From chemistry-request@server.ccl.net Mon Jul 17 22:12:26 2000 Received: from ms.dicp.ac.cn ([159.226.159.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA21186 for ; Mon, 17 Jul 2000 22:12:20 -0400 Received: from lgh ([159.226.159.123]) by ms.dicp.ac.cn (8.8.5/SCO5) with SMTP id KAA15755 for ; Tue, 18 Jul 2000 10:07:56 +0800 (CST) Message-Id: <200007180207.KAA15755@ms.dicp.ac.cn> Date: Tue, 18 Jul 2000 10:17:4 -0800 From: Li Guo Hui To: "CHEMISTRY@ccl.net" Subject: question about compiling FORTRAN codes under LINUX and SGI Organization: Dalian Institute of Chemical Physics X-mailer: FoxMail 3.0 beta 1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear Netters: I had compiled FORTRAN codes under linux with g77 and SGI with f77, but it gave me the following warning under linux: x.f: In subroutine 'x': x.f:126: warning: call b(s, ij, it, bb) 1 x.f: b1: call b(o1, o2, it, bb) 2 Argument #1 of 'B' is one type at(2) but is some other type at (1) [info -f g77 M GLOBALS] But under SGI with f77, it is compiled without any warning and error. Could you tell me the reason? I hope someone can help me do it correctly. thank you very much!!! From chemistry-request@server.ccl.net Mon Jul 17 22:17:59 2000 Received: from ms.dicp.ac.cn ([159.226.159.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA21234 for ; Mon, 17 Jul 2000 22:17:51 -0400 Received: from lgh ([159.226.159.123]) by ms.dicp.ac.cn (8.8.5/SCO5) with SMTP id KAA15816 for ; Tue, 18 Jul 2000 10:14:08 +0800 (CST) Message-Id: <200007180214.KAA15816@ms.dicp.ac.cn> Date: Tue, 18 Jul 2000 10:23:17 -0800 From: Li Guo Hui To: "CHEMISTRY@ccl.net" Subject: Can f77 or g77 program from comercial company make it correctly? Organization: Dalian Institute of Chemical Physics X-mailer: FoxMail 3.0 beta 1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear Netters: another question about f77 or g77 under linux from chenhua@ms.dicp.ac.cn: Are there comercial programs for f77 or g77 under linux which can make my question correctly? if yes, which is the best performance/price? its webaddress? thank you very much!!! From chemistry-request@server.ccl.net Tue Jul 18 02:23:09 2000 Received: from hydra.chem.rug.nl (hydra.chem.rug.nl [129.125.35.229]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA22155 for ; Tue, 18 Jul 2000 02:23:08 -0400 Received: from [129.125.7.13] (theochem1.chem.rug.nl [129.125.7.13]) by hydra.chem.rug.nl (AIX4.2/UCB 8.7/8.7) with ESMTP id IAA27786 for ; Tue, 18 Jul 2000 08:23:01 +0200 (MET DST) Mime-Version: 1.0 X-Sender: swart@hydra.chem.rug.nl Message-Id: In-Reply-To: <200007180207.KAA15755@ms.dicp.ac.cn> References: <200007180207.KAA15755@ms.dicp.ac.cn> Date: Tue, 18 Jul 2000 08:25:30 +0200 To: CHEMISTRY@ccl.net From: Marcel Swart Subject: Re: CCL:question about compiling FORTRAN codes under LINUX and SGI Content-Type: text/plain; charset="us-ascii" ; format="flowed" >Dear Netters: >I had compiled FORTRAN codes under linux with g77 and SGI with f77, >but it gave me the following warning >under linux: > >x.f: In subroutine 'x': >x.f:126: warning: > call b(s, ij, it, bb) > 1 >x.f: b1: call b(o1, o2, it, bb) > 2 >Argument #1 of 'B' is one type at(2) but is some other type at (1) >[info -f g77 M GLOBALS] > >But under SGI with f77, it is compiled without any warning and error. >Could you tell me the reason? >I hope someone can help me do it correctly. >thank you very much!!! This means probably that you have not declared either s or o1 explicitly, and f77 at SGI takes the default for this (real), while this default does not seem to be present with g77, or is different from the explicit declaration of either s or o1. -- ------------------------------------------------ drs. Marcel Swart Theoretical Chemistry (MSC) Molecular Dynamics (GBB) Rijksuniversiteit Groningen Chemistry Department Nijenborgh 4 9747 AG Groningen The Netherlands tel : +31 - (0)50 - 3634377 fax : +31 - (0)50 - 3634441 E-mail : m.swart@chem.rug.nl WWW: http://theochem.chem.rug.nl/~marcel/ ------------------------------------------------ From chemistry-request@server.ccl.net Tue Jul 18 09:08:30 2000 Received: from mail-f.bcc.ac.uk (mail-f.bcc.ac.uk [128.40.23.81]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA24751 for ; Tue, 18 Jul 2000 09:08:24 -0400 Received: from ri.ac.uk (actually host davy.ri.ac.uk) by mail-f.bcc.ac.uk with SMTP (XT-PP); Tue, 18 Jul 2000 14:08:04 +0100 Received: from tyndall.ri.ac.uk by ri.ac.uk (5.x/SMI-SVR4) id AA05647; Tue, 18 Jul 2000 14:06:51 +0100 Received: from localhost by tyndall.ri.ac.uk (980427.SGI.8.8.8) id OAA82965; Tue, 18 Jul 2000 14:08:02 +0100 (BST) Date: Tue, 18 Jul 2000 14:08:01 +0100 From: "DFT on Complex Oxides; Workshop/School at the DFRL, 2001" X-Sender: dft@tyndall To: chemistry@ccl.net Subject: DFT school and workshop: Study of Complex Oxides Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, we would like to attract your attention to the following event that will take place at the Royal Institution of Great Britain, in central London (UK) in May 2001. "Density Functional Theory for the Study of Complex Oxides" a combined school and workshop. A preliminary programme is now ready and is available on line at the following address: http://www.ri.ac.uk/DFT2001 If you would like to receive further information, you can pre-register on line, or contact the organisers at dft@ri.ac.uk We look forward to hearing from you. Yours sincerely, the local organising committee =============================================================================== Density Functional Theory for the Study of Complex Oxides The Royal Institution of Great Britain, London, 14-18 May 2001 Organising Committee: M. Alfredsson, F. Cora' and A.A. Sokol (Davy-Faraday Research Laboratory, The Royal Institution of Great Britain, 21 Albemarle Street, London W1X 4BS - UK) J.D. Gale (Dept. of Chemistry, Imperial College, Exhibition Road, London SW7 2AY - UK) N.M. Harrison (CCLRC - Daresbury Laboratory, Daresbury, Warrington, WA4 4AD - UK) e-mail: dft@ri.ac.uk Tel. + 44 - 207 - 4092992 Fax. + 44 - 207 - 6293569 Conference web site: http://www.ri.ac.uk/DFT2001 =============================================================================== From chemistry-request@server.ccl.net Tue Jul 18 09:07:20 2000 Received: from max.mpi-muelheim.mpg.de (moritz.mpi-muelheim.mpg.de [192.108.70.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA24739 for ; Tue, 18 Jul 2000 09:07:15 -0400 Received: from localhost (terstege@localhost) by max.mpi-muelheim.mpg.de (8.10.0.Beta12/8.10.0.Beta12) with ESMTP id e6ID6wH26510 for ; Tue, 18 Jul 2000 15:06:58 +0200 (MET DST) Date: Tue, 18 Jul 2000 15:06:58 +0200 (MET DST) From: Frank Terstegen To: CHEMISTRY@ccl.net Subject: G98:Problems with MASSAGE and PSEUDOPOTENTIALS Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="0-353378643-963925618=:16043" This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. --0-353378643-963925618=:16043 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Gaussian users, we have problems using the basis with GEN and pseudopotentials with PSEUDO=CARDS along with MASSAGE. GEN with PSEUDO=CARDS works fine this is also true for GEN with MASSAGE but not if all three are together. Does anyone hit the same problem and know to handle it. The input file is attached to this mail. I have put a charge somewhere in space only for testing purpose (no physical relevance). Thank you for your help. 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--0-353378643-963925618=:16043-- From chemistry-request@server.ccl.net Tue Jul 18 09:44:58 2000 Received: from mailimailo.univ-rennes1.fr (mailimailo.univ-rennes1.fr [129.20.131.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA24982 for ; Tue, 18 Jul 2000 09:44:58 -0400 Received: from ensc-rennes.fr (balaban.rech.ensc-rennes.fr [129.20.16.67]) by mailimailo.univ-rennes1.fr (8.9.3/jtpda-5.3.3) with ESMTP id PAA22689 for ; Tue, 18 Jul 2000 15:44:34 +0200 (MET DST) Sender: david@univ-rennes1.fr Message-ID: <39745EBC.529A0C48@ensc-rennes.fr> Date: Tue, 18 Jul 2000 15:42:21 +0200 From: David Enot X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Summary: logP database Content-Type: multipart/alternative; boundary="------------B16DFDAE3DA252A3AD800243" --------------B16DFDAE3DA252A3AD800243 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, Last week, I asked a question about free database with compounds and their logP. 1- You can calculate freely logP at these addresses: http://www.acdlabs.com/ilab http://esc-plaza.syrres.com/interkow/kowdemo.htm http://www.daylight.com/daycgi/clogp http://clogp.pomona.edu/medchem/chem/clogp/drugs/index.html 2- You can obtain a release of Xlogp and database with 1800 compounds at these sites: ftp://ftp2.ipc.pku.edu.cn/pub/software/xlogp/ http://mdl.ipc.pku.edu.cn/ 3- You can also access to another database and their experimental logP here: http://www.scivision.com/gProdPage/tReviews/SciLogPUltra/TestYourOwn.html Thanks very much to Gustavo Seabra, Poda Gennady, Gavin Shear, Stefan Seidler and Mario Citra -- *************************************************** * * * David ENOT * * Laboratoire de Chimie Quantique * * et Modelisation Moleculaire * * * * Ecole Nationale Superieure de Chimie de Rennes * * Avenue du General Leclerc * * 35700 RENNES, FRANCE * * * * david.enot@ensc-rennes.fr * * Tel: +33 2 99871333 * * Fax: +33 2 99871399 * * * *************************************************** --------------B16DFDAE3DA252A3AD800243 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit     Hello,

    Last week, I asked a question about free database with compounds and their logP.

1- You can calculate freely logP at these addresses:
        http://www.acdlabs.com/ilab
        http://esc-plaza.syrres.com/interkow/kowdemo.htm
        http://www.daylight.com/daycgi/clogp
        http://clogp.pomona.edu/medchem/chem/clogp/drugs/index.html

2- You can obtain a release of Xlogp and database with 1800 compounds at these sites:
        ftp://ftp2.ipc.pku.edu.cn/pub/software/xlogp/
        http://mdl.ipc.pku.edu.cn/

3- You can also access to another database and their experimental logP here:
        http://www.scivision.com/gProdPage/tReviews/SciLogPUltra/TestYourOwn.html

    Thanks very much to Gustavo Seabra, Poda Gennady, Gavin Shear, Stefan Seidler and Mario Citra 

-- 
***************************************************
*                                                 *
*  David ENOT                                     *
*  Laboratoire de Chimie Quantique                *
*              et Modelisation Moleculaire        *
*                                                 *
*  Ecole Nationale Superieure de Chimie de Rennes *
*  Avenue du General Leclerc                      *
*  35700 RENNES, FRANCE                           *
*                                                 *
*  david.enot@ensc-rennes.fr                      *
*  Tel: +33 2 99871333                            *
*  Fax: +33 2 99871399                            *
*                                                 *
***************************************************
  --------------B16DFDAE3DA252A3AD800243-- From chemistry-request@server.ccl.net Tue Jul 18 12:21:24 2000 Received: from goshen.rutgers.edu (0@goshen.rutgers.edu [165.230.180.150]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA25769 for ; Tue, 18 Jul 2000 12:21:24 -0400 Received: from eden.rutgers.edu (molly.envsci.rutgers.edu [165.230.5.148]) by goshen.rutgers.edu (8.8.8/8.8.8) with ESMTP id MAA08515 for ; Tue, 18 Jul 2000 12:21:09 -0400 (EDT) Message-ID: <39748731.8D26726F@eden.rutgers.edu> Date: Tue, 18 Jul 2000 12:34:57 -0400 From: "Mary O'Connor" X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Protonation enthalpies Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers I would appreciate any advice on how to calculate protonation enthalpies from ab initio calculations. Does AM1 work for molecules containing halogens? Thank-you for any help you can give me. Mary O'Connor Rutgers University New Brunswick, NJ From chemistry-request@server.ccl.net Tue Jul 18 12:12:34 2000 Received: from jamie.chem.unt.edu (jamie.chem.unt.edu [129.120.66.42]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA25721 for ; Tue, 18 Jul 2000 12:12:33 -0400 Received: from jamie.chem.unt.edu (localhost [127.0.0.1]) by jamie.chem.unt.edu (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id LAA42154; Tue, 18 Jul 2000 11:13:41 -0500 (CDT) Sender: naga@jamie.chem.unt.edu Message-ID: <39748234.2EE2404A@jamie.chem.unt.edu> Date: Tue, 18 Jul 2000 11:13:41 -0500 From: "G. Naga Srinivas" X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP27) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net CC: edjsc@uohyd.ernet.in Subject: Summary:CO frequencies in Organometallic Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLs, Here is a summary of the responses to the inquiry I posted recently. I apologize for the mistake in the reference. the correct reference is J. Phys. Chem. 1996, 100, 16502. Thank you to everyone who responded. My original question and responses to it: > I am trying to compare the calculated CO vibrational frequencies >with experimental >frequencies in Organometallics. But the scaling factors suggested for >organic compounds >in J. Phys. Chem. 1996, 100, 16052 producing large errors. Are there >any special scaling >factors for organometallic CO vibrational frequencies. >From: Sérgio Emanuel Galembeck > > We are studying vibrational spectra of ruthenium >carbonyl complexes by PM3 tm method, and >scale factors produced by this paper is >well reproduced. >From: "Li Zhenhua" > Hi, A paper by Bytheway I and Wong MW is about the >scaling factors of DFT >method for inorganic compounds. Hope it can help you. > >The prediction of vibrational frequencies of inorganic molecules using >density functional theory >CHEM PHYS LETT 282: (3-4) 219-226 JAN 16 1998 >From: Kalathingal Thomas Giju > >First of all, I would like to say that there is no absolute >scale factor which you can use for any molecule. The scale >factors reported in literature are somewhat arbitrary. >That means the scaling factors suggested for organic compounds >may lead to errors with organometallic compounds. A better >way of getting reasonable scale factors is to perform a >vibrational mode to mode scaling by comparing experimentally >known carbonyl complexes at a level of your choice. >For a clear example on how to do it is given in the following >article. >E. D. Jemmis, K. T. Giju, J. Leszczynski, K. Sundararajan, K. Sankaran, >V. Vidya, and K. S. Viswanathan J. Mol. Struct. 1999, 510, 59-68. > >Dr. Giju T. Kalathingal >Department of Chemistry and Biochemistry >University of Delaware >Newark, Delaware 19716, USA. >URL: http://dogstar.duch.udel.edu/~gijukt/ From chemistry-request@server.ccl.net Tue Jul 18 18:25:50 2000 Received: from mailer.psc.edu (mailer.psc.edu [128.182.58.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA27286 for ; Tue, 18 Jul 2000 18:25:50 -0400 Received: from pscuxc.psc.edu (pscuxc.psc.edu [128.182.66.177]) by mailer.psc.edu (8.9.3/8.9.3/psc) with ESMTP id SAA24285 for ; Tue, 18 Jul 2000 18:25:49 -0400 (EDT) Received: from localhost (wymore@localhost) by pscuxc.psc.edu (8.9.3/8.9.3/psc) with ESMTP id SAA02992 for ; Tue, 18 Jul 2000 18:25:49 -0400 (EDT) Date: Tue, 18 Jul 2000 18:25:48 -0400 (EDT) From: Troy Wymore To: chemistry@server.ccl.net Subject: Delphi pk calculation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Delphi experts, I am attempting to calculate pK shifts in an active site cysteine residue. To carry out the calculation, I have largely followed the examples in Delphi version 3.0 on histidine in trypsin and explanations laid out in a paper by Yang et al. "On the calculation of pKas in proteins" PROTEINS, 1993, 15:252-265. I start out using a box fill of 20% and dipolar boundary conditions and then focussing in three steps to 90% box fill. My reaction field energies converge in the last two calculations. No problem with dG(solv) When I do the same analogous procedure to get the dG(dipoles + charges), my total energies from the bottom of the frc file are not converging and they totally dominate the result. For charged cysteine with partial charges on the protein: 56.93215 kt For neutral cysteine with partial charges on the protein: 28.74323 kt I am using PARSE3 sizes and CHARMM charges and I center the active site residue before doing the calcs. Should the total energies converge at larger box fills? Should they be so large? Perhaps I should try using a minimized structure instead of the x-ray coordinates. Any help on this would be much appreciated. Troy Wymore Pittsburgh Supercomputing Center