From chemistry-request@www.ccl.net Fri Mar 5 07:48:07 1999 Received: from srepo200.univ-mrs.fr (srepo200.univ-mrs.fr [194.57.196.56]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA09214 Fri, 5 Mar 1999 07:48:06 -0500 (EST) Received: from srepo200.univ-mrs.fr (localhost [127.0.0.1]) by srepo200.univ-mrs.fr (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id NAA08750 for ; Fri, 5 Mar 1999 13:50:16 +0100 Sender: marsal@srepo200.univ-mrs.fr Message-ID: <36DFD307.167E@srepo200.univ-mrs.fr> Date: Fri, 05 Mar 1999 13:50:15 +0100 From: MARSAL Philippe X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX64 6.4 IP27) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: CCL:potential surfaces Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit -Dear ccls I would like to understand why when working in cartesian coordinates and diagonalizing the hessian matrix on a potential surface at a point witch is not a stationnary point I find only 3 zero eigenvalues (what about the rotations). Thanks- _______________________________________________________________________ MARSAL Philippe "Laboratoire de Chimie Theorique" SREP CNRS - UMR 6517 "Chimie, Biologie et Radicaux libres" Universite de Provence Faculte de Saint-Jerome Avenue Escadrille Normandie - Niemen 13397 MARSEILLE Cedex 20 - France Phone # : (ext) + 04-91-28-84-14 FAX # : (ext) + 04-91-98-85-12 ________________________________________________________________________ From chemistry-request@www.ccl.net Fri Mar 5 08:27:02 1999 Received: from bulldog.unca.edu (root@bulldog.unca.edu [152.18.64.9]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA09476 Fri, 5 Mar 1999 08:27:01 -0500 (EST) Received: from jmartell.facstaff.unca.edu (dhcp1-182.facstaff.unca.edu [152.18.20.181]) by bulldog.unca.edu (8.9.1a/8.9.1) with SMTP id IAA05043; Fri, 5 Mar 1999 08:27:02 -0500 (EST) Message-Id: <199903051327.IAA05043@bulldog.unca.edu> Comments: Authenticated sender is From: "Jaime Martell" Organization: UNC Asheville To: CCL , Patrick Bultinck Date: Fri, 5 Mar 1999 08:28:23 -500 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:QC journals 'in trouble' Reply-to: jmartell@bulldog.unca.edu Priority: normal In-reply-to: X-mailer: Pegasus Mail for Win32 (v2.53/R1) Content-Transfer-Encoding: 7BIT > > The trouble is mainly with journals like 'ours' e.g. J. Mol. Struct. > (THEOCHEM). A lot of the quantum chemistry specific journals do not > have high impact factors. If you consider the way these are > calculated, that's not suprising, and does not indicate low quality > of the journals. Except maybe for THEOCHEM. I've given up on them, but last time I checked there were an awful lot of low quality papers there. > now that were are in the branch 'Chemistry, physical'. To get in the > top ten (percent even), we need to 'beat' things like 'Advances in > Physical chemistry', and a lot of review journals. That is > practically impossible, even very well-known journals like J. Am. > Chem. Soc. have trouble 'beating' things like 'Chemical Reviews'. I have a hard time believing that a publication in JACS will not score you enough points. Regarding physical chemistry journals, why not publish in J. Phys. Chem.? In the ACS series, it is second in reputation only to JACS, and surely must have a high impact factor. Between J. Phys. Chem. and J. Chem. Phys. you will find most of the highest quality theoretical chemistry papers. > > Another option might be that Ghent University does no longer pursue > this. But we are leading in bibliometrics, and a LOT of things that > started in Ghent have come spread all over the world. So, it seems > to me, we might better not be taking chances. Or fine tune the policy to be more realistic. Good luck. Jaime Martell, Ph.D. Research Assistant Professor and Camille & Henry Dreyfus Fellow Department of Chemistry University of North Carolina at Asheville Asheville, NC 28805-8511 Phone: (828) 232-5170 Fax: (828) 232-5179 E-mail: WWW: "Ignorance is its own punishment" From chemistry-request@www.ccl.net Fri Mar 5 08:38:51 1999 Received: from ntsvexch.albmolecular.com (mail.albmolecular.com [205.247.153.6]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA09918 Fri, 5 Mar 1999 08:38:50 -0500 (EST) Received: by Ntsvexch with Internet Mail Service (5.0.1457.3) id <1WP5GYWY>; Fri, 5 Mar 1999 08:41:33 -0500 Message-ID: <80F79FF3ECD6D1119D9000805FCC602A309C18@Ntsvexch> From: "Andruski, Stephen W." To: "'CCL'" Subject: MIF format Date: Fri, 5 Mar 1999 08:41:32 -0500 X-Priority: 3 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1457.3) Content-Type: text/plain Does anyone out there know the status of the MIF (Molecular Information File) format. Searching the CCL archives, the most recent message on this topic I found was ~1993. I have searched the Internet and cannot find any information out there, though a number of years ago the format specification and preliminary data dictionary were available (I have copies, but no longer remember whose Web site they were on). This file format seems like such a good idea for the archiving and transmittal of molecular data (MO calculations, MM calculations, multiple conformations, X-ray data, etc.) in a single file. Much like the CIF format now widely used for crystallographic data, the content is extensible using data dictionaries and could accommodate a large amount of different data for different uses. My gut feeling is that no group or Society has taken the lead in promoting this file format and interest has therefor waned. Perhaps the ACS Division of Computers in Chemistry would be an appropriate group to do this. I hope that there is some interest out there. I will gladly summarize the responses I get. Thank you. Steve Andruski > *********************************** > Dr. Stephen W. Andruski > Senior Research Chemist II > Albany Molecular Research, Inc. > 21 Corporate Circle > Albany, New York 12203 USA > Tel. (518) 464-0279, Ext. 3303 > Fax (518) 464-0289 > http://www.albmolecular.com > E-mail: stephena@albmolecular.com > ************************************ > > From chemistry-request@www.ccl.net Fri Mar 5 08:53:30 1999 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id IAA10441 Fri, 5 Mar 1999 08:53:29 -0500 (EST) Message-Id: <199903051353.IAA10441@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Fri, 05 Mar 1999 14:41:30 +0100 Comments: Authenticated sender is From: "Tamas Gunda" To: "Victor E. Kuz'min" Date: Fri, 5 Mar 1999 14:41:21 +1 MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7BIT Subject: Re: CCL:CCL:Drawings--->Stuctural file CC: chemistry@www.ccl.net Priority: normal X-mailer: Pegasus Mail for Windows (v2.42a) > > > Dear Colleagues, > Whether there is a software for conversion of a graphics image of > molecular structure ( for example: *.gif, *.jpg, .. etc) in files such > as *.mol, *.hin, *.pdb, ..? This is a peculiar kind of OCR for the > structural formulas. It will enable for scanned drawings to get the > structural file. Is it possible? I shall be grateful for any guidelines > or tips. > > With best regards, > VEK As far as I remember, there is a program called Kekule somewhere out there, which was designed to convert scanned structural images to molfiles Hope this helps Tamas ************************************************************************ Dr Tamas E. Gunda phone: (+36-52) 316666-2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 http://www.klte.hu/~gundat H-4010 Debrecen Hungary ************************************************************************ From chemistry-request@www.ccl.net Fri Mar 5 09:01:51 1999 Received: from mail.chemie.fu-berlin.de (root@mail.chemie.fu-berlin.de [160.45.24.23]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA11540 Fri, 5 Mar 1999 09:01:24 -0500 (EST) Received: from bragg.chemie.fu-berlin.de([160.45.24.11]) (1436 bytes) by mail.chemie.fu-berlin.de via sendmail with P:smtp/R:bind_hosts/T:inet_zone_bind_smtp (sender: ) id for ; Fri, 5 Mar 1999 15:01:21 +0100 (CET) (Smail-3.2.0.101 1997-Dec-17 #18 built 1999-Feb-17) Date: Fri, 5 Mar 1999 15:01:21 +0100 (MET) From: Roland Meier To: chemistry@www.ccl.net Subject: Conform analysis of n-membered rings Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I got a mail from Peter Comba, and this mail contained a couple of back and forth mails on conf analysis of rings and if there people that know more about appropriate software. I am using already quite a while D Cremers PUCKRING with good sucess for my own structures. The phi values that come out here need special care and one needs to read Cremers papers in Isr J Chem to get a feeling how to select a useful numbereing scheme for the ring atoms. The PLATON does it too and this is freeware as far as I know In Platon, however, the phi values for 5mem rings , are garbadge for my purposes but the Qs that come out are okay. A straighforward tool for published structures is the CSD combination of QUEST and VISTA . In this, one should know someting about the numbering scheme. Then, nice Q vs phi diagrams can be done for any collection of 5mem rings. see also Dunitz/Buergi "Structure and Correlation" Pt I + II VCH (1995 ??) Dr Roland Meier From chemistry-request@www.ccl.net Fri Mar 5 11:03:23 1999 Received: from mail.chemie.fu-berlin.de (root@mail.chemie.fu-berlin.de [160.45.24.23]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA17815 Fri, 5 Mar 1999 11:03:22 -0500 (EST) Received: from Dirac.Chemie.FU-Berlin.DE(dirac.chemie.fu-berlin.de[160.45.24.166]) (2142 bytes) by mail.chemie.fu-berlin.de via sendmail with P:smtp/R:bind_hosts/T:inet_zone_bind_smtp (sender: ) id for ; Fri, 5 Mar 1999 17:03:19 +0100 (CET) (Smail-3.2.0.101 1997-Dec-17 #18 built 1999-Feb-17) Received: by Dirac.Chemie.FU-Berlin.DE (Smail3.2.0.98) id ; Fri, 5 Mar 1999 17:03:08 +0100 (MET) Message-Id: From: melchers@chemie.fu-berlin.de (Bernd Melchers) Subject: CCL:Summary: AMD-K6/linux for G98 To: chemistry@www.ccl.net Date: Fri, 5 Mar 1999 17:03:08 +0100 (MET) X-Mailer: ELM [version 2.4 PL24 ME8d] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit 'Jerry C.C. Chan wrote:' > > > K6 is slower than PentiumII (with the same clock). Especially on floating > point operations. This is not OS dependent, so I wouldn't expect better some words again to this theme: there are benchmarks comparing the brand new AMD-K6-III (*not* the AMD-K6-2-3D!) against the Pentium III which show that even the AMD-K6-III@400MHz outperforms the Pentium-III@500MHz (for a special application benchmark!): http://www.ga-source.com/cgi-bin/gaimage.cgi?images/amd/Slide6.JPG it is not only the floating point unit, which makes the Pentium-II and the Celeron fast, it is also the builtin second level cache. The AMD-K6-III now has also an on dye second level cache. The floating point unit itself is not faster than the one of the AMD-K6-II. Some additional points: Celeron CPUs are using 66 MHz Busspeed, compared to 100 MHz for Pentium II and K6. Celeron and K6 CPUs are not able to do multiprocessing. Compilers usually optimize the code for Pentium or Pentium-II CPUs, but there is a compiler which optimize also for the K6: pgcc, have a look at ftp://ftp.goof.com/pub/pcg/source/ But Gaussian98 and CHARMM is not able to be compiled by the g77 part of pgcc or egcs . Ciao Bernd Melchers -- Bernd Melchers | melchers@FU-Berlin.DE Freie Universitaet Berlin | "We don't write software, we compose it." AG Macromolecular Modelling - Prof. Dr. E.W. Knapp for more information see http://userpage.chemie.fu-berlin.de/~melchers/ From chemistry-request@www.ccl.net Fri Mar 5 11:30:11 1999 Received: from servidor.unam.mx (servidor.unam.mx [132.248.10.5]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA18626 Fri, 5 Mar 1999 11:30:10 -0500 (EST) Received: from localhost (apisan@localhost) by servidor.unam.mx (8.8.8/8.8.8) with SMTP id KAA26303; Fri, 5 Mar 1999 10:27:45 -0600 (CST) Date: Fri, 5 Mar 1999 10:27:44 -0600 (CST) From: Pisanty Baruch Alejandro-FQ To: Jaime Martell cc: CCL , Patrick Bultinck Subject: Re: CCL:QC journals 'in trouble' In-Reply-To: <199903051327.IAA05043@bulldog.unca.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Patrick and all, let's be brief since this is not a mainstream CCL topic. Patrick's original mail on impact factors shows the fundamental illness of bibliometric research for all its claims of objectivity. The fact is that the impact factors are skewed in favor of secondary sources which aggregate the results of a number of original papers. That is why even JACS and other major, highly respected and highly quoted journals don't make it to the top, whereas all forms of reviews do. This is not meant to disparage reviews! - just to add perspective, recognizing that some of the very major journals are also in the top. Specialized knowledge gets lost in this turmoil. Whether it be theoretical chemistry or tannery, specialized journals just don't cut it for bibliometers. Yet bibliometry is most surely here to stay and, as Patrick makes it clear, is a well established church with dogmas and rituals which will not move. So my way of thinking is along Jaime Martell's last line: tune policy, personalize assessments of researchers (we ARE persons!). Alx . . . . . . . . . . . . . . . . . . . . . . . . . . Dr. Alejandro Pisanty, Director General de Servicios de Computo Academico (Director, Computing Academic Services) Universidad Nacional Autonoma de Mexico (UNAM) Ciudad Universitaria, 04510 Mexico City DF MEXICO Tel. (+52-5) 622-8541, 622-8542; Fax 622-8540 . . . . . . . . . . . . . . . . . . . . . . . . . . From chemistry-request@www.ccl.net Fri Mar 5 11:31:53 1999 Received: from giasbma.vsnl.net.in (giasbma.vsnl.net.in [202.54.4.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA18696 Fri, 5 Mar 1999 11:31:51 -0500 (EST) Received: from giasbmc.vsnl.net.in (giasbmc [202.54.4.6]) by giasbma.vsnl.net.in (8.8.8/8.8.8) with SMTP id WAA18002 for ; Fri, 5 Mar 1999 22:10:29 +0500 (IST) Date: Fri, 5 Mar 1999 21:43:51 -0500 (GMT) From: Amit Galande To: CHEMISTRY@www.ccl.net Subject: topological indices Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Can any one provide me with very basic references regarding topological indices,topography like what these terms exactly mean >from theoretical point of view .(and not from the software point of view ) thanking you in anticipation amit galande From chemistry-request@www.ccl.net Fri Mar 5 13:56:26 1999 Received: from dirac.cnrs-orleans.fr (dirac.cnrs-orleans.fr [163.9.6.67]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA22871 Fri, 5 Mar 1999 13:56:25 -0500 (EST) Received: (from hinsen@localhost) by dirac.cnrs-orleans.fr (AIX4.3/UCB 8.8.8/8.7) id TAA19246; Fri, 5 Mar 1999 19:53:39 +0100 Date: Fri, 5 Mar 1999 19:53:39 +0100 Message-Id: <199903051853.TAA19246@dirac.cnrs-orleans.fr> X-Authentication-Warning: dirac.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: marsal@srepo200.univ-mrs.fr CC: chemistry@www.ccl.net In-reply-to: <36DFD307.167E@srepo200.univ-mrs.fr> (message from MARSAL Philippe on Fri, 05 Mar 1999 13:50:15 +0100) Subject: Re: CCL:potential surfaces References: <36DFD307.167E@srepo200.univ-mrs.fr> > I would like to understand why when working in cartesian coordinates and > diagonalizing the hessian matrix on a potential surface at a point witch > is not a stationnary point I find only 3 zero eigenvalues (what about > the rotations). Not being at a stationary point means that there is a non-zero energy gradient. So when you rotate the whole system, the energy gradient follows the rotation as well. The difference between the rotated and the original gradient is thus not zero, meaning that this motion does not correspond to a zero eigenvalue. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@www.ccl.net Fri Mar 5 19:11:47 1999 Received: from smtp.263.net ([202.96.44.19]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id TAA27251 Fri, 5 Mar 1999 19:11:45 -0500 (EST) Message-Id: <199903060011.TAA27251@www.ccl.net> Received: (fmail 23849 invoked from network); 6 Mar 1999 08:11:35 -0000 Received: from unknown (HELO luoxch) (166.111.10.117) by 202.96.44.19 with SMTP; 6 Mar 1999 08:11:35 -0000 Date: Sat, 6 Mar 1999 8:12:12 +0800 From: lvtunj Reply-To: lvtun@263.net To: ccl discution Subject: SPL problem X-mailer: FoxMail 2.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi everyone: Is there anyone has written SPL for sybyl's DIANA block so that it can treat with sets of *.upl and *.lol file automaticlly?I have 200 pairs of *.upl file and *.lol file to treat, but my spl donot work,can anyone read code I list below and give me some advice? SET CGQ_TIMEOUT 0 DIANA READ SEQUENCE hu.seq m1 modify molecule name m1 "hu" for j in %range(1 45) if %lt($j 10) setvar lolfile %cat("hupat0" $j ".lol") setvar uplfile %cat("hupat0" $j ".upl") setvar jobname %cat("Hb0" $j) setvar pdbname %cat("Hb0" $j ".pdb") endif if %gteq($j 10) setvar lolfile %cat("hupat" $j ".lol") setvar uplfile %cat("hupat" $j ".upl") setvar jobname %cat("Hb" $j) setvar pdbname %cat("Hb0" $j ".pdb") endif DIANA SUBMIT UPPER_DISTANCE_LIMITS $uplfile \ LOWER_DISTANCE_LIMITS $lolfile \ COORDINATE_OUTPUT_FILES $pdbname \ NUM_STRUCTS 2 255555 \ MINIMIZATION_PARAMS * 8.0 0.0 4000 800 1000 YES \ JOBNAME $jobname \ DONE endfor sincerely yours LVTUN Dept.Biosci&Biotech Tsinghua University Beijing,10084 P.R.China LVTUN@263.NET From chemistry-request@www.ccl.net Fri Mar 5 19:41:15 1999 Received: from ex1.ncsa.uiuc.edu (ex1.ncsa.uiuc.edu [141.142.3.16]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA27384 Fri, 5 Mar 1999 19:41:14 -0500 (EST) Received: from mx1.ncsa.uiuc.edu (mx1.ncsa.uiuc.edu [141.142.3.15]) by ex1.ncsa.uiuc.edu (8.9.3/8.9.3) with ESMTP id SAA28592 for ; Fri, 5 Mar 1999 18:41:17 -0600 (CST) Received: from mckelvey (mckelvey.ncsa.uiuc.edu [141.142.41.30]) by mx1.ncsa.uiuc.edu (8.9.2/8.9.2) with SMTP id SAA19680 for ; Fri, 5 Mar 1999 18:41:16 -0600 (CST) Message-Id: <3.0.5.32.19990305184115.02323a40@pop.ncsa.uiuc.edu> X-Sender: mckelvey@pop.ncsa.uiuc.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Fri, 05 Mar 1999 18:41:15 -0600 To: chemistry@www.ccl.net From: John McKelvey Subject: GA-QPLS Codes Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-md5sum: 65fe580cf845ed035c4e57ad02a987cf X-md5sum-Origin: mx1.ncsa.uiuc.edu My previous query to CCL on available PLS codes was quite good! Many thanks! Could I try another? I recently ran a cross a paper on GA-Quadratic PLS, GA-QPLS, that appeared to be quite robust. Is there a possible source for such a code available? Thanks! John McKelvey NCSA