From chemistry-request@server.ccl.net Fri Mar 29 09:42:09 2002 Received: from TheWorld.com ([199.172.62.106]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2TEg9p24873 for ; Fri, 29 Mar 2002 09:42:09 -0500 Received: from world.std.com (root@world-f.std.com [199.172.62.5]) by TheWorld.com (8.9.3/8.9.3) with ESMTP id JAA19049 for ; Fri, 29 Mar 2002 09:42:04 -0500 Received: (from jle@localhost) by world.std.com (8.9.3/8.9.3) id JAA17215 for chemistry@ccl.net; Fri, 29 Mar 2002 09:42:03 -0500 (EST) Date: Fri, 29 Mar 2002 09:42:03 -0500 (EST) From: Joe M Leonard Message-Id: <200203291442.JAA17215@world.std.com> To: chemistry@ccl.net Subject: Linux/x86 compiler question Folks, I've been trying to develop numerically-intensive code on an x86/Linux box (RedHat) after years of working on SGI's. To date, I've found that the double-precision floating-point performance of gcc isn't quite as good as IRIX C, and I wonder whether it's the compiler, the chipset or both... Has anybody tried different compilers with things like GAMESS or Amber? Has there been noticeable improvement with these or similar codes? Are there alternate chipset/compiler Linux's which I should be looking at? Thanks in advance! Joe Leonard jle@theworld.com (formerly jle@world.std.com - ISP changed name) From chemistry-request@server.ccl.net Fri Mar 29 03:42:45 2002 Received: from hermes.bmc.uu.se ([130.238.39.245]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2T8gip19993 for ; Fri, 29 Mar 2002 03:42:45 -0500 Received: from XRAY.bmc.uu.se ([130.238.37.10]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with ESMTP id se; Fri, 29 Mar 2002 09:42:29 +0100 Received: from zorn.bmc.uu.se (IDENT:spoel@zorn.bmc.uu.se [130.238.37.95]) by XRAY.bmc.uu.se (8.11.6/8.8.7) with ESMTP id g2T8jp132734; Fri, 29 Mar 2002 09:45:51 +0100 Date: Fri, 29 Mar 2002 10:45:12 +0100 (CET) From: David van der Spoel X-Sender: spoel@zorn.bmc.uu.se To: Kaiming Wang cc: chemistry@ccl.net Subject: Re: CCL:Any good paper on Grid-based interactions? In-Reply-To: <20020328221032.34127.qmail@web20503.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 28 Mar 2002, Kaiming Wang wrote: > >Hello, >I wonder if you can tell me some good articles on the methods of >grid-based potential calculations. The more detail and more updated, the better. Autodock uses it. @Article{Morris98a, author = {G. M. Morris and D. S. Goodsell and R. S. Halliday and R. Huey and W. E. Hart and R. K. Belew and A. J. Olson}, title = {Automated docking using a {L}amarckian genetic algorithm and an empirical binding free energy function}, journal = {J. Comp. Chem.}, year = 1998, volume = 19, pages = {1639-1662} } Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Fri Mar 29 10:07:38 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2TF7cp25541 for ; Fri, 29 Mar 2002 10:07:38 -0500 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id KAA23960; Fri, 29 Mar 2002 10:07:35 -0500 (EST) Date: Fri, 29 Mar 2002 10:07:34 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: jonathan.hirst@nottingham.ac.uk Subject: 02.07.31 Exploring Modern Computational Chemistry Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Fri, 29 Mar 2002 11:19:02 +0000 From: Jonathan Hirst To: jkl@ccl.net Subject: Conference: Exploring Modern Computational Chemistry 31Jul-2Aug02 Conference Announcement Exploring Modern Computational Chemistry July 31 - August 2, 2002 University of Nottingham The second circular, with full details on registration, accommodation, etc. is now available at: http://www.nottingham.ac.uk/chemistry/emc2 ------------------------------------------------------------- Conference: Exploring Modern Computational Chemistry, Nottingham 2002 http://www.nottingham.ac.uk/chemistry/emc2 Dr Jonathan Hirst School of Chemistry, University of Nottingham University Park, Nottingham NG7 2RD Tel: +44 115 951 3478; FAX: +44 115 951 3562 Email: jonathan.hirst@nottingham.ac.uk URL: www.nottingham.ac.uk/chemistry/staff/hirst/hirst.html From chemistry-request@server.ccl.net Fri Mar 29 13:04:14 2002 Received: from mxout4.cac.washington.edu ([140.142.33.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2TI4Ep28915 for ; Fri, 29 Mar 2002 13:04:14 -0500 Received: from mailscan-out1.cac.washington.edu (mailscan-out1.cac.washington.edu [140.142.32.17]) by mxout4.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with SMTP id g2TI41MQ032664 for ; Fri, 29 Mar 2002 10:04:01 -0800 Received: FROM mailhost1.u.washington.edu BY mailscan-out1.cac.washington.edu ; Fri Mar 29 10:03:48 2002 -0800 Received: from donald (borg.chem.washington.edu [128.95.128.134]) by mailhost1.u.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with SMTP id g2TI3lgK005625 for ; Fri, 29 Mar 2002 10:03:48 -0800 From: "Carsten Detering" To: "ChemistryList" Subject: CCL:Any good paper on Grid-based interactions? Date: Fri, 29 Mar 2002 18:48:40 +0100 Message-ID: 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 IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 > >Hello, >I wonder if you can tell me some good articles on the methods of >grid-based potential calculations. The more detail and more updated, the better. Essentially, there are three ways of calculating grid-based potentials out there: the first is used in AutoDocks AutoGrid Morris, G. M., D. S. Goodsell, et al. (1996). "Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4." J. Comp. Aid. Mol. Des. 10: 293-304, Morris, G. M., D. S. Goodsell, et al. (1998). "Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Funcition." J. Comp. Chem. 19(14): 1639-1662., SCF described in: Mehler, E. L. and T. Solmajer (1991). "Electrostatic effects in proteins: comparison of dielectric and charges models." Protein Engineering 4(8): 903-910.original grid method described by Goodford Goodford, P. J. (1985). "A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules." J. Med. Chem. 28: 849-857. There are programs like MEAD Bashford, D. and K. Gerwert (1992). "Electrostatic Calculations of the pKa Values of Ionizable Groups in Bacteriorhodopsin." J. Mol. Biol. 224: 473-486. Bashford, D. and M. Karplus (1990). Biochemistry 29: 10219-10225. or like DELPHI (MSI) Honig, B. and A. Nicholls (1995). "Classical Electrostatics in Biology and Chemistry." Science 268: 1144-1149. which calculate electrostatics by solving the PB equation. The above mentioned three ways are especially useful for calculating the electrostatic interaction in solution. The new release of DOCK5 (Kuntz et. al., UCSF) will use a Generalized-Born approach. Hope this helps you. Carsten ------------------------ Carsten Detering,Ph.D University of Washington Seattle, WA 98195 Phone: 206 543 5081 email: detering@u.washington.edu From chemistry-request@server.ccl.net Fri Mar 29 20:30:09 2002 Received: from mx.seanet.com ([199.181.164.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2U1U8p07752 for ; Fri, 29 Mar 2002 20:30:08 -0500 Received: from Debug (ssl.seanet.com [199.181.164.13]) by mx.seanet.com (8.11.6/8.11.6) with SMTP id g2U1Tx928577 for ; Fri, 29 Mar 2002 17:30:03 -0800 (PST) Message-Id: <200203300130.g2U1Tx928577@mx.seanet.com> To: chemistry@ccl.net From: Mark Thompson Subject: gaussian integrals package Date: Fri, 29 Mar 2002 17:30:03 US/Pacific X-Mailer: Endymion MailMan Professional Edition v3.0.35 Are there any stand-alone gaussian integrals packages out there that one can get source code access to? Mark