From chemistry-request@server.ccl.net Fri Oct 6 02:18:20 2000 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA27047 for ; Fri, 6 Oct 2000 02:18:20 -0400 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id CAA24902 for ; Fri, 6 Oct 2000 02:18:13 -0400 (EDT) Sender: desingh@mailbox.syr.edu Message-ID: <39DD6FD4.6FB98835@syr.edu> Date: Fri, 06 Oct 2000 02:23:16 -0400 From: Deepak Singh Organization: Birge Group, Dept. Of Chemistry, Syracuse Univ. X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: Helical hydrophobicity moments Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCLers Does anyone know of any good freeware that will plot the component of helical hydrophobic moments? QUANTA does this, but the quality of the graphics is not good enough. A UNIX (preferably) or windows program will do. Thank you Deepak. -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Fri Oct 6 04:22:02 2000 Received: from hermes.bmc.uu.se (hermes.bmc.uu.se [130.238.39.159]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA27703 for ; Fri, 6 Oct 2000 04:22:02 -0400 Received: from alpha2.bmc.uu.se ([130.238.37.65]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with SMTP id se for ; Fri, 6 Oct 2000 10:23:10 +0200 Received: from werkman.bmc.uu.se by alpha2.bmc.uu.se (5.65v3.2/1.1.10.5/07Jan00-1145AM) id AA32393; Fri, 6 Oct 2000 10:21:51 +0200 Date: Fri, 6 Oct 2000 08:22:50 +0200 (CEST) From: David X-Sender: spoel@werkman.bmc.uu.se To: chemistry@ccl.net Subject: Multipole in Gaussian Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am curious as to how Gaussian (98) computes multipole moments. For neutral molecules only the dipole is position independent. The Quadrupole is customarily computed with respect to the center of mass for most small molecules such as water and ammonia. But how does Gaussian do it? -- Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Fri Oct 6 04:47:09 2000 Received: from mailhost1.rdg.ac.uk (sumh1.rdg.ac.uk [134.225.16.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA27799 for ; Fri, 6 Oct 2000 04:47:08 -0400 Received: from indyp.chemistry ([134.225.168.35] helo=scsgind2) by mailhost1.rdg.ac.uk with esmtp (University of Reading Email Service) id {13hT9g-0004ND-00} for CHEMISTRY@server.ccl.net; Fri, 06 Oct 2000 09:47:00 +0100 Received: from reading.ac.uk (localhost [127.0.0.1]) by scsgind2 (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id JAA11239 for ; Fri, 6 Oct 2000 09:47:05 -0100 (BST) Sender: dave@reading.ac.uk Message-ID: <39DDADA8.73A32F50@reading.ac.uk> Date: Fri, 06 Oct 2000 09:47:04 -0100 From: Dave Price Organization: none-what-so-ever X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Comp Chem Mailing List Subject: Help with a DFT reference needed. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear fellow computational chemists, Some time ago I heard Nick Handy, Cambridge, quote E. Bright Wilson on DFT. The quote was regarding a simple explanation of why the electron density fully describes a system- 1) The total electron density defines the number of electrons in the system; 2) The cusps in the density define the nuclear co-ordinates; 3) The height of each cusp defines the nuclear charge at each nucleus and thus the configuration of the elements in the molecule; 4) Knowing the total number of electrons and the elements present gives us the charge of the system. Thus, the system is fully defined. OK. Now, does anyone have a reference for this E. Bright Wilson explanation? Any help much appreciated. Cheers, Dave -- ------------------------------------------------------------------------ Dr. David W. Price, Tel: +44 (0)118 9875123 extn 7415 Department of Chemistry, Fax: +44 (0)118 9316331 University of Reading, mailto:d.w.price@reading.ac.uk Whiteknights, READING http://www.chem.rdg.ac.uk/g50/mmrg/dave/dave.html RG6 6AD U.K. ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Fri Oct 6 08:50:58 2000 Received: from gip.u-picardie.fr (gip.u-picardie.fr [193.49.184.17]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA29587 for ; Fri, 6 Oct 2000 08:50:57 -0400 Received: from labo5 (labo5.sa.u-picardie.fr [195.83.150.83]) by gip.u-picardie.fr (8.9.3/8.9.3) with SMTP id OAA32345 for ; Fri, 6 Oct 2000 14:50:45 +0200 Date: Fri, 6 Oct 2000 14:50:45 +0200 Message-Id: <200010061250.OAA32345@gip.u-picardie.fr> X-Sender: fyd-phar@mailx.u-picardie.fr X-Mailer: Windows Eudora Light Version 1.5.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: =?iso-8859-1?Q?Fran=E7ois?= Yves Dupradeau Subject: AmberFFC 1.0 Dear All, I am pleased to announce the release of AmberFFC, a program to Convert all the AMBER Force Fields available in the public domain (amber91, amber91X, amber94, amber96, amber98 and amber99; http://www.amber.ucsf.edu/amber) for use with commercial molecular modeling packages. In its current version (version 1.0, written May 2000, released October 2000) AmberFFC creates the AMBER force fields for the CDiscover molecular mechanics module of Molecular Simulation Inc. (MSI, http://www.msi.com) by transforming the AMBER amino acid and nucleic acid topology database and force field parameter files to the MSI file format. This program is suitable for any modeler who is interested in (i) using the current AMBER force fields with MSI molecular modeling package and/or (ii) comparing the results obtained with the AMBER and MSI software. It has been entirely written with the Perl programming language, making it highly flexible and portable on different operating systems and platforms. Easy to use, AmberFFC is freely available for academic laboratories through the world-wide web at the site http://www.u-picardie.fr/UPIC/UPJV/recherche/labos/bpd/AmberFFC.htm after signing a license. The first version of this program was written in May 2000 by : A. Dejoux (1), P. Cieplak (2), G. Moyna (3) and F.-Y. Dupradeau (1) (1) Faculte de Pharmacie, Amiens, France. (2) Dept. Chem., University of Warsaw, Poland. (3) Dept. Chem. & Biochem., University of Sciences in Philadelphia, USA. All your suggestions are welcome, Sincerely, Francois -- F.-Y. Dupradeau, Ph.D. http://www.u-picardie.fr/UPIC/UPJV/recherche/labos/bpd/fyd.htm email : fyd@u-picardie.fr From chemistry-request@server.ccl.net Fri Oct 6 10:41:36 2000 Received: from dep.chem.rug.nl (dep.chem.rug.nl [129.125.7.81]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA30071 for ; Fri, 6 Oct 2000 10:41:36 -0400 Received: from [129.125.7.13] (theochem1.chem.rug.nl [129.125.7.13]) by dep.chem.rug.nl (8.9.3/8.9.3/Debian 8.9.3-21) with ESMTP id QAA22956; Fri, 6 Oct 2000 16:41:22 +0200 X-Authentication-Warning: dep.chem.rug.nl: Host theochem1.chem.rug.nl [129.125.7.13] claimed to be [129.125.7.13] Mime-Version: 1.0 X-Sender: swart@hydra.chem.rug.nl Message-Id: In-Reply-To: <39DDADA8.73A32F50@reading.ac.uk> References: <39DDADA8.73A32F50@reading.ac.uk> Date: Fri, 6 Oct 2000 16:45:49 +0200 To: Dave Price From: Marcel Swart Subject: Re: CCL:Help with a DFT reference needed. Cc: CHEMISTRY@ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" >Dear fellow computational chemists, > Some time ago I heard Nick Handy, Cambridge, quote >E. Bright Wilson on DFT. The quote was regarding a simple explanation >of why the electron density fully describes a system- > >1) The total electron density defines the number of electrons in the >system; >2) The cusps in the density define the nuclear co-ordinates; >3) The height of each cusp defines the nuclear charge at each nucleus >and thus the configuration of the elements in the molecule; >4) Knowing the total number of electrons and the elements present >gives us the charge of the system. > >Thus, the system is fully defined. OK. Now, does anyone have a >reference >for this E. Bright Wilson explanation? It was at a (spectroscopy?) conference somewhere, but i forgot the details. Sorry. -- Marcel Swart Theoretische Chemie (MSC) / Moleculaire Dynamica (GBB) Rijksuniversiteit Groningen Nijenborgh 4 9747 AG Groningen The Netherlands m.swart@chem.rug.nl http://go.to/m.swart From chemistry-request@server.ccl.net Fri Oct 6 10:55:10 2000 Received: from piglet.chem-eng.nwu.edu (piglet.chem-eng.nwu.edu [129.105.205.250]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA30169 for ; Fri, 6 Oct 2000 10:55:09 -0400 Received: (qmail 28322 invoked by uid 1119); 6 Oct 2000 14:54:57 -0000 Message-ID: <20001006145457.28718.qmail@piglet.chem-eng.nwu.edu> Date: 6 Oct 2000 09:54:57 -0500 X-Mailer: exmh version 2.0.2 2/24/98 To: chemistry@ccl.net cc: help@gaussian.com Subject: g98 unfchk conversion X-URL: http://winnie.chem-eng.northwestern.edu/~scott/ From: Scott McMillan Reply-To: Scott McMillan Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Fri, 06 Oct 2000 09:54:57 -0500 Sender: scott@piglet.chem-eng.nwu.edu Hello, I am trying to convert a formatted (ascii) g98 checkpoint file to a binary checkpoint file with the g98 utility unfchk. When I do so, I get the following error: % unfchk lafer_opt.fchk lafer_opt_pop.chk Read checkpoint file lafer_opt.fchk Write formatted file lafer_opt_pop.chk UFChkP allocation failure: iend,mxcore= 3336038 3000000 Error termination via Lnk1e. Segmentation fault It seems that unfchk has a staticly allocated array that my fchk file is too big for. I've tried unfchk on several platforms (Tru64, Linux, HPUX) with the same result. We don't have the g98 source, so I can't increase the size of whatever needs to be allocated myself. Is there anything I can do? Thanks, Scott -- Scott McMillan - smcmilla@northwestern.edu Institute for Environmental Catalysis Department of Chemical Engineering, Northwestern University http://winnie.chem-eng.northwestern.edu/ From chemistry-request@server.ccl.net Fri Oct 6 15:51:46 2000 Received: from fcindy5.NCIFCRF.GOV (fcindy5.NCIFCRF.GOV [129.43.50.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA31348 for ; Fri, 6 Oct 2000 15:51:45 -0400 Received: (from catfee@localhost) by fcindy5.NCIFCRF.GOV (SGI-SGI-8.9.3/8.9.3) id PAA38804 for chemistry@ccl.net; Fri, 6 Oct 2000 15:46:47 -0400 (EDT) Date: Fri, 6 Oct 2000 15:46:47 -0400 (EDT) From: CATFEE Message-Id: <200010061946.PAA38804@fcindy5.NCIFCRF.GOV> To: chemistry@ccl.net Subject: CATFEE Announcement Reply-To: catfee@fcindy5.NCIFCRF.GOV *** CATFEE *** The Drug Design Challenge (Meeting on the Critical Assessment of Techniques for Free Energy Evaluation) Targets announcement: Targets are now available at CATFEE. Visit our page at: http://uqbar.ncifcrf.gov/~catfee/ Raul E. Cachau (NCI-SAIC) Krzysztof Fidelis (LLNL) Adrian E. Roitberg (NIST-Geo Centers) CATFEE: Critical Assessment of Techniques for Free Energy Evaluation e-Mail: catfee@uqbar.ncifcrf.gov; Fax/Voice: +1-209-8825286 From chemistry-request@server.ccl.net Fri Oct 6 16:09:47 2000 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA31513 for ; Fri, 6 Oct 2000 16:09:47 -0400 Received: from geneseo.ks.uiuc.edu (geneseo.ks.uiuc.edu [130.126.120.127]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id PAA09405 for ; Fri, 6 Oct 2000 15:09:47 -0500 (CDT) Received: (from johns@localhost) by geneseo.ks.uiuc.edu (8.9.1b+Sun/8.9.1) id PAA05087 for chemistry@ccl.net; Fri, 6 Oct 2000 15:09:42 -0500 (CDT) Date: Fri, 6 Oct 2000 15:09:42 -0500 From: John Stone To: chemistry@ccl.net Subject: Announce: VMD 1.6a3 is available Message-ID: <20001006150941.F4896@geneseo.ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0i Dear CCL, We have just made VMD 1.6a3 available for download on the VMD downloads page: http://www.ks.uiuc.edu/Development/Download/download.cgi VMD is a 3-D molecular visualization tool for Unix and Windows systems, supporting quite a range of hardware. VMD 1.6 Alpha 3 fixes PR 114 (Cartoon rep problems with certain molecules), and has a bunch of small user interface improvements some of which were only on Windows, and some which are on all versions. We're now providing pre-compiled binaries for Linux on PowerPC and Alpha processors, which are new to this release. I intend to continue providing these binaries as long as we have access to such machines. We have also recently started adding Python support into VMD, although it isn't visible in the binary distributions we're making available at this time, it will begin to be more prominent in future revs of VMD. Those individuals curious about Python support in VMD that are willing to play with bleeding edge code may feel free to send us email and get in on the ground floor of VMD's Python support. I've included the latest README features-diff at the tail of this email for your perusal. We welcome your feedback on this latest version, tell us what you think! Thanks, John Stone vmd@ks.uiuc.edu What's new in VMD 1.6? ---------------------- New Features o New support for Linux on Alpha processors o New support for Linux on PowerPC processors o New support for generation of RenderMan .RIB files from VMD scenes. o New VMD Python scripting interface (developmental stage) General Improvements and Bug Fixes o Windows version of VMD now implements mouse capture so that you can drag the mouse outside of the graphics window while doing rotations, translations, scaling, and other mouse dragging operations. o Improved interactive rendering speed of molecular surfaces by a factor of two or more on most platforms. o Improved OpenGL materials rendering and gave VMD better looking default material properties. o Tachyon ray tracer binaries are now packaged along with VMD on all supported platforms. o Added the ability for Tcl code to capture VMD events as through the logfile mechanism, but through a Tcl variable, so that one VMD can easily remote control other VMD's through a bit of Tcl sockets code. o Significant speed increases for many common VMD commands, many commands are 5 to 200 times faster now, using new Tcl 8.x interpreter interface. o Made it easier to customize size/position of the VMD command window on Unix versions of VMD. o Built with FLTK 1.0.9 o Built with VRPN 5.01 o Fixed PRs: 60, 106, 108, 109, 110, 111, 112, 114 User Interface Changes o New Tcl/Tk based RMSD fit GUI o Save state uses a GUI dialog now when possible. User Documentation Updates o Updated various sections in User's guide, particularly relating to new rendering features, RMSD fit, etc. o Started lengthy update to Programmer's guide. o Added commit email capability to CVS, may make it an option for read-only CVS users as well. -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns@ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078