From katagiri@nrim.go.jp Thu Jul 9 01:46:48 1998 Received: from kugane.nrim.go.jp (kugane.nrim.go.jp [144.213.2.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id BAA08550 Thu, 9 Jul 1998 01:46:46 -0400 (EDT) Received: from momokusa.nrim.go.jp ([144.213.240.13]) by kugane.nrim.go.jp (8.8.8+2.7Wbeta7/NRIMSep-97) with ESMTP id OAA11397; Thu, 9 Jul 1998 14:46:46 +0900 (JST) Received: from localhost (momokusa.nrim.go.jp [144.213.240.13]) by momokusa.nrim.go.jp (8.8.7+2.7Wbeta7/3.6Wbeta6) with SMTP id OAA02882; Thu, 9 Jul 1998 14:46:44 +0900 (JST) Date: Thu, 9 Jul 1998 14:46:44 +0900 (JST) From: KATAGIRI Masahiko Message-Id: <199807090546.OAA02882@momokusa.nrim.go.jp> To: chemistry@www.ccl.net Cc: T.Somasundaram@qub.ac.uk MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp Subject: LaPack on SX4 X-Subject: LaPack on SX4 X-Mailer: LaMail Dear CCLer's I would like to compile LaPack on NEC SX4. Does anyone have optimized LaPack code or Makefile on SX4? Any information will be appreciated. Thanks in advance. regards, -Masa Katagiri katagiri@nrim.go.jp From dgeuenic@tu-bs.de Thu Jul 9 03:43:30 1998 Received: from rzcomm1.rz.tu-bs.de (rzcomm1.rz.tu-bs.de [134.169.9.107]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA10683 Thu, 9 Jul 1998 03:43:24 -0400 (EDT) Received: from rzab0.rz.tu-bs.de (daemon@rzab0.rz.tu-bs.de [134.169.9.28]) by rzcomm1.rz.tu-bs.de (8.8.6/8.8.6) with ESMTP id JAA25872 for ; Thu, 9 Jul 1998 09:42:54 +0200 (METDST) Received: from tu-bs.de (ppp364.ts.rz.tu-bs.de) by rzab0.rz.tu-bs.de with ESMTP (1.37.109.24/15.6) id AA160900164; Thu, 9 Jul 1998 09:42:44 +0200 Sender: NetUser1@ws.rz.tu-bs.de Message-Id: <35A490A4.BE4926AA@tu-bs.de> Date: Thu, 09 Jul 1998 09:43:00 +0000 From: Daniel Geuenich X-Mailer: Mozilla 4.05 [en] (X11; I; Linux 2.0.33 i586) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: Summary addendum:3D-grid of current density tensors Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL-lers, about two weeks ago I summarized my question concerning the computation of a 3D-grid of current density tensors. The only answer I got to this time said that my problem is not solvable with G94. After this I received this message from Ernst-Udo Wallenborn: >Hi Daniel, > > >i should've answered your question, but i just didn't find the time. > >On Tue, 23 Jun 1998, Daniel Geuenich wrote: >> >> I am interested in generating a plot of the current density. >> When using the NMR=CSGT or NMR=IGAIM keyword, Gaussian 94 >> prints only one current density tensor, but what I need is >> a calculation of the current density tensor over a >> 3-dimensional grid of points. > > > >Doug Fox is only partially right. While g94 does not include the >feature you request as a regular option, and Bader's AIMPAC code is a >bad starting point for trying to include it, Jerzy Cioslowski's >implementation of CSGT in g94 does calculate this. If you don't mind >hacking link 1002 (basically you have to include a couple of >write statements at the right point) you can get a printout of the >current density tensor field on the grid used by g94. You can >then refine the data (remap onto a different grid for example) >and visualize it using your favourite visualisation system (avs >would be my advice). > >This is suboptimal of course, for one would like to have something >like a subroutine CurrTens(moldata,grid), but it did work for us. >(Wallenborn, Haldimann, Klaerner, and Diederich, Chem. Eur. J., >submitted) > > >-- >Ernst-Udo Wallenborn >Laboratorium fuer Physikalische Chemie >ETH Zuerich Many thanks to Ernst-Udo Wallenborn! From darrena@chem.leeds.ac.uk Thu Jul 9 06:07:50 1998 Received: from chemistry.leeds.ac.uk (chmsun1.leeds.ac.uk [129.11.12.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id GAA12966 Thu, 9 Jul 1998 06:07:49 -0400 (EDT) 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 LAA12485 for ; Thu, 9 Jul 1998 11:07:47 +0100 (BST) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Message-Id: Date: Thu, 9 Jul 1998 11:02:33 +0100 To: chemistry@www.ccl.net From: Darren Andrews Subject: Big Frequency Calcs. with little resources Does anybody know how to calculate frequencies with large systems, i.e., about 380 basis functions at the HF level with limited file sizes? I have a linux box with a max file size of 2Gb, and also 512M of RAM. If I use GAMESS(US) to calculate the frequencies it craps out at the 2Gb file limit (I guess it has to write all the integrals to disk first) even though I ran a direct calculation. I tried G92 on an SGI, because I was told it would handle the direct calculation without writing big files to disk first, but it just kind of stopped with no explanation after a few days. Anyone have a solution? 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 herbert.homeier@chemie.uni-regensburg.de Thu Jul 9 07:15:24 1998 Received: from rrzs2.rz.uni-regensburg.de (rrzs2.rz.uni-regensburg.de [132.199.1.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA14440 Thu, 9 Jul 1998 07:15:23 -0400 (EDT) Received: from rchs4.chemie.uni-regensburg.de (rchs4.chemie.uni-regensburg.de [132.199.48.4]) by rrzs2.rz.uni-regensburg.de (8.8.8/8.8.8) with SMTP id NAA17299 for ; Thu, 9 Jul 1998 13:15:16 +0200 (MET DST) Date: Thu, 9 Jul 1998 13:17:18 +0200 From: Herbert Homeier t4720 Message-Id: <9807091117.AA28749@rchs4.chemie.uni-regensburg.de> To: chemistry@www.ccl.net Subject: Change of URL Dear CCL readers, please note that the WWW server at rchs1.chemie.uni-regensburg.de (or equivalently, rchs1.uni-regensburg.de) ceased to function due to hardware problems and will not be available in future. Please use the WWW server www.chemie.uni-regensburg.de instead, and please, update all links in your bookmarks/ html pages accordingly. Thus, any old URLs like http://rchs1.chemie.uni-regensburg.de/ ... http://rchs1.uni-regensburg.de/ ... should be replaced by http://www.chemie.uni-regensburg.de/ ... In particular, this applies to the list of Chemistry Servers and Resources (via Theoretical Chemistry, University of Regensburg) that should be accessed now via http://www.chemie.uni-regensburg.de/external.html and the Chemistry Conference Listing that should be accessed now via http://www.chemie.uni-regensburg.de/~hoh05008/KONFERENZEN/ Sorry for all the inconveniences. Best regards Herbert Homeier -- Priv.-Doz. Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg, D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX: +49-941-943 4719 email: herbert.homeier@na-net.ornl.gov WWW: http://www.chemie.uni-regensburg.de/~hoh05008 From hinsen@dirac.cnrs-orleans.fr Thu Jul 9 12:17:55 1998 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 MAA20593 Thu, 9 Jul 1998 12:17:49 -0400 (EDT) Received: (from hinsen@localhost) by dirac.cnrs-orleans.fr (AIX4.3/UCB 8.7/8.7) id SAA20908; Thu, 9 Jul 1998 18:16:10 +0200 (DFT) Date: Thu, 9 Jul 1998 18:16:10 +0200 (DFT) Message-Id: <199807091616.SAA20908@dirac.cnrs-orleans.fr> From: Konrad Hinsen To: smithja@ucarb.com CC: chemistry@www.ccl.net In-reply-to: (smithja@ucarb.com) Subject: Re: CCL:Summary: Visualization of molecules and arbitrary geometric o bjects References: > This reminds me of a related feature I've always wanted to see in > modeling packages. I'd like to be able to select a subset of atoms in a >... > I think that quantifying the shape and size of molecular fragments > (cavities) is an important, useful and often overlooked aspect of most > molecular modeling packages. The essential problem is the use of "packages", i.e. monolithic programs, for molecular modelling. It is unlikely that any such package will ever provide all features you want, and so in practice you have to adapt your wishlist to what's available. Even if a program is available in source code, few people are able to make substantial modifications or additions, because the complexity of a big program code requires significant programming experience and plenty of time. During the last two years I have developed an alternative approach: a molecular modelling toolkit, i.e. a library of useful operations in molecular modelling, to be used with (and to a large part written in) Python, a high-level general-purpose easy-to-learn programming language. This library contains basic functions that are always needed (system construction, import/export, geometric operations, etc.), plus a large range of more specialized techniques. It even includes some of the techniques that were asked for in the post I am replying to. With this fundamental stuff out of the way, implementing additional specialized methods becomes much easier. Moreover, it is not necessary to understand or even look at any of the original code of the library, even though this might be helpful in some cases. To give an example, I was able to add a complete new forcefield (admittedly a simple one) in an afternoon, including testing, and without modifying or even looking at any of the original files. For those who want to know more about this approach, have a look at http://starship.skyport.net/crew/hinsen/mmtk.html -- ------------------------------------------------------------------------------- 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 paul.wilkie@virgin.net Thu Jul 9 19:21:02 1998 Received: from newmail.virgin.net (newmail.virgin.net [194.168.54.44]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id TAA28689 Thu, 9 Jul 1998 19:21:01 -0400 (EDT) Received: from virgin.net ([194.168.121.161]) by newmail.virgin.net (Post.Office MTA v3.5 release 217 ID# 0-52107U250000L250000S0V35) with ESMTP id net; Thu, 9 Jul 1998 23:20:59 +0000 Message-ID: <35A54F84.5289B4C6@virgin.net> Date: Fri, 10 Jul 1998 00:17:25 +0100 From: Paul Wilkie Reply-To: paul.wilkie@virgin.net X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: KATAGIRI Masahiko CC: chemistry@www.ccl.net Subject: Insulin Receptor with ATP References: <199807090546.OAA02882@momokusa.nrim.go.jp> Content-Type: text/plain; charset=x-user-defined Content-Transfer-Encoding: 7bit Dear CCL'ers, I am a PhD research student at the University of Sunderland, England. Having recently i.e. yesterday, downloaded the active form of the Insulin Receptor Kinase with ATP, I have had endless troubles. The main problem is that when I load in the receptor, the bond order for the ATP and the phosphorylated tyrosine residues is not recognized causing the full receptor complex to return a " Could not assign charge " statement even when I charge the appropriate residues. Although this is a problem that can be, and has been, dealt with, it is highly annoying. I would be interested in hearing from anyone who has experienced similar difficulties with 1ir3.pdb from Brookhaven and if there is a simplier solution other than the long-handed approach that I have had to use i.e. changing the bond order's manually etc etc. I would also like to hear from those who are also modeling kinase's esp EGFR and Insulin. Cheers, Paul Wilkie