From owner-chemistry@ccl.net Tue Feb 13 05:12:57 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id FAA25480; Tue, 13 Feb 1996 05:08:52 -0500 Received: from chsun.eunet.ch for bgobbi@CHBS.CIBA.COM by bedrock.ccl.net (8.7.1/950822.1) id FAA11636; Tue, 13 Feb 1996 05:08:42 -0500 (EST) Received: from Ciba-GW.CHBS.CIBA.COM by chsun.eunet.ch (8.6.10/1.34) id LAA18952; Tue, 13 Feb 1996 11:08:34 +0100 Received: from Central.CHBS.CIBA.COM by Ciba-GW.CHBS.CIBA.COM (4.1/Ciba2.0-R1.0) id AA07545; Tue, 13 Feb 96 11:08:48 +0100 Received: from wirz.chbs (cgchb.uss.is.chbs) by Central.CHBS.CIBA.COM id AA20281; Tue, 13 Feb 1996 11:08:30 +0100 (5.65c8/Ciba2.0-C1.1) Received: from is7w_gobbial1 ([192.37.10.47]) by wirz.chbs id AA06748; Tue, 13 Feb 96 11:08:29 +0100 (4.1/SMI-3.2-CG-1.1A) Message-Id: <9602131008.AA06748@wirz.chbs> Comments: Authenticated sender is From: "Alberto Gobbi" To: Chemistry@ccl.net Date: Tue, 13 Feb 1996 11:08:36 +1 Subject: CCL: logP Reply-To: bGobbi@CHBS.CIBA.COM Priority: normal X-Mailer: Pegasus Mail for Windows (v2.22) We are using the clogp program from the pomona college which is solled by daylight Inc.: www.daylight.com Alberto From owner-chemistry@ccl.net Tue Feb 13 07:57:59 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id HAA26491; Tue, 13 Feb 1996 07:53:02 -0500 Received: from batata.fh.huji.ac.il for masha@mickey.fh.huji.ac.il by bedrock.ccl.net (8.7.1/950822.1) id HAA17293; Tue, 13 Feb 1996 07:52:44 -0500 (EST) Received: from mickey.fh.huji.ac.il by batata.fh.huji.ac.il via ESMTP (950215.SGI.8.6.10/930416.SGI.AUTO) for <@batata.fh.huji.ac.il:CHEMISTRY@ccl.net> id OAA00928; Tue, 13 Feb 1996 14:53:27 +0200 Received: by mickey.fh.huji.ac.il (950511.SGI.8.6.12.PATCH526/940406.SGI.AUTO) id OAA14118; Tue, 13 Feb 1996 14:53:18 +0200 Date: Tue, 13 Feb 1996 14:53:15 +0000 (IST) From: MASHA Niv Subject: HBr lowest potentials To: CHEMISTRY@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am a PhD student in prof. R.B.Gerber's group in Fritz HAber Center at Hebrew U.,Jerusalem. I am interested in running dynamics that involves also lowest potential curves of HBr molecule. In a paper published in Chem. Physics 118 (1987), p. 333-343, by D.A.CHAPMAN, K.BALASUBRAMANIAN and S.H.LIN curves for 12 lowest electronic states of HBr molecule were presented. I am looking for data points or functional fits of those potentials. I was unable to find e-mail addresses of any of the authors. So i would be very happy to get their e-mail addresses or any other related (to the authors or to the topic) information. Thank you very much, please DON't send the answer to the net (i am not connected) but to my e-mail: masha@batata.fh.huji.ac.il Masha Niv From J63C002%HUSZEG11.BITNET@phem3.acs.ohio-state.edu Tue Feb 13 08:42:59 1996 Received: from phem3 for J63C002%HUSZEG11.BITNET@phem3.acs.ohio-state.edu by www.ccl.net (8.6.10/950822.1) id IAA26885; Tue, 13 Feb 1996 08:39:35 -0500 From: Received: from HUSZEG11.BITNET (MAILER@HUSZEG11) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01I15PSDR57K8WW22Z@phem3.acs.ohio-state.edu>; Tue, 13 Feb 1996 08:39:28 EST Received: from HUSZEG11.BITNET (J63C002) by HUSZEG11.BITNET (Mailer R2.10 ptf000) with BSMTP id 9701; Tue, 13 Feb 96 14:39:36 +0100 Date: Tue, 13 Feb 1996 14:38:57 +0100 Subject: Convergence problems in MNDO program To: Computational Chemistry List Message-id: <01I15PSDR57M8WW22Z@phem3.acs.ohio-state.edu> X-Envelope-to: chemistry@www.ccl.net Content-transfer-encoding: 7BIT Dear netters, I am using an old version of the MNDO program (QCPE No. 353) as a part of another program (the so called DDRP) for determining reaction paths. The MNDO program calculates the total energy values in various points of the potential energy surface of the system investigated. Our main program is working without any problem, it is very stabil, but the part - which is basically a truncated MNDO program - is very slow and often doesn't converge at all. This version of MNDO contains an old iteration method of M. J. S. Dewar and P. K. Weiner (Comput. Chem. 2,31,1978). Well, I determined to implement an improved iteration algorithm developed especially for the MNDO program (P. Badziag and F. Solms, Comput. Chem. 12,233,1988). This iteration algorithm was very similar to that in the original program and I thought, it can be built without any problem into the subroutine BORDER of the MNDO and other parts of the program can remain unchanged. The algorithm of Badziag and Solms was said to be superiour over other known methods (for example those implemented into the program package AMPAC). Unfortunately the description of this algorithm was not enough to reproduce this iteration method. I have tried to carry out this iteration scheme based on the description with and without any change. The new version is working now but my results are not very promising. It follows what I want to ask: 1. Can somebody send me the improved subroutine BORDER - and perhaps also other parts of the program - which must be changed? 2. Can you give me E-mail address of Badziag or Solms? 3. Any other suggestion? Thanks in advance any suggestion. If there is interest in this problem and I receive any answer, I will write a summary. Best regards Dr. Gyula Domotor From owner-chemistry@ccl.net Tue Feb 13 08:58:00 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id IAA27002; Tue, 13 Feb 1996 08:48:49 -0500 Received: from uldns1.unil.ch for Frederic.Billois@ict.unil.ch by bedrock.ccl.net (8.7.1/950822.1) id IAA23091; Tue, 13 Feb 1996 08:48:45 -0500 (EST) Message-Id: <199602131348.IAA23091@bedrock.ccl.net> Received: from pcbep5004a.unil.ch (actually pcbep5004a) by uldns1 with SMTP (PP); Tue, 13 Feb 1996 14:48:28 +0100 X-Sender: fbillois@ulys.unil.ch X-Mailer: Windows Eudora Version 2.1.1 Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Date: Tue, 13 Feb 1996 14:48:18 +0100 To: chemistry@ccl.net From: Frederic Billois Subject: logP Created, developed and extensively tested at the Institute of=20 Medicinal Chemistry of the University of Lausanne , CLIP is a package with the following capabilities:=20 Computation and representation of the Molecular Lipophilicity Potential= (MLP)=20 on the solvent-accessible surface of molecules and macromolecules;=20 Calculation of n-octanol/water partition coefficients (log Poct) from the= MLP on the solvent-accessible surface;=20 Calculation of virtual log P values for individual conformers, and= exploration of the lipophilicity range accessible to a compound;=20 Computation and representation of the MLP in a given region of space around molecules and macromolecules;=20 Computation and incorporation of the MLP into Comparative Molecular Field=20 Analysis (CoMFA)=A9.=20 Information about CLIP, publications can be found on the web at: http://www.unil.ch/pharm/clip/ -------------------------------------------------------------- Frederic Billois Universite de Lausanne Section de Pharmacie. Institut de Chimie Therapeutique. CH-1015 Dorigny-Lausanne Suisse Tel :+41.21.692.45.24 =20 Fax :+41.21.692.45.05 Internet: Frederic.Billois@ict.unil.ch WWW : http://www.unil.ch/pharm/ict/docs/ict.html ---------------------------------------------------------------- From Schiffer@MSMWIA.hoechst.hoechst-ag.d400.de Tue Feb 13 10:28:01 1996 Received: from ixgate02.dfnrelay.d400.de for Schiffer@MSMWIA.hoechst.hoechst-ag.d400.de by www.ccl.net (8.6.10/950822.1) id KAA28302; Tue, 13 Feb 1996 10:27:30 -0500 X400-Received: by mta d400relay in /PRMD=dfnrelay/ADMD=d400/C=de/; Relayed; Tue, 13 Feb 1996 16:24:42 +0100 X400-Received: by /PRMD=HOECHST-AG/ADMD=D400/C=DE/; converted (ia5-text,undefined); Relayed; Tue, 13 Feb 1996 16:22:28 +0100 X400-Received: by /PRMD=HOECHST-AG-MSM/ADMD=DBP/C=DE/; Relayed; Tue, 13 Feb 1996 13:21:10 +0100 Date: Tue, 13 Feb 1996 13:21:10 +0100 X400-Originator: Schiffer@MSMWIA.hoechst.hoechst-ag.d400.de X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=hoechst-ag-msm/ADMD=dbp/C=de/;960213122110] Original-Encoded-Information-Types: teletex X400-Content-Type: P2-1984 (2) Content-Identifier: CSI NC V3.0 From: "Schiffer, Heinz, Dr., WIA / SC" Message-ID: <001C553E.MAI*/S=Schiffer/OU=MSMWIA/O=HOECHST/PRMD=hoechst-ag/ADMD=dbp/C=de/@MHS> To: CCL (Receipt Notification Requested) (Non Receipt Notification Requested) Subject: Contouring code/algorithm Jeff Gosper and Conor McMenamin asked for information about programs to produce contour plots of 3-D data points. In my view the easiest and probably fastest algorithm is the one of Brickmann et al. : Wolfgang Heiden, Michael Schlenkrich and Jurgen Brickmann Triangulation algorithms for the representation of molecular surface properties J. Comp. Aided Mol. Design 4 (1990) 255-269 W. Heiden, T. Goetze, and J. Brickmann Fast Generation of Molecular Surfaces from 3D Data Fields with an Enhanced "Marching Cube" Algorithm J. Comp. Chem. 14 (1993) 246-250 ---------------------------------------------------------------------------- ----------------------------------------- Dr. Heinz Schiffer Phone : ++49-69-305-2330 Hoechst AG Fax : ++49-69-305-81162 Scientific Computing Email : schiffer at 65926 Frankfurt am Main - wia.hoechst-ag.d400.de - msmwia.hoechst.hoechst-ag.d400.de ---------------------------------------------------------------------------- ----------------------------------------- From ALHINAI@FRCU.EUN.EG Tue Feb 13 10:43:00 1996 Received: from FRCU.EUN.EG for ALHINAI@FRCU.EUN.EG by www.ccl.net (8.6.10/950822.1) id KAA28313; Tue, 13 Feb 1996 10:28:07 -0500 From: Received: from FRCU.EUN.EG by FRCU.EUN.EG (PMDF V4.2-11 #3805) id <01I167RUEPC4000179@FRCU.EUN.EG>; Tue, 13 Feb 1996 17:27:24 O Date: Tue, 13 Feb 1996 17:27:24 +0000 (O) Subject: SUM: DeFT under linux To: chemistry@www.ccl.net Message-id: <01I167RUEPC6000179@FRCU.EUN.EG> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hello everybody A few weeks ago i sent the following message : >Dear netters > >I am trying to compile the density functional code DeFT on a pentium 75 >running linux 1.2.1 using f2c and gcc. > >The compilation of the code was quite simple and reletively fast, the only >warning reported was : >" local variable ...... never used " which i believe is harmless . > >The linking of the object however gave an error : >" main.o : could not read symbols : Bad value " > >I do not know what to do with it, i would appreciate any help. > >Ashraf Talib Al-Hinai > I recived several comments on the issue. I was advised to use the f77 script rather than the two steps , f2c and gcc. This did not solve the problem but it did make the work much easier. The other comments were about the sizes of the arrays in the main.f . A small reduction in the sizes of the arrays made the linking work. I would like to thank all the ccl'ers who responded to my message. Ashraf From owner-chemistry@ccl.net Tue Feb 13 13:28:03 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id NAA00401; Tue, 13 Feb 1996 13:26:04 -0500 Received: from gusun for choic@gusun.acc.georgetown.edu by bedrock.ccl.net (8.7.1/950822.1) id NAA07493; Tue, 13 Feb 1996 13:26:02 -0500 (EST) Received: (choic@localhost) by gusun (SMI-8.6/8.6.4) id NAA11192; Tue, 13 Feb 1996 13:25:22 -0500 Date: Tue, 13 Feb 1996 13:25:21 -0500 (EST) From: Cheol Choi To: chemistry@ccl.net Subject: DFT and Raman Activity? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, Recently, I've tried to do vibrational calculation with G94 using DFT methods. It nicely gave me the vibrational frequencies and IR intensities but not vibrational Raman activities. I simply used FREQ keyword in the input file. Couldn't G94 calculate Raman activities with DFT methods? Thanks, Cheol Ho Choi Georgetown Univ. From haney@netcom.com Mon Feb 12 15:09:33 1996 Received: from netcom14.netcom.com for haney@netcom.com by www.ccl.net (8.6.10/950822.1) id PAA18557; Mon, 12 Feb 1996 15:09:32 -0500 Received: by netcom14.netcom.com (8.6.12/Netcom) id MAA18053; Mon, 12 Feb 1996 12:08:09 -0800 From: haney@netcom.com (Dr. David N. Haney) Message-Id: <199602122008.MAA18053@netcom14.netcom.com> Subject: Re: CCL:logP To: jaouad@goliat.ugr.es (Jauoad El Bahraoui) Date: Mon, 12 Feb 1996 12:08:09 -0800 (PST) Cc: chemistry@www.ccl.net In-Reply-To: from "Jauoad El Bahraoui" at Feb 12, 96 02:55:44 pm jaouad@goliat.ugr.es writes: > Please tell me about programs does permit the calculation of the > partition coefficients octanol-water (logP) ? > regards. HINT is a third-party program that works in the molecular modeling environment of Biosym's InsightII, Tripos's Sybyl or Chemical Design's Chem-X. HINT calculates logP using a library for proteins, nucleic acids and certain other materials. HINT can calculate logP of any molcule in its "calculate mode" using rules based on the chemical fragment types, and a translation of the fragment method of Leo and Abraham. In addition to calculating logP, HINT calculates (1) 3-D visual maps that aid in the 3-D understanding of hydrophobicity for small and large molecules, and (2) molecular interaction constants (including hydrophobic, electrostatic and VDW) useful for studying binding of drugs to proteins or proteins to proteins. Information about HINT, publications and seminars can be found on the web at: http://www.i2020.net/edusoft/hint/hint.html -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * * http://www.i2020.net/edusoft/haney/haney.html * ************** Email - haney@netcom.com *************** From owner-chemistry@ccl.net Thu Feb 8 10:32:00 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA05573; Thu, 8 Feb 1996 10:31:59 -0500 Received: from uscmail.usc.es for qftramos@usc.es by bedrock.ccl.net (8.7.1/950822.1) id KAA13408; Thu, 8 Feb 1996 10:31:50 -0500 (EST) Received: by uscmail.usc.es (5.67b/1.34) id AA13336; Thu, 8 Feb 1996 16:33:06 +0100 Date: Thu, 8 Feb 1996 16:33:06 +0100 (MET) From: Antonio Fernandez Ramos To: chemistry@ccl.net Subject: Fortran 77 to PowerMac? Dear netters: Anybody knows if is available a free f77 for PowerMac? Thanks in advice. From vuckovic@hyper.com Mon Feb 12 10:15:31 1996 Received: from www.hyper.com for vuckovic@hyper.com by www.ccl.net (8.6.10/950822.1) id KAA14997; Mon, 12 Feb 1996 10:15:23 -0500 Received: (from vuckovic@localhost) by www.hyper.com (8.6.12/8.6.12) id KAA20698 for chemistry@www.ccl.net; Mon, 12 Feb 1996 10:25:21 -0500 From: Dragan Vuckovic Message-Id: <199602121525.KAA20698@www.hyper.com> Subject: HyperChem Workshop-Germany To: chemistry@www.ccl.net Date: Mon, 12 Feb 1996 10:25:20 -0500 (EST) Hypercube, Inc. in association with Science direct presents an Introductory HyperChem Workshop on Computational Chemistry April 24 -26, 1996 , University of Paderborn Paderborn, Germany For more information contact me at vuckovic@hyper.com, or Dr. Heinz Hofmann ,Science direct Sandrangen 3, D-91257 Pegnitz-Buchau, Germany e-mail: 100411.2306@compuserve.com Tel. +49-(0)9241- 91216 Fax: +49-(0)9241 - 91217 For a complete description of the workshop and the registration form, check Hypercube's home page at http://www/hyper.com or check conference listings: gopher://www.ccl.net:73/1m/info/conferences ftp://www.ccl.net/pub/chemistry/info/conferences ___________________________________________________________________ Dr. Dragan Lj. Vuckovic phone: (519) 725-4040 International Marketing Manager fax: (519) 725-5193 Hypercube, Inc. e-mail: vuckovic@hyper.com 419 Phillip Street URL: http://www.hyper.com Waterloo, Ontario Canada, N2L 3X2