From chemistry-request@server.ccl.net Thu Jul 13 00:43:16 2000 Received: from franc.ucdavis.edu (franc.ucdavis.edu [169.237.105.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id AAA21786 for ; Thu, 13 Jul 2000 00:43:15 -0400 Received: from sigma.ucdavis.edu (sigma.ucdavis.edu [169.237.38.51]) by franc.ucdavis.edu (8.9.3/8.9.3/IT4.3.3) with ESMTP id VAA21292 for ; Wed, 12 Jul 2000 21:43:09 -0700 (PDT) Received: (from medvedev@localhost) by sigma.ucdavis.edu (8.9.3/UCD4.0.1) id VAA18087 for chemistry@ccl.net; Wed, 12 Jul 2000 21:43:08 -0700 (PDT) From: "Dmitry M. Medvedev" Message-Id: <10007122143.ZM18085@sigma.ucdavis.edu> Date: Wed, 12 Jul 2000 21:43:06 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: DelPhi questions Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear netters, I am trying to make certain calculations using DelPhi distributed by MSI, release 97.2. I've run into some problems I can't solve. Here they are: 1. When I don't center the grid on the center of the molecule, then the site potential file (file.frc) is completely screwed up, showing ridiculous values of potential and total electrostatic energy. Why is it so? 2. The values of total electrostatic energy reported in log file and in site potenial file are different. This difference is small if I center the grid on the center of the molecule, and is large if the center of the grid is far from the center of the molecule. What is the reason for this difference? 3. The convergence criterion does not seem to work. When I changed energy convergence criterion from 0.000001 to 0.1, nothing changed in the calculation. How can I make this criterion work? 4. What do centers of assigned positive and negative charges in grid units (gu) reported in log file mean? 5. What are the values of potentials given in the log file? 6. I was trying to calculate (as a test) the change of energy of an ion when I changed its radius from 1.35A to 9.35A. I used grids centered on the ion with grid steps from 1A to 0.02A, using focussing boundary conditions. The charge of ion was 1e, the internal dielectric permeability was 4, the external dielectric permeability was 80. I found that when the grid step was in the range approximately from 0.2A to 06A, the desolvation penaly was close to the correct value (42.1kT with T=298K), but for smaller values of the grid step is started to deviate from this value. Why does it happen? 7. Could anyone explain what DelPhi does with spectral radius? I don't understand what is written in the manual. Thanks in advance, Dmitry From chemistry-request@server.ccl.net Thu Jul 13 04:19:25 2000 Received: from ovrisc.mdche.u-szeged.hu (ovrisc.mdche.u-szeged.hu [160.114.101.224]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA22704 for ; Thu, 13 Jul 2000 04:19:24 -0400 Received: from localhost by ovrisc.mdche.u-szeged.hu (AIX 3.2/UCB 5.64/4.03) id AA20457; Thu, 13 Jul 2000 10:16:26 +0100 Date: Thu, 13 Jul 2000 10:16:26 +0100 (NFT) From: Hetenyi Csaba To: chemistry@server.ccl.net Subject: problems compiling autodock (fwd) Message-Id: Mime-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="-1603115552-1231836461-963476238=:20299" Content-Id: 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. ---1603115552-1231836461-963476238=:20299 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-ID: Hi, I have some problem with compilation of autodock. I use an SGI R4400 for running the program. Till this time I could use the precompiled binaries, but a new problem occured: I need more grid points than 128 /ca. 400/ and, therefore I have to compile the source. I have changed the MAX_GRID_PTS value to 400 in autocomm.h and managed to compile the autogrid sources. However, when I made the same change in autocomm.h file in autodock library, the compilation was not succesful: the main.o file had not a correct format according to the error-message of the compiler. Could you please write me how it is possible to use autodock with more than 128 grid points. There would be an other possibility to change the grid spacing to a larger value than .375 so as to cover the whole target /which I need to/, but I feel using this /smaller/ one is better /the number of succesful dockings was greater in the latter case/. /Please, find attached the modified Makefile for autodock, I used. I made the compilations on an R5000, because we had the compiler licensed on that computer only./ Thank you for your help. 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service by hotmail.com with Microsoft SMTPSVC; Thu, 13 Jul 2000 02:09:05 -0700 Received: from 193.132.141.231 by lw4fd.law4.hotmail.msn.com with HTTP; Thu, 13 Jul 2000 GMT X-Originating-IP: [193.132.141.231] From: "Douglas Smith`" To: williams@bucknell.edu, chemistry@ccl.net Subject: Re: CCL:QSAR Date: Thu, 13 Jul 2000 05:09:05 EDT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 13 Jul 2000 09:09:05.0102 (UTC) FILETIME=[FE605EE0:01BFECA9] Oxford Molecular Group is in the beta testing phase, and will within about 4 weeks, release Tsar for Windows. This is the same as our Tsar product on SGI workstations, with all the same functionality including 2D and 3D descriptors, calculations, VAMP (Tim Clark) and Corina (John Gasteiger) back ends, etc. However, the price point for the full package is only $9900 on the PC, compared to over $40,000 list on the SGI. Contact me (at dsmith@oxmol.com) for more details if you wish them. We will be formally launching the program at the ACS meeting in Washington and the European QSAR meeting in Dusseldorff in late August. Doug Smith Product Manager Decision Support programs Oxford Molecular Group dsmith@oxmol.com >From: Brian Williams >To: chemistry@ccl.net >Subject: CCL:QSAR >Date: Fri, 7 Jul 2000 15:22:28 -0400 (EDT) > >This is probably a FAQ, but an organic colleague of mine is interested in >knowing more about what packages or code might be available to do QSAR. We >are a PUI ("Primarily Undergraduate Institution") and are looking to this >in >as cost-effective manner as possible. I myself have used molecular >modelling/computational chemistry at very basic levels with packages such >as >Spartan and HyperChem, but know little about QSAR. Thanks for any advice. > >Brian Williams >Dept. Chemistry >Bucknell University > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To >Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net >70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: >jkl@ccl.net > > > > > ________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com From chemistry-request@server.ccl.net Thu Jul 13 05:14:05 2000 Received: from hotmail.com (f270.law4.hotmail.com [216.33.148.148]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA22904 for ; Thu, 13 Jul 2000 05:14:04 -0400 Received: (qmail 13862 invoked by uid 0); 13 Jul 2000 09:11:55 -0000 Message-ID: <20000713091155.13861.qmail@hotmail.com> Received: from 193.132.141.231 by www.hotmail.com with HTTP; Thu, 13 Jul 2000 02:11:55 PDT X-Originating-IP: [193.132.141.231] From: "Douglas Smith" To: chemistry@ccl.net Subject: Re: CCL:Are atoms spherical? Date: Thu, 13 Jul 2000 05:11:55 EDT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Excuse me for coming into this late.... A few years ago, we published a paper entitled: "Polarizability of Molecular Orbitals," J. Phys. Chem. 1994, 98, 6903-6905 that might be of interest to those following this thread. Doug Smith ________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com From chemistry-request@server.ccl.net Thu Jul 13 06:34:58 2000 Received: from jivdhan.unipune.ernet.in (jivdhan.unipune.ernet.in [196.1.114.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA23192 for ; Thu, 13 Jul 2000 06:34:54 -0400 Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.9.0/UnipuneMailhubV1.3) with ESMTP id PAA00564 for ; Thu, 13 Jul 2000 15:50:27 +0530 Received: (from spgejji@localhost) by chem.unipune.ernet.in (8.8.7/8.8.7) id QAA20710 for CHEMISTRY@ccl.net; Thu, 13 Jul 2000 16:30:03 +0530 Date: Thu, 13 Jul 2000 16:30:03 +0530 From: "Shridhar P. Gejji" Message-Id: <200007131100.QAA20710@chem.unipune.ernet.in> To: CHEMISTRY@ccl.net Subject: Clusters !!! I would like to know the details about the following. What is the largest water cluster studied within ab initio framework? And what level of theory? I will appreciate the answers greatly. Thank you. S. P. Gejji From chemistry-request@server.ccl.net Thu Jul 13 10:03:50 2000 Received: from misnoc.mis.bio-rad.com (misnoc.mis.bio-rad.com [198.211.153.71]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA25062 for ; Thu, 13 Jul 2000 10:03:49 -0400 Received: from 68yse by misnoc.mis.bio-rad.com (SMI-8.6/SMI-SVR4) id HAA27564; Thu, 13 Jul 2000 07:04:07 -0700 Reply-To: From: "Marie Scandone" To: "'CCL'" Subject: add to CCL list service Date: Thu, 13 Jul 2000 10:03:40 -0400 Message-ID: <000001bfecd3$26582a30$85a5d3c6@sadtler.biorad.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Marie Scandone Database Product Manager Sadtler Division, Bio-Rad Laboratories 3316 Spring Garden Street Philadelphia, PA 19104-2596 Phone: 215.349.7349 Fax: 215.662.0585 Email: marie_scandone@bio-rad.com Web: http://www.sadtler.bio-rad.com From chemistry-request@server.ccl.net Thu Jul 13 19:18:38 2000 Received: from ice.lanl.gov (ice.lanl.gov [128.165.22.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA27673 for ; Thu, 13 Jul 2000 19:18:38 -0400 Received: from localhost (localhost [[UNIX: localhost]]) by ice.lanl.gov (8.9.3/8.9.3) id RAA09517 for chemistry@ccl.net; Thu, 13 Jul 2000 17:18:36 -0600 From: Matt Challacombe Reply-To: MChalla@LANL.Gov Organization: Group T-12, Theoretical Chemistry and Molecular Physics To: chemistry@ccl.net Subject: Stability of 1GHz AMD/Linux Date: Thu, 13 Jul 2000 17:16:01 -0600 X-Mailer: KMail [version 1.0.29] Content-Type: text/plain References: <001501bfe511$5c3bf060$d43b8286@dorf.rwthaachen.de> <14690.2563.245509.868855@yogi.pc1.uni-duesseldorf.de> In-Reply-To: <14690.2563.245509.868855@yogi.pc1.uni-duesseldorf.de> MIME-Version: 1.0 Message-Id: <0007131718350B.27815@ice> Content-Transfer-Encoding: 8bit Hi, I'm curious to here anyones experience with high clockspeed AMD CPUs running LINUX, especially the stability of this platform running G98 compiled with PGI compilers. Thanks, Matt +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ + Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ + + Los Alamos National Laboratory email: mchalla@t12.lanl.gov + + Theoretical Division pager: (505) 949-0096 + + Group T-12, Mail Stop B268 phone: (505) 665-5905 + + Los Alamos, New Mexico 87545 fax: (505) 665-3909 + + + + "The secret to mountain biking is pretty simple. The slower you go + + the more likely it is you'll crash." -- Julie Furtado + +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@server.ccl.net Thu Jul 13 23:00:32 2000 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.8.7/8.8.7) with SMTP id XAA28544 for ; Thu, 13 Jul 2000 23:00:15 -0400 Received: from iris.sipp.ac.cn (202.127.25.133) by iris.sipp.ac.cn (EMWAC SMTPRS 0.81) with SMTP id ; Fri, 14 Jul 2000 11:03:28 +0800 Sender: user@ccl.net Message-ID: <396E739A.A5548C23@iris.sipp.ac.cn> Date: Fri, 14 Jul 2000 10:57:46 +0900 From: Mao Xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: deprotonation rate Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello everyone: I want to know about the activation free energy of the following reaction: 1. H2O---> H+ + OH- 2. CH3CH2OH----> CH3CH2O- + H+ 3. NH2CH2CH2OH---> +NH3CH2CH2O- I think I calculate them with Arrhenius equation, but I do not know where I can get the observed rate constants. Does anyone have some experients about my problem. Hope you can help me. Thanks. Regards, mao ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Xiang Mao | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~