC Berkeley Extension will offer a three-day course, "An Overview of Computational Chemistry for Biomedical Applications," on Mon., Nov. 17 through Wed., Nov.19, from 9 am to 5 pm at UC Extension Downtown, 150 Fourth St., San Francisco. Course fee is $1,295 and includes computer use, connect time and extensive course materials. Those registering 30 days in advance receive a $50 discount. Team enrollments may be discounted to $1,195 per person for three or more people. (Early registration discounts do not apply to team enrollments.) For a brochure, call (415) 323-8143 or e-mail eiw@unx.berkeley.edu To register, call (510) 642-4111 or visit the course website at http://www.unex.berkeley.edu:4243/chem Instructors are Michael Colvin, Ph.D., a research chemist in the Biology and Biotechnology Research Program at Lawrence Livermore National Laboratories, and Douglas Henry, Ph.D., a senior scientist at MDL Information Systems, Inc. This hands-on course introduces computer-assisted molecular modeling, with an emphasis on practical application of the simulations and on understanding the strengths and limitations of different methods. Participants will gain an overview of the range of chemical modeling methods from first-principles quantum chemistry on small biochemicals to hueristic homology-searching on large proteins. The computer lab will be open for three hours at end of each day's session for the completion of course labs and work on modeling projects related to private research. From mauro@carbon.foodsci.unibo.it Fri Oct 3 13:28:19 1997 Received: from carbon.foodsci.unibo.it for mauro@carbon.foodsci.unibo.it by www.ccl.net (8.8.3/950822.1) id MAA10400; Fri, 3 Oct 1997 12:35:33 -0400 (EDT) Received: from localhost (mauro@localhost) by carbon.foodsci.unibo.it (8.7.5/8.7.3) with SMTP id SAA29601 for ; Fri, 3 Oct 1997 18:37:10 +0200 Date: Fri, 3 Oct 1997 18:37:10 +0200 (MET DST) From: "Mauro A. Cremonini" To: chemistry@www.ccl.net Subject: ab initio calculation on heme In-Reply-To: <3.0.1.32.19971001114816.008347b0@cherwell.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, can anybody point me to some fundamental publication about ab intio calculation of hemes? In particular I would be glad to know which basis set is best suited for calculating spin delocalization from iron to heme. Thank you very much. Mauro ============================================ Mauro Andrea Cremonini, PhD Food Science and Technology Laboratory University of Bologna Via Ravennate 1020 - Cesena - Italy FAX:+39.547.382348 e-mail: mauro@carbon.foodsci.unibo.it 73 de IK4QIX ============================================ From omar@boston.sgi.com Fri Oct 3 13:32:18 1997 Received: from deliverator.sgi.com for omar@boston.sgi.com by www.ccl.net (8.8.3/950822.1) id MAA10442; Fri, 3 Oct 1997 12:38:53 -0400 (EDT) Received: from sgibos.boston.sgi.com (sgibos.boston.sgi.com [169.238.34.4]) by deliverator.sgi.com (950413.SGI.8.6.12/970507) via ESMTP id JAA24641; Fri, 3 Oct 1997 09:38:45 -0700 env-from (omar@boston.sgi.com) Received: from arkham.boston.sgi.com by sgibos.boston.sgi.com via ESMTP (951211.SGI.8.6.12.PATCH1042/940406.SGI) id MAA04248; Fri, 3 Oct 1997 12:38:25 -0400 Received: from boston.sgi.com (localhost [127.0.0.1]) by arkham.boston.sgi.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id MAA12838; Fri, 3 Oct 1997 12:38:17 -0400 Sender: omar@boston.sgi.com Message-ID: <34351F79.11BBAB6C@boston.sgi.com> Date: Fri, 03 Oct 1997 12:38:17 -0400 From: "Omar G. Stradella" Organization: Silicon Graphics, Inc. X-Mailer: Mozilla 4.03C-SGI [en] (X11; I; IRIX 6.2 IP22) MIME-Version: 1.0 To: Christian Klein CC: CCL Subject: Re: CCL:Summary: Fortran for Irix 6.x References: <3434F34B.167E@uic.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Christian Klein wrote: > > Thanks to all who responded! > > Here is the outcome: > > SGI does provide Fortran compilers for the latest Irix versions. Both > f77 and f90/95 compilers can be bought as part of a package (MIPSpro > Compilers package), which also includes C and C++. Some responders > acknowledged the good performance of these compilers. > > >From a conversation with an SGI sales representative, however, I > concluded that the cheapest solution for our lab will cost at least > $1500, and probably twice as much. > > Free, or cheaper, compilers do not seem to be available. > > Konrad Hinsen wrote that he used to work with f2c and did not experience > any trouble, although the generated code is somewhat slower than the one > from "genuine" Fortran compilers. The problem with our source is, that > it is quite large and we hope that a recompilation with a genuine > Fortran compiler works smoother than the f2c, so we can get along with > fewer changes. > > Chris > Hi Chris, I'm almost sure that UIC is a member of the Varsity Program, if that's the case you can try to get in contact with the "contact" person in your University to see if you can get the compiler from them. For more datails about the Varsity Program, check: http://www.sgi.com/silicon_campus/varsity_NA.html Hope this hels, Omar. -- +---------------------------------------------------------------------+ Omar G. Stradella, Ph.D. Supercomputing Applications Silicon Graphics, Inc. Computational Chemistry One Cabot Road, Hudson, MA 01749, USA N 42 22'41" W 71 33'45" E-mail: omar@boston.sgi.com Phone: +1-978-567-2258 FAX: +1-978-562-4755 http://www.sgi.com/ChemBio http://reality.sgi.com/omar +-------- Ph-nglui mglw'nafh Cthulhu R'lyeh wgah'nagl fhtagn -------+ From hinsen@lmspc1.ibs.fr Fri Oct 3 13:34:13 1997 Received: from ibs.ibs.fr for hinsen@lmspc1.ibs.fr by www.ccl.net (8.8.3/950822.1) id MAA10417; Fri, 3 Oct 1997 12:37:27 -0400 (EDT) Received: from lmspc1.ibs.fr (hinsen@lmspc1.ibs.fr [192.134.36.141]) by ibs.ibs.fr (8.6.12/8.6.12) with ESMTP id SAA13321; Fri, 3 Oct 1997 18:37:48 +0100 Received: (from hinsen@localhost) by lmspc1.ibs.fr (8.8.5/8.8.5) id SAA29053; Fri, 3 Oct 1997 18:36:29 +0200 Date: Fri, 3 Oct 1997 18:36:29 +0200 Message-Id: <199710031636.SAA29053@lmspc1.ibs.fr> From: Konrad Hinsen To: cklein@uic.edu CC: chemistry@www.ccl.net In-reply-to: <3434F34B.167E@uic.edu> (message from Christian Klein on Fri, 03 Oct 1997 08:29:47 -0500) Subject: Re: CCL:Summary: Fortran for Irix 6.x > Konrad Hinsen wrote that he used to work with f2c and did not experience > any trouble, although the generated code is somewhat slower than the one > from "genuine" Fortran compilers. The problem with our source is, that > it is quite large and we hope that a recompilation with a genuine > Fortran compiler works smoother than the f2c, so we can get along with > fewer changes. Maybe it's worth pointing out what f2c really is and does. It is based on a genuine Fortran compiler, the first one available for Unix systems, and which has been the basis for some Fortran 77 compilers offered by various manufacturers. Due its "generic Unix" origin, the code generator was a well isolated and easily replacable piece. f2c is nothing but a version of this Fortran compiler with a code generator that spits out C code. So f2c is as much a Fortran compiler as any other; it supports the full Fortran 77 standard. The reason why f2c + a C compiler is usually less efficient than a direct Fortran compiler is that some optimization approaches are lost due to the intermediate representation as C code. The Fortran standard contains some rules that enable important optimization (at the cost of reliability) which C code does not permit. And Fortran has optimizable built-in numerical operations where C uses a library approach which makes optimization more difficult (though not impossible). So if speed is not of extreme importance, f2c can be a fully sufficient replacement for a Fortran compiler. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------- From XIENING@MEENA.CC.UREGINA.CA Fri Oct 3 21:28:22 1997 Received: from veena.cc.uregina.ca for XIENING@MEENA.CC.UREGINA.CA by www.ccl.net (8.8.3/950822.1) id VAA12679; Fri, 3 Oct 1997 21:01:21 -0400 (EDT) Received: from meena.cc.uregina.ca by meena.cc.uregina.ca (PMDF V5.1-8 #20153) id <01IODP3ST2ME94IEXM@meena.cc.uregina.ca> for chemistry@www.ccl.net; Fri, 3 Oct 1997 18:41:54 CST Date: Fri, 03 Oct 1997 18:41:54 -0600 (CST) From: Ning Xie Subject: reasonable geometry In-reply-to: <3434F34B.167E@uic.edu> To: chemistry@www.ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Good day! cclers, We are using Gaussian 94 calculating the energy of the complex formed between permanganate and ZnCl2. We suppose that ZnCl2 is tetrahedral with two chloride atoms, an oxygen atom from permangate ion and another oxygen atom from acetone (solvent) as ligands. We want to keep the geometry of permanaganate ion tetrahedral. But after optimization, three oxygen atoms and manganese are almost on the same plane and the remaining oxygen atom joins acetone (CH3COCH3--->CH3COCH2OH). I tried to fix the geometry of permanganate ion as tetrahedral by defining its bond lengths and bond angles as constant at the start of the calculation. It doesn't seem to be working. Is there somebody out there who would give me a hint? Thank you very much for your help. ========================================================================= | NING XIE Tel: (306)585-5262 (O) | | Chemistry Department (306)585-2184 (H) | | University of Regina Fax: (306)585-4894 | | Regina, SK E-Mail: xiening@meena.cc.uregina.ca | | Canada S4S 0A2 | ========================================================================= From uucp@msi.com Thu Oct 2 16:41:19 1997 Received: from bioc1.msi.com for uucp@msi.com by www.ccl.net (8.8.3/950822.1) id QAA03958; Thu, 2 Oct 1997 16:19:16 -0400 (EDT) Received: by bioc1.msi.com (5.64/0.0) id AA12575; Thu, 2 Oct 97 13:19:35 -0700 Received: from news.msi.com(146.202.0.224) by bioc1.msi.com via smap (V2.0) id xma012561; Thu, 2 Oct 97 13:19:05 -0700 Received: by news.msi.com (4.1/SMI-4.1) id AA01688; Thu, 2 Oct 97 13:06:52 PDT Newsgroups: msi.comp-chem-list Path: uucp From: Bob Funchess Subject: Re: CCL:Presentation graphics X-Nntp-Posting-Host: iris76 Content-Type: text/plain; charset=us-ascii To: Steve.Bowlus@sandoz.com Message-Id: <3434017B.BB47E473@msi.com> Sender: uucp@msi.com Content-Transfer-Encoding: 7bit Organization: Molecular Simulations Inc. References: <0034700006889867000002*@MHS> Mime-Version: 1.0 Date: Thu, 2 Oct 1997 20:18:03 GMT X-Mailer: Mozilla 4.02 [en] (X11; I; IRIX 6.2 IP22) Steve.Bowlus@sandoz.com wrote: > > I'm looking for a converter program which will take a screen capture > image (e.g. an RGB file from the SGI snapshot utility, or a > postscript file generated from it) and generate a high quality > postscript file. By high quality, I mean with the jaggies removed > from letters and edges of smooth curves, and some color/pattern > dithering for shaded surfaces, etc. Most printers will automatically handle dithering for any color they can't reproduce as a pure tone, so you're probably better off leaving that and concentrating on smoothing the edges unless you _really_ dislike the way the printer's doing it. In general, there's no magic way to recover lost detail, though some of the painting/photo-refinishing programs these days are capable of amazing things and would be worth looking into. Normally the feature you need will be called something like "smooth" or "blur", or possibly "convolve" or "filter". If you don't have access to a program like that, you could try rescaling the image to the size (in terms of number of pixels) that you need, and then using a convolution function to blur the jagged edges a bit; SGI has tools for doing this sort of thing in the imgtools subsystem on the IRIX CD-ROMs. There are also some programs available from their website (go to http://www.sgi.com/ and poke around a bit). As for the text, personally I'd suggest removing it from the original bitmapped image whenever possible and adding real postscript text later using showcase or something similar. It may be tricky to do that if the text overlaps something other than the background, though. Regards, Bob Funchess -- Dr. Robert B. Funchess bobf@msi.com Senior Scientist, Scientific Support Voice (619) 458-9990 x738 Molecular Simulations Inc. FAX (619) 458-0431 9685 Scranton Road San Diego, CA 92121-3752 http://www.msi.com/ From krajesh@giasdla.vsnl.net.in Fri Oct 3 23:28:23 1997 Received: from giasdla.vsnl.net.in for krajesh@giasdla.vsnl.net.in by www.ccl.net (8.8.3/950822.1) id WAA13182; Fri, 3 Oct 1997 22:30:03 -0400 (EDT) Received: from localhost by giasdla.vsnl.net.in (SMI-8.6/SMI-SVR4) id HAA22495; Sat, 4 Oct 1997 07:59:55 +0530 Date: Sat, 4 Oct 1997 07:59:55 +0530 (IST) From: Rajesh Kumar Grover X-Sender: krajesh@giasdlb To: CCL cc: surjit@netearth.iitd.ernet.in Subject: Questions regarding MOPAC Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi!, We wish to thank the readers of CCL for the useful suggestions and advice for my query regarding MOPAC calculation on FADH2. We have the following doubts regarding which help and suggestions would be greatly appreciated. 1. How are we to react to messages like " THE LINE MINIMIZATION FAILED TWICE IN A ROW. TAKE CARE! SCF FIELD WAS ACHIEVED " and " GRADIENT TEST NOT PASSED, BUT FURTHER WORK NOT JUSTIFIED SCF FIELD WAS ACHIEVED " 2. A veriety of Z-matrix (on the basis of reference atoms used for the definition of bond, angles and dihedrals) could be written for the same molecule. Is there a prefered/right way for writing Z-matrices? 3. Are there any informative reference books/articles on applications of MOPAC? We are aware of Tim Clark's Handbook and J.P.P. Stewart's MOPAC manual. In specific, are there any articles dealing with charge transfer studies using MOPAC? Thank you for the time, Regards, Surjit / Bhawana. ____________________________ Surjit B.Dixit PhD Candidate Telephone:+91 11 666979 Extn.:7602 Chemistry Department, Facsimile:+91 11 6862037 Indian Institute of Technology, Email : surjit@chemistry.iitd.ernet.in Hauz Khas, surjit@netearth.iitd.ernet.in New Delhi 110016, India.