From wdi@mail2.organik.uni-erlangen.de Mon Feb 9 20:10:56 1998 Received: from faui45.informatik.uni-erlangen.de for wdi@mail2.organik.uni-erlangen.de by www.ccl.net (8.8.3/950822.1) id TAA03432; Mon, 9 Feb 1998 19:57:03 -0500 (EST) Received: from mail2.organik.uni-erlangen.de (cygnus.organik.uni-erlangen.de [131.188.128.10]) by faui45.informatik.uni-erlangen.de (8.8.8/8.1.16-FAU) with ESMTP id BAA29559 for ; Tue, 10 Feb 1998 01:57:04 +0100 (MET) Received: from wtewael.organik.uni-erlangen.de (wtewael.organik.uni-erlangen.de [131.188.128.216]) by mail2.organik.uni-erlangen.de (8.8.6/8.1.2-FAU) with ESMTP id BAA16845 for ; Tue, 10 Feb 1998 01:56:40 +0100 (MET) Received: (from wdi@localhost) by wtewael.organik.uni-erlangen.de (8.8.7/8.1.59-FAU) id AAA06391 for chemistry@www.ccl.net; Tue, 10 Feb 1998 00:56:27 GMT From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9802100156.ZM6389@ccc.chemie.uni-erlangen.de> Date: Tue, 10 Feb 1998 01:56:21 +0100 In-Reply-To: "Dr. Bruno Manunza" "CCL:postscript editor" (Feb 9, 18:34) References: Reply-To: Wolf-Dietrich.Ihlenfeldt@TORVS.CCC.Uni-Erlangen.DE X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Re: CCL:postscript editor On Feb 9, 18:34, Dr. Bruno Manunza wrote: > Subject: CCL:postscript editor > > On Mon, 9 Feb 1998, Shin-Inn Chen wrote: > > > dear netters: > > i need a program that can read the postscript file and modify the > > figure. does any one know where can i download the program like this? > > any suggestion will be appreciated. > > > Dear Shin, > on UNIX/LINUX, Win and Mac you may use ImageMagick which do exactly > what you need. > > have a look at it at: > http://www.wizards.dupont.com/cristy/ImageMagick.html > > Bye > Bruno (plus several other helpful messages not included here). I have a suspicion that the original request may have been misunderstood. Until now, all postings referred to programs which can read an EPS file and export it as some kind of bitmap and support the addition of annotations and other image manipulations on the bitmap. A good selection of these programs has been presented in the previous posts. However, EDITING a PostScript file is another problem. For example, if you want do delete a line which crosses other elements this will be an awkward procedure in a typical image processing program, and in any case you will lose the advantage of the original file format, for example scalability without artefacts etc. There are programs available which contain an embedded PostScript interpreter and allow direct manipulation of the PostScript strokes and other basic elements. Unfortunately, these programs tend to be rather expensive. The freeware program 'pstoedit' (part of the X11R6 distribution, also available from numerous ftp repositories, check with archie, most current version appears to be 2.50) will read a PostScript or PDF file and output its contents in various vector formats (mif, fig, cgm, wmf, gnuplot, dxf, etc.) which can be loaded into a vector drawing program and manipulated in a more comfortable way than with bitmap image manipulation programs. Note however that this program only processes lines and text, embedded images etc. are lost in the conversion process. You also need a PostScript interpreter program, for example ghostscript. Of course, you can also use your standard text editor to edit the original file directly. PostScript is plain Ascii and inherently just another programming language. Direct editing is not so difficult as it may sound if you simply remove items - just a few hours ago I edited an MSI Cerius II output file to get rid of some annoying logos. All you need is a PostScript language documentation manual and a PostScript display program to avoid wasting paper during the editing steps. -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 >From jrh@qc.ag-berlin.mpg.de Mon Feb 9 20:04 EST 1998 Received: from ccl.net for jrh@qc.ag-berlin.mpg.de by www.ccl.net (8.8.3/950822.1) id UAA03448; Mon, 9 Feb 1998 20:04:57 -0500 (EST) Received: from helios.qc.ag-berlin.mpg.de (helios.QC.AG-Berlin.MPG.DE [141.20.74.13]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id UAA12687 for ; Mon, 9 Feb 1998 20:04:55 -0500 (EST) Received: by helios.qc.ag-berlin.mpg.de (AIX 3.2/UCB 5.64/4.03) id AA22828; Tue, 10 Feb 1998 02:04:56 +0100 Date: Tue, 10 Feb 1998 02:04:56 +0100 From: jrh@qc.ag-berlin.mpg.de (Joerg-Ruediger Hill) Message-Id: <9802100104.AA22828@helios.qc.ag-berlin.mpg.de> To: ccl@ccl.net Subject: Viewmol 2.1.1 released (bug fix) Viewmol 2.1.1 has been released. This is a bug fix for version 2.1 and concerns mainly Linux users. The new version has been statically linked with libGLw.a for Linux, since I got a number of complaints about it from people who couldn't find this library in their distribution (it should be part of Mesa). The new version also fixes a bug with respect to the Post- script output. There have been a number of problems that people wanted to compile Viewmol and got a message about '__eprintf not found' from the linker. Thanks to John-David Ray Rocha I could trace that down to a problem with libtiff, but I can't really tell the reason for the problem. I have tried to compile Viewmol on quite a number of different systems and OSes and never encountered such a problem. The only reason I can think of is, that you did not compile libtiff on the same machine you are compiling Viewmol on. Unfortunately, commercial OSes usually have to get patched a few times before they actually work and even if the OS claims to be version x.y.z on two machines it can be different due to different installed patches. The only remedy to this situation is to compile anything on the same machine. Jörg-R. Hill From rick@donet.com Tue Feb 10 04:11:26 1998 Received: from cookie.donet.com for rick@donet.com by www.ccl.net (8.8.3/950822.1) id DAA05203; Tue, 10 Feb 1998 03:30:48 -0500 (EST) Received: from [206.173.99.56] ([206.173.99.56]) by cookie.donet.com (8.8.7/8.8.7) with SMTP id DAA02151 for ; Tue, 10 Feb 1998 03:30:31 -0500 Message-Id: <199802100830.DAA02151@cookie.donet.com> Subject: Hello, my name is Rick Gies... Date: Tue, 10 Feb 98 03:30:59 -0000 x-sender: rick@donet.com x-mailer: Claris Emailer 2.0v2, June 6, 1997 From: Rick Gies To: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-transfer-encoding: quoted-printable Hello: I would like to take this opportunity to introduce myself to you. My = name is Rick Gies and I am a recent graduate of Wright State = University in Dayton, Ohio. I have recently taken over website development and related sales for = Advanced American Biotechnology (AAB). AAB is a company that offers = Biotech software and systems for research, medicine, agriculture & = industry. Our software & instrumentation can be used for such = applications as electrophoresis, TLC, gel documentation, image = analysis, and more. I would like to invite you to our website to check out the great = deals we have on Biotech software and systems. I know you will be = happy that you did, because our products have more functions & are = more than 30% lower than similar products, and they are also much = easier to use. The AAB Biotech Website can be accessed on the Web at: http://www.meddoctor.com/aabi/aab.html If you have any questions about our products or need assistance = please don=B9t hesitate to ask, I will do my best to serve you. Sincerely, Rick Gies also--> When you come by our website please check out the demo software that = is available. During February we are offering an EXCLUSIVE higher = education 10% discount on all software! ------------------------------------------------- AAB (Advanced American Biotechnology) http://www.meddoctor.com/aabi/aab.html Phone 937 431-0596 EMail: rick@meddoctor.com 18 Windows, 14 Mac, 24 DOS programs: 1D, 2D, DNA, PCR, RFLP, RAPD, colony count, particle sizing, = Dots-ELISA, FISH, Chromosomes Karyotyping, telemicroscopy. ALSO AVAILABLE: Gel documentation, UV fluorescence, chemiluminescence, densitometers, = & scanners. -------------------------------------------------- From mahieu@univ-littoral.fr Tue Feb 10 05:11:01 1998 Received: from lilserv.univ-lille1.fr for mahieu@univ-littoral.fr by www.ccl.net (8.8.3/950822.1) id EAA05562; Tue, 10 Feb 1998 04:58:21 -0500 (EST) Received: from opale.univ-littoral.fr (opale.univ-littoral.fr [193.49.203.13]) by lilserv.univ-lille1.fr (8.8.7/jtpda-5.1) with SMTP id KAA11201 for ; Tue, 10 Feb 1998 10:57:34 +0100 (MET) Received: by opale.univ-littoral.fr; id AA26420; Tue, 10 Feb 1998 11:04:02 +0100 Message-Id: <2.2f.32.19980210095713.0068277c@opale.univ-littoral.fr> X-Sender: mahieu@opale.univ-littoral.fr X-Mailer: Windows Eudora Pro Version 2.2f (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 10 Feb 1998 10:57:13 +0100 To: chemistry@www.ccl.net From: mahieu joris Subject: CCL: Normal Coordinate Analysis question Dear Net Chemists, I need a program which converts the force matrix in cartesien coordinates obtained by ab-initio or semi-empirical methods to the force constants in complete internal coordinates. Thanks. ************************************************** MAHIEU Joris Laboratoire de Synthese Organique et Environnement Universite du Littoral Dunkerque (France) E-mail : mahieu@univ-littoral.fr ************************************************** From schiffer@h1tw0036.hoechst.com Tue Feb 10 06:11:02 1998 Received: from mailgate.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id FAA05628; Tue, 10 Feb 1998 05:13:45 -0500 (EST) Received: by mailgate.hoechst.com id LAA08038; Tue, 10 Feb 1998 11:16:51 +0100 Received: from unknown(134.81.76.36) by mailgate id sma008023; Tue Feb 10 11:16:34 1998 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id LAA21537; Tue, 10 Feb 1998 11:10:14 +0100 Message-ID: <34E02785.41C6@h1tw0036.hoechst.com> Date: Tue, 10 Feb 1998 11:10:13 +0100 From: "Dr. Heinz Schiffer" Organization: Hoechst Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Computational Chemistry List Subject: ACES2/HFINSTABILITY Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, I have some problems getting the right UHF solution running ACES2 nearby the transition state for OO---H on the MP2 level (O-H = 2.85 a.u., O-O=2.239694, OOH=116.4239). With my basis set (SVP) the energy according to TURBOMOLE is -149.972924 Hartree. . Running ACES2 I get -149.936211 Hartree and <0|S*S|0> = 0.765. This solution is not stable, and with the keyword HFSTABILITY=FOLLOW I get the right solution of -149.972924 Hartree and <0|S*S|0> =1.472. However, doing the same calculation with ACES2 again with GUESS=MOREAD I again get the wrong answer. So it seams to me, that after using the key word HFSTABILITY=FOLLOW there are no stored eigen vectors in the JOBARC file. But I need these to perform a transition state search on the MP2 level. Can anyone help me with that ? Ciao Heinz ----------------------------------------------------------------------- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst Research & Technology Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main Schiffer@CRT.hoechst.com From salvador@itqb.unl.pt Tue Feb 10 07:11:03 1998 Received: from gatekeeper.itqb.unl.pt for salvador@itqb.unl.pt by www.ccl.net (8.8.3/950822.1) id GAA05810; Tue, 10 Feb 1998 06:16:09 -0500 (EST) Received: (from uucp@localhost) by gatekeeper.itqb.unl.pt (8.8.6/8.8.6) id LAA03788 for ; Tue, 10 Feb 1998 11:22:15 GMT Received: from ctqb04.itqb.unl.pt(193.136.182.4) by gatekeeper.itqb.unl.pt via smap (V1.3) id sma003771; Tue Feb 10 11:22:09 1998 Received: from milou.itqb.unl.pt by CTQB04 (MX V3.1) with SMTP; Tue, 10 Feb 1998 12:20:56 EST Message-ID: <1.5.4.32.19980210111958.00670b94@ctqb04.itqb.unl.pt> X-Sender: salvador@ctqb04.itqb.unl.pt X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 10 Feb 1998 11:19:58 +0000 To: chemistry@www.ccl.net From: Armindo Salvador Subject: PowBioSys PowBioSys - International Symposium on Power-Law Modelling of Biological Systems Oeiras (Portugal), October 4-7, 1998 This is the SECOND ANNOUNCEMENT and CALL FOR ABSTRACTS for PowBioSys. This symposium is centred on, but not restricted to, developments of the power-law formalism and on its applications to biological problems, >from the molecular to the ecological levels. The following types of contributions are welcome: * mathematical contributions bearing on or applying the power-law formalism; * applications of the power-law formalism to biological problems; * other applications of the power-law formalism (Chemistry, Physics, Economics, Engineering, etc.); * contributions that do not involve the power-law formalism but fall within the scope of the biological themes of the sessions. The contributions can be presented as seminars, posters, or software demonstrations. For more information and registration please visit the website at http://www.itqb.unl.pt/sss5/ Armindo Salvador Gr. de Bioquimica e Biologia Teoricas | Lab. de Sistemas Micro-heterogeneos Instituto Rocha Cabral | Inst. de Tecnologia Quimica e Biologica Cc. Bento da Rocha Cabral, 14 | Apartado 127 P-1250 LISBOA | P-2780 OEIRAS Portugal From schiffer@h1tw0036.hoechst.com Tue Feb 10 09:11:04 1998 Received: from mailgate.hoechst.com for schiffer@h1tw0036.hoechst.com by www.ccl.net (8.8.3/950822.1) id IAA06376; Tue, 10 Feb 1998 08:34:40 -0500 (EST) Received: by mailgate.hoechst.com id OAA19551; Tue, 10 Feb 1998 14:36:52 +0100 Received: from unknown(134.81.76.36) by mailgate id sma019516; Tue Feb 10 14:34:58 1998 Received: from h1tw0024 by h1tw0036 via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) id OAA21836; Tue, 10 Feb 1998 14:28:28 +0100 Message-ID: <34E055FC.167E@h1tw0036.hoechst.com> Date: Tue, 10 Feb 1998 14:28:28 +0100 From: "Dr. Heinz Schiffer" Organization: Hoechst Research & Technology X-Mailer: Mozilla 2.0 (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Computational Chemistry List Subject: ACES2 / Transition State Optimization Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Netters, does anyone knows how to for the ACES2 program to start a transition state optimization with an exact Hessian ? I tried several variants, but never succeded. Ciao Heinz -- Dr. Heinz Schiffer Phone ++49-69-305-2330 Hoechst Research & Technology Fax ++49-69-305-81162 Scientific Computing, G864 Email schiffer@h1tw0036.hoechst.com 65926 Frankfurt am Main Schiffer@CRT.hoechst.com From darrena@chem.leeds.ac.uk Tue Feb 10 11:11:07 1998 Received: from chemistry.leeds.ac.uk for darrena@chem.leeds.ac.uk by www.ccl.net (8.8.3/950822.1) id KAA07130; Tue, 10 Feb 1998 10:37:05 -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 PAA11935 for ; Tue, 10 Feb 1998 15:36:35 GMT Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 10 Feb 1998 15:36:15 +0000 To: chemistry@www.ccl.net From: Darren Andrews Subject: Gaussian scratch space limitation Dear all, I'm having problems with AO integral files on a G92 job. My job needs more than 2Gigs of disk space (7Gig scratch disk), but the job craps out with an I/O error when it gets to 2Gig integral file size. I guess it's to do with the 32 bit OS (Irix5.3 on a SG Indy) limiting the maximum file size to 2Gig. Is there a way to increase the maximum size of the integral file, or limit the size of the written file, i.e., don't write all the integrals out? Of course, it may be something else entirely. 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 smb@smb.chem.niu.edu Tue Feb 10 11:22:23 1998 Received: from cz2.chem.niu.edu for smb@smb.chem.niu.edu by www.ccl.net (8.8.3/950822.1) id KAA07024; Tue, 10 Feb 1998 10:14:50 -0500 (EST) Received: from cz.chem.niu.edu by cz2.chem.niu.edu via SMTP (920330.SGI/920502.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA02765; Tue, 10 Feb 98 08:44:17 -0600 Received: from smb.chem.niu.edu by cz.chem.niu.edu via SMTP (920330.SGI/890607.SGI) (for @cz2.chem.niu.edu:CHEMISTRY@www.ccl.net) id AA03893; Tue, 10 Feb 98 09:11:47 -0600 Received: from smb by smb.chem.niu.edu via SMTP (940816.SGI.8.6.9/940406.SGI) for id JAA07374; Tue, 10 Feb 1998 09:13:46 -0600 Sender: smb@smb.chem.niu.edu Message-Id: <34E06EA9.2781@smb.chem.niu.edu> Date: Tue, 10 Feb 1998 09:13:45 -0600 From: Steven Bachrach X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP12) Mime-Version: 1.0 To: computational chemistry list Subject: Diff. EQ Requirements in PhD programs Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit This is a bit off the subject, but should be of interest to many of the folks on this list. We are currently revamping our PhD requirements. The issue of requiring a course in Differential Equations is now a subject of intense interest. The ACS Committee on Professional Training no longer requires Diff. Eq. to obtain the certified ACS BS degree. Given that decision, we have opted to no longer required Diff. Eq. for admission. The question before us is should Diff. Eq. still be a requirement for completion of the PhD? Preliminary inquiries have indicated that a number of schools have already eliminated the Diff. Eq. requirement for their PhD program. I would like to get some feedback on how other PhD programs are dealing with this requirement. You may, of course, direct your responses to me or the list. I can summarize for the list - if you wish to remain anonymous, please let me know. Thanks Steve -- Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From jvaara@sun3.oulu.fi Tue Feb 10 12:11:06 1998 Received: from oulu.fi for jvaara@sun3.oulu.fi by www.ccl.net (8.8.3/950822.1) id LAA07917; Tue, 10 Feb 1998 11:47:18 -0500 (EST) Received: from cc.oulu.fi (jvaara@sun3.oulu.fi [130.231.240.13]) by oulu.fi (8.8.5/8.8.5) with ESMTP id SAA06412; Tue, 10 Feb 1998 18:47:17 +0200 (EET) Received: (from jvaara@localhost) by cc.oulu.fi (8.8.5/8.8.5) id SAA06792; Tue, 10 Feb 1998 18:47:16 +0200 (EET) From: Juha Vaara Message-Id: <199802101647.SAA06792@cc.oulu.fi> Subject: f-primitive for Te To: chemistry@www.ccl.net Date: Tue, 10 Feb 1998 18:47:16 +0200 (EET) Cc: Juha.Vaara@oulu.fi (Juha Vaara) X-Mailer: ELM [version 2.4ME+ PL15 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi, could somebody share his/her knowledge of a suitable exponent of a Gaussian f-type polarization primitive for tellurium? Please indicate reference as well. Thanks in advance, Juha ----------------------------------------------------------------------- Dr. Juha Vaara tel. + 358 - (0)8 - 553 1332 Department of Physical Sciences fax + 358 - (0)8 - 553 1287 NMR Research Group email Juha.Vaara@oulu.fi University of Oulu URL http://cc.oulu.fi/~jvaara P.O.Box 333, FIN-90571 Oulu, Finland From gerald@ccl.net Tue Feb 10 12:20:15 1998 Received: from ccl.net for gerald@ccl.net by www.ccl.net (8.8.3/950822.1) id LAA07807; Tue, 10 Feb 1998 11:31:37 -0500 (EST) Received: from oscdesk53.ccl.net (oscdesk53.ccl.net [192.148.249.53]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id LAA07736; Tue, 10 Feb 1998 11:31:36 -0500 (EST) From: Gerald Lushington Received: for gerald@ccl.net by oscdesk53.ccl.net (8.7.1/920428.1525) id LAA07671; Tue, 10 Feb 1998 11:31:36 -0500 (EST) Message-Id: <199802101631.LAA07671@oscdesk53.ccl.net> Subject: Re: CCL:G:Gaussian scratch space limitation To: darrena@chemistry.leeds.ac.uk (Darren Andrews) Date: Tue, 10 Feb 1998 11:31:36 -0500 (EST) Cc: chemistry@www.ccl.net In-Reply-To: from "Darren Andrews" at Feb 10, 98 03:36:15 pm X-Mailer: ELM [version 2.4 PL24 ME5a] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit There's a nice detailed discussion on this problem, and how to get around it, available on our Web site at: http://www.asc.hpc.mil/PET/CCM/asc-tips/asc-tips.html Gerry Lushington PET-CCM Research Specialist Ohio Supercomputer Center 1224 Kinnear Rd. Columbus OH 43212-1163 Ph. 614-292-6036 Fax 614-292-7168 e-mail: gerald@ccl.net > > Dear all, > > I'm having problems with AO integral files on a G92 job. My job needs more > than 2Gigs of disk space (7Gig scratch disk), but the job craps out with an > I/O error when it gets to 2Gig integral file size. I guess it's to do with > the 32 bit OS (Irix5.3 on a SG Indy) limiting the maximum file size to > 2Gig. Is there a way to increase the maximum size of the integral file, or > limit the size of the written file, i.e., don't write all the integrals > out? Of course, it may be something else entirely. > > > 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. > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: darrena@chem.leeds.ac.uk > -- Original Sender From: Address: darrena@chemistry.leeds.ac.uk > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From mchalla@ice.lanl.gov Tue Feb 10 12:30:31 1998 Received: from ice.lanl.gov for mchalla@ice.lanl.gov by www.ccl.net (8.8.3/950822.1) id LAA07589; Tue, 10 Feb 1998 11:22:01 -0500 (EST) Received: from localhost (mchalla@localhost) by ice.lanl.gov (8.8.5/8.8.5) with SMTP id JAA02514; Tue, 10 Feb 1998 09:17:09 -0700 Date: Tue, 10 Feb 1998 09:17:09 -0700 (MST) From: Matt Challacombe T-12 To: mahieu joris cc: chemistry@www.ccl.net Subject: Re: CCL:Normal Coordinate Analysis question In-Reply-To: <2.2f.32.19980210095713.0068277c@opale.univ-littoral.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Mahieu, Check out ANHTRAX written by myself and available from QCPE. It reads Cartesian force constants (2nd and 3rd order) >from G92 (or 90 or 88? -- I can't remember now...) and transforms them to non-redundant user specified internal coordinates. The ref is "COORDINATE TRANSFORMATIONS OF CUBIC FORCE-CONSTANTS AND TRANSFERABILITY OF ANHARMONIC-FORCE CONSTANTS IN INTERNAL COORDINATES" CHALLACOMBE M, CIOSLOWSKI J JOURNAL OF CHEMICAL PHYSICS v. 95(#2) pp. 1064-1068 1991 Cheers, Matt PS. What are the complete internal coordinates? +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ Matt Challacombe Los Alamos National Laboratory http://www.t12.lanl.gov/~mchalla/ Theoretical Division email: mchalla@t12.lanl.gov Group T-12, Mail Stop B268 phone: (505) 665-5905 Los Alamos, New Mexico 87545 fax: (505) 665-3909 +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ On Tue, 10 Feb 1998, mahieu joris wrote: > Dear Net Chemists, > > I need a program which converts the force matrix in cartesien > coordinates obtained by ab-initio or semi-empirical methods to the force > constants in complete internal coordinates. > > Thanks. > > ************************************************** > MAHIEU Joris > Laboratoire de Synthese Organique et Environnement > Universite du Littoral > Dunkerque (France) > E-mail : mahieu@univ-littoral.fr > ************************************************** > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: mahieu@univ-littoral.fr > -- Original Sender From: Address: mahieu@univ-littoral.fr > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From MARYJO@neu.edu Tue Feb 10 13:11:07 1998 Received: from NUHUB.DAC.NEU.EDU for MARYJO@neu.edu by www.ccl.net (8.8.3/950822.1) id MAA08323; Tue, 10 Feb 1998 12:49:20 -0500 (EST) From: Received: from neu.edu by neu.edu (PMDF V5.1-8 #24746) id <01ITEYIM1G748X54HU@neu.edu> for chemistry@www.ccl.net; Tue, 10 Feb 1998 12:49:03 EST Date: Tue, 10 Feb 1998 12:49:02 -0500 (EST) Subject: polariz functions? To: chemistry@www.ccl.net Message-id: <01ITEYIM3BPU8X54HU@neu.edu> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Hello Everybody. Does anyone have any opinion or experience with the following problem: I am trying to get an accurate description of the bonding in ligated heavy alkaline earths. Polarization functions, or some sort of good quality augmented basis will be needed The structures are unexpected, with anomalous bond angles about the alkaline earth. Does anybody have an opinion about the relative merits of AM1, MNDO, and PM3 for this type of problem? (We have good crystal geometries. We are interested in the bonding properties.) Thanks in advance, Mary Jo Ondrechen From daniel.parish@roche.com Tue Feb 10 13:19:26 1998 Received: from gecko.pal.roche.com for daniel.parish@roche.com by www.ccl.net (8.8.3/950822.1) id MAA08355; Tue, 10 Feb 1998 12:53:44 -0500 (EST) Received: from pdxpr6 (pdxpr6.pal.roche.com [141.167.40.118]) by gecko.pal.roche.com (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id JAA07695 for ; Tue, 10 Feb 1998 09:53:10 -0800 Message-Id: <3.0.2.32.19980210095150.0091b3f0@gecko.pal.roche.com> X-Sender: daniel@gecko.pal.roche.com X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.2 (32) Date: Tue, 10 Feb 1998 09:51:50 -0800 To: chemistry@www.ccl.net From: Daniel Parish Subject: Mailing list for MSI's Catalyst software Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Greetings CCLers, For some time now I have been toying with the idea of starting a mailing list specifically for users of the software package Catalyst. For those of you unfamiliar with it, Catalyst is a commercial pharmacophore generation/database searching package sold by MSI. Although MSI maintains its own mailing list for Catalyst (catalyst-l), traffic on their list appears to be virtually nonexistent. I'm not sure whether this reflects a lack of need for such a list or whether users are uncomfortable with the list because it is maintained by MSI. I'd like some feedback on whether you think an independent catalyst mailing list would be useful and who among you would be interested in subscribing/contributing to such a list if it were available. If there is sufficient interest I will be happy to maintain this new list and, having a great deal of practical (and impractical :^) ) experience using Catalyst, happy to share my expertise as well. Please email your comments directly to me and I will summarize to the list if necessary. Regards, Daniel __*_____Daniel W. Parish ____*_____Roche Bioscience ______*_____daniel.parish@roche.com ________*_____650/855-6314 (Phone) 650/852-1875 (FAX) From patter@pollux.chem.umn.edu Tue Feb 10 15:11:07 1998 Received: from pollux.chem.umn.edu for patter@pollux.chem.umn.edu by www.ccl.net (8.8.3/950822.1) id OAA08699; Tue, 10 Feb 1998 14:13:17 -0500 (EST) Received: from localhost by pollux.chem.umn.edu via SMTP (950413.SGI.8.6.12/950213.SGI.AUTOCF) id NAA11999; Tue, 10 Feb 1998 13:12:43 -0600 Date: Tue, 10 Feb 1998 13:12:42 -0600 (CST) From: "Eric V. Patterson" To: Darren Andrews cc: chemistry@www.ccl.net Subject: Re: CCL:G:Gaussian scratch space limitation In-Reply-To: <199802101631.LAA07671@oscdesk53.ccl.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Darren, As pointed out by Gerald Lushington, there is a fairly nice workaround implemented in G94. However, you indiated that you're using G92. If you do not have access to G94, your choices are much more limited. What sort of calculation are you performing? If this is an MP2, as I suspect it might be, then you should try the MP2=verystingy and MAXDISK keywords. Depending on the number of basis functions you have, you might be flat out of luck. - Eric ######################################################################### >From the desk of: Dr. Eric V. Patterson Postdoctoral Associate Lecturer: Chemistry 8003 Department of Chemistry voice: (612) 624-1535 University of Minnesota FAX: (612) 626-7541 207 Pleasant St. SE email: patter@pollux.chem.umn.edu Minneapolis, MN 55455 WWW: http://pollux.chem.umn.edu/~patter On Tue, 10 Feb 1998, Gerald Lushington wrote: > There's a nice detailed discussion on this problem, and how to get around it, > available on our Web site at: > > http://www.asc.hpc.mil/PET/CCM/asc-tips/asc-tips.html > > Gerry Lushington > PET-CCM Research Specialist > Ohio Supercomputer Center > 1224 Kinnear Rd. > Columbus OH 43212-1163 > Ph. 614-292-6036 > Fax 614-292-7168 > e-mail: gerald@ccl.net > > > > > Dear all, > > > > I'm having problems with AO integral files on a G92 job. My job needs more > > than 2Gigs of disk space (7Gig scratch disk), but the job craps out with an > > I/O error when it gets to 2Gig integral file size. I guess it's to do with > > the 32 bit OS (Irix5.3 on a SG Indy) limiting the maximum file size to > > 2Gig. Is there a way to increase the maximum size of the integral file, or > > limit the size of the written file, i.e., don't write all the integrals > > out? Of course, it may be something else entirely. > > > > > > 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. > > > > > > > > -------This is added Automatically by the Software-------- > > -- Original Sender Envelope Address: darrena@chem.leeds.ac.uk > > -- Original Sender From: Address: darrena@chemistry.leeds.ac.uk > > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > > Web: http://www.ccl.net/chemistry.html > > > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: gerald@ccl.net > -- Original Sender From: Address: gerald@ccl.net > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From elewars@alchemy.chem.utoronto.ca Tue Feb 10 17:11:15 1998 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id QAA09598; Tue, 10 Feb 1998 16:14:38 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id QAA06293 for chemistry@www.ccl.net; Tue, 10 Feb 1998 16:14:35 -0500 (EST) Date: Tue, 10 Feb 1998 16:14:35 -0500 (EST) From: "E. Lewars" Message-Id: <199802102114.QAA06293@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: BENCHMARKS: THANKS AND COMMENTS Tuesday 1998 Feb 10 Re SOME BENCHMARKS FOR G94 ON A PENTIUM PRO (mailed Feb 3) Hello, Thanks to all who responded to my email: Joseph Bausch, Gary Kedziora, Alexander Turner, Stephane.humbel, John Shelley and Daniel Tunega. Responding to questions and comments: 1) (JB) My PentiumPro is 200 MHz (128 MB RAM, 6 GB disk); ca. $3000 US. 2) GK says you can get a decent DEC Alpha for $5000--10000. My only info' on the DEC whose times I reported is what it says in the Gaussian book "Exploring Chemistry...": DEC AlphaServer, 5 GB disk, 250 RAM. 3) AT says the DEC is very fast cf. SGI for ab initio (but can be more trouble to set up). 4) S.h reported that job 2_05a took 4.3 min on an SGI O2 R10000 (150 MHz). 5) JS my machine: PentiumPro etc; [(1) above]; the DEC: I have only the info I reported. Maybe a 300 MHz Pentium II is faster than a PentiumPro. Only one way to find out. 6) DT and GK: websites for DEC and for specs: http://www.microway.com www.aspsys.com http://www.specbench.org http://performance.netlib.com Thanks again to all who wrote. E. Lewars elewars@trentu.ca =================== The info I posted a week ago: The designations 2_05a etc are those used in "Exploring Chemistry..." Short jobs (< 20 min on DEC) | Medium jobs (0.3 h--<2h on DEC) job Time, min | job Time, h DEC Pentium Ratio | DEC Pentium Ratio 2_05a 3.0 8.0 2.7 |2_06 0.74 1.5 2.0 2_05b 2.8 6.7 2.4 |3_05a 1.0 3.2 3.2 2_05c 2.8 3.5 1.3 |3_05b 1.8 4.4 2.4 4_04d 7.3 6.8 0.9 |e4_02d 0.34 0.57 1.7 4_04e 6.0 10.2 1.7 |4_05a 0.92 1.9 2.1 4_04f 17.6 47 2.7 |e5_02 0.71 1.4 2.0 e9_02 3.9 2.9 0.7 |5_02 1.2 2.5 2.1 5_03a 0.75 2.6 3.5 5_03b 1.2 3.7 3.1 e6_06 0.50 0.80 1.6 6_03x 0.90 2.5 2.8 6_04 0.58 1.5 2.6 6_06d 0.53 1.1 2.1 6_08 0.62 0.87 1.4 8_01c 0.70 1.3 1.9 Long jobs (>=2 h on DEC) job Time, h DEC Pentium Ratio 3_06b 11.2 36 3.2 4_05b 2.0 4.7 2.4 5_04 3.4 10.5 3.1 e6_04 3.6 9.2 2.6 6_03 5.8 18.0 3.1 6_07b 2.0 7.3 3.7 10_04c 4.5 11.7 2.6 10_05a 4.1 12.4 3.0 10_05b 4.0 12.5 3.1 ------------------------------------------------------- ============================================== From tokarskj@bms.com Tue Feb 10 21:11:10 1998 Received: from cliff.bms.com for tokarskj@bms.com by www.ccl.net (8.8.3/950822.1) id UAA11899; Tue, 10 Feb 1998 20:53:30 -0500 (EST) Received: from alchemy.bms.com by cliff.bms.com (PMDF V5.1-10 #22413) with SMTP id <01ITFFJBNFVM00VKDF@cliff.bms.com> for chemistry@www.ccl.net; Tue, 10 Feb 1998 20:52:15 EST Received: from alchemy by alchemy.bms.com via SMTP (950413.SGI.8.6.12/930416.SGI) for id UAA10199; Tue, 10 Feb 1998 20:53:30 -0500 Date: Tue, 10 Feb 1998 20:53:30 -0500 From: John Tokarski Subject: 3D-QSAR methodology Sender: tokarskj@bms.com To: chemistry@www.ccl.net Message-id: <34E1049A.41C6@alchemy.bms.com> MIME-version: 1.0 X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX64 6.4 IP30) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Hello fellow modellers, I woulk like to tap the CCL's wealth of knowledge with respect to recent advances in 3D-QSAR analysis methodologies. In that a 3D-QSAR analysis requires the consideration of alignment and conformation anything new in these areas is of important also. Also of interest is new types of descriptors as well as better ways of calculating old ones. Advances in statistical approaches in 3D-QSAR is of interest also. If there is enough interest I will post a summary. Thank you in advance. John Tokarski -- John S. Tokarski, Ph.D MS H23-07, Computer-Assisted Drug Design Department of Macromolecular Structure Bristol-Myers Squibb Pharmaceutical Research Institute P.O. Box 4000, Princeton, NJ 08543-4000 PH: (609)252-6154 FAX: (609)252-6030 EMAIL: Tokarskj@alchemy.bms.com For UPS or FedEx: Rt. 206 and Provinceline Road, Lawrenceville, NJ 08648