From chemistry-request@server.ccl.net Tue Sep 24 04:12:42 2002 Received: from oulu.fi (root@[130.231.240.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8O8Cfw14772 for ; Tue, 24 Sep 2002 04:12:41 -0400 Received: from paju.oulu.fi (paju.oulu.fi [130.231.240.20]) by oulu.fi (8.8.5/8.8.5) with ESMTP id LAA08526 for ; Tue, 24 Sep 2002 11:12:40 +0300 (EET DST) Received: from paju.oulu.fi (paju.oulu.fi [130.231.240.20]) by paju.oulu.fi (8.8.5/8.8.5) with ESMTP id LAA20566 for ; Tue, 24 Sep 2002 11:12:40 +0300 (EEST) Date: Tue, 24 Sep 2002 11:12:40 +0300 (EEST) From: =?ISO-8859-1?Q?Atte_Sillanp=E4=E4?= X-X-Sender: asillanp@paju.oulu.fi Reply-To: atte.sillanpaa@oulu.fi To: chemistry@ccl.net Subject: visualization of charges on surface Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, I'd like to plot the electrostatic potential on a cosmo cavity surface. I have performed the calculations using Turbomole, which has the GRID option to plot properties on 3D grids. This is where I get my potential. However, the surface, which in this case is the cosmo-cavity, on which I'd like to map the electrostatic potential, is defined by points in space, that is, their xyz-coordinates. Does anyone know of a program that is able to read these points and create the surface from it? The program I've used till now, gOpenMol, is able to take an isosurface of a property of choice, and map another 3D-grid property on that, but in this case, as my surface is not defined my a 3D grid, this approach does not work. Any suggestions? Cheers, atte.sillanpaa@oulu.fi +358 (0)8 553 1681 (work), KE 368 Dept. of Physical Chemistry +358 (0)40 592 7369 (gsm) Po-BOX 3000 FIN-90014 University of Oulu FINLAND | Entropy requires no maintenance. | From chemistry-request@server.ccl.net Tue Sep 24 04:28:26 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8O8SPw15122 for ; Tue, 24 Sep 2002 04:28:25 -0400 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 17tkz9-0004RR-00; Tue, 24 Sep 2002 08:23:59 +0000 Date: Tue, 24 Sep 2002 08:23:59 +0000 (GMT) From: Szilveszter Juhos To: Rick Venable cc: Computational Chemistry List Subject: Re: CCL:help about the computing ability of my cluster In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 23 Sep 2002, Rick Venable wrote: > + Use Linux 2.2.x kernel and apply the 'tcpfix' patch Is there any effort to make a similar patch for 2.4 kernels? Szilva From chemistry-request@server.ccl.net Mon Sep 23 15:30:22 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8NJUMw23835 for ; Mon, 23 Sep 2002 15:30:22 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id PAA07075; Mon, 23 Sep 2002 15:18:13 -0400 (EDT) Date: Mon, 23 Sep 2002 15:18:13 -0400 From: Rick Venable To: Andrij Baumketner cc: chemistry@ccl.net Subject: Re: CCL:CHARMM: Is there any problem with velocity Verlet in c28b2 ? In-Reply-To: Message-ID: ReplyTo: Rick_Venable@nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII In my initial reply to the original question on NVT dynamics I stated: On Wed, 18 Sep 2002, Rick Venable wrote: > I tried some tests with VVER at one point, with fairly > unsatisfactory results-- plots of the total Hamiltonian vs. time > (which should be flat) had fairly large fluctuations compared to > extended system methods using the CPT keyword. I should note that the large Hamiltonian fluctuations are most likely due to the use of the NOSE thermostat together with VVER algorithm, which I believe is the only way to do NVT with that integrator in CHARMM. (The weak coupling method of Berendsen is not strict NVT, and requires additional heat baths for multiphase systems such as water/octane, lipid bilayers, and a protein in water.) =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Tue Sep 24 11:34:00 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8OFY0w25604 for ; Tue, 24 Sep 2002 11:34:00 -0400 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id LAA10053; Tue, 24 Sep 2002 11:33:50 -0400 (EDT) Sender: richard@cornell.edu Message-ID: <3D9085DD.6530B3CD@cornell.edu> Date: Tue, 24 Sep 2002 11:33:49 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: Atte =?iso-8859-1?Q?Sillanp=E4=E4?= CC: chemistry@ccl.net Subject: Re: CCL:visualization of charges on surface References: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g8OFY0w25605 Atte Sillanpää wrote: > > Hello all, > > I'd like to plot the electrostatic potential on a cosmo cavity > surface. I have performed the calculations using Turbomole, which has > the GRID option to plot properties on 3D grids. This is where I get my > potential. However, the surface, which in this case is the > cosmo-cavity, on which I'd like to map the electrostatic potential, is > defined by points in space, that is, their xyz-coordinates. Does > anyone know of a program that is able to read these points and create > the surface from it? You can use simple trilinear interpolation to map the potential values > from the grid to the points (www.opendx.org can do this), but I assume the real problem you have is that the points do not have a connection table. Triangulating a general 2D surface in 3-space is not trival since there can be genuine ambiguity. There are programs that attempt to do it however. If I recall correctly, some of the early molecular surface codes which generated dot surfaces attempted triangulation in this fashion. I also recall a paper some years ago in a SIGGRAPH journal on this subject but I can't find it at the moment. I'm not familiar with how cosmo cavity is defined. If it is a collection of spheres of given radius, then you may be able to treat them like a bunch of atoms and compute a triangulated surface using a molecular surface algorithm. Good luck. Richard Gillilan MacCHESS, Cornell > The program I've used till now, gOpenMol, is able > to take an isosurface of a property of choice, and map another 3D-grid > property on that, but in this case, as my surface is not defined my a > 3D grid, this approach does not work. > > Any suggestions? > > Cheers, > > atte.sillanpaa@oulu.fi +358 (0)8 553 1681 (work), KE 368 > Dept. of Physical Chemistry +358 (0)40 592 7369 (gsm) > Po-BOX 3000 > FIN-90014 University of Oulu > FINLAND > | Entropy requires no maintenance. | > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Sep 24 15:28:58 2002 Received: from mail.ccmsi.us ([143.132.103.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8OJSww31129 for ; Tue, 24 Sep 2002 15:28:58 -0400 Received: from Falcon [10.30.6.25] by mail.ccmsi.us (SMTPD32-7.07) id ACFA9B006C; Tue, 24 Sep 2002 14:28:58 -0500 Message-ID: <00a101c26400$a15699a0$19061e0a@ccmsi.us> From: "Yevgeniy Podolyan" To: Subject: Registration deadline for CCTCC-11 is October 1 ! Date: Tue, 24 Sep 2002 14:28:58 -0500 Organization: Jackson State University MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Dear Colleagues! This is to remind you that the registration deadline for the 11th Conference on Current Trends in Computational Chemistry is approaching very fast. Only one week has left (the deadline is October 1). Please, visit our conference web site (http://ccmsi.us/cctcc) for details and registration. We hope to see you in November. Sincerely, 11th CCTCC Organizing Committee From chemistry-request@server.ccl.net Tue Sep 24 13:00:39 2002 Received: from sd.accelrys.com ([64.165.22.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8OH0dw27537 for ; Tue, 24 Sep 2002 13:00:39 -0400 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id g8OH8jl12190 for chemistry@ccl.net; Tue, 24 Sep 2002 10:08:45 -0700 From: Jeffrey Nauss Received: from sandmail01.sd.accelrys.com (sandmail01.sd.accelrys.com [172.30.160.90]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id g8OH8jf12181 for ; Tue, 24 Sep 2002 10:08:45 -0700 MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Subject: Accelrys Drug Design Workshops in Cambridge, UK To: Message-ID: Date: Tue, 24 Sep 2002 10:00:32 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 09/24/2002 10:00:34 AM Content-type: text/plain; charset=us-ascii Accelrys Inc. will be holding a series of Rational Drug Design workshops at their European Headquarters in Cambridge, UK, during November 2002. On November 26-27, the "Introduction to Cerius2 for Life Sciences" workshop will be offered. This course provides an overview of molecular modeling techniques for applications in drug design and combinatorial chemistry using the Cerius2 graphical user interface. This workshop is aimed at new customers in the pharmaceutical industry and involved in drug design who would like to begin using modeling in their research. Basic usage of Cerius2 will be examined with an introduction to some of the more advanced applications including QSAR, structure-based drug design, and combinatorial chemistry. A knowledge of basic UNIX commands is required On November 28-29, the "Small Molecule and Drug Design with Cerius2" workshop will be conducted. This course is an advanced workshop for applications in drug design using the Cerius2 graphical user interface. This workshop is aimed at our customers in the pharmaceutical industry and involved in drug design who would like to make more effective use of modeling in their research. QSAR techniques will explored in detail. Also structure-based drug design methodologies will also be described in details. Attendees should either have extensive experience with Cerius2 or have attended the "Introduction to Cerius2 for Life Sciences" workshop. Fees for the 2-day course are $1200 commercial, $900 government, and $660 academic. Registration is on-line at URL http://www.accelrys.com/training/RDD/registration.php. Further detailed information about these and other Accelrys training workshops can be found at the Accelrys website ( http://www.accelrys.com/training). Please do not hesitate to contact me should you have any questions. Thank you very much. Elizabeth Crookenden Training Coordinator + 44 (0) 1223 228691 -- Jeffrey L. Nauss, Ph.D. Manager, Discovery Studio Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss@accelrys.com http://www.accelrys.com/training From chemistry-request@server.ccl.net Tue Sep 24 23:12:21 2002 Received: (from root@localhost) by server.ccl.net (8.11.6/8.11.0) id g8P3CL719317 for chemistry@server.ccl.net; Tue, 24 Sep 2002 23:12:21 -0400 Received: from paoli (62.211.18.137) by smtp2.cp.tin.it (6.5.019) id 3D8FF22F00068B7B; Tue, 24 Sep 2002 21:26:52 +0200 Message-ID: <00b201c26400$8d0221e0$8912d33e@tin.it> From: "Paolo Accomazzi" To: chemistry@ccl.net Cc: "Vittorio Accomazzi" Subject: Molecular Orbitals Visualization Shareware Date: Tue, 24 Sep 2002 21:28:24 +0200 Let me introduce a new shareware software for Molecular Orbitals visualization, which uses a technique called "Volume Rendering" for the 3D visualization of the orbital. It is called Voxel Time Orbital Viewer. Using Volume Rendering the software allows to change the threshold interactively without any recomputation, enhancing interactivity. The process is simple and really straightforward, and facilitate the understanding of the distribution of density in space. You can find more information on how Volume Rendering can enhance orbital Visualization at http://www.voxeltime.com/Pages/OrbitalViewerIntroduction.html and you can download the software from http://www.voxeltime.com/Pages/OrbitalViewer.html Our adresses: For information regarding Volume Rendering technique: voxel@voxeltime.com For questions about orbital file format: paolo@accomazzi.it Best Regards - Paolo Accomazzi ============================= From chemistry-request@server.ccl.net Tue Sep 24 23:18:31 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g8P3IV719526 for ; Tue, 24 Sep 2002 23:18:31 -0400 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id g8P3IWb17824; Tue, 24 Sep 2002 23:18:32 -0400 (EDT) Date: Tue, 24 Sep 2002 23:18:29 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: ECCC9 - March 2003 - Call for Papers Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Tue, 24 Sep 2002 16:20:00 -0400 (EDT) From: Robert Q. Topper To: jkl@ccl.net Cc: TOPPER ROBERT Subject: ECCC9 - March 2003 - Call for Papers (fwd) ***************************************************************************** 9th ELECTRONIC COMPUTATIONAL CHEMISTRY CONFERENCE MARCH 2003 http://eccc9.cooper.edu ***************************************************************************** Robert Q. Topper, Ph.D. email: topper@cooper.edu Associate Professor of Chemistry phone: (212) 353-4378 School of Engineering fax: (212) 353-4341 The Cooper Union for the Advancement of Science and Art subway: take the 6 to Astor Place 51 Astor Place or the N/R to 8th street New York, NY 10003 and you're there! ***************************************************************************** http://www.cooper.edu/engineering/chemechem/ ***************************************************************************** ---------- Forwarded message ---------- Date: Tue, 17 Sep 2002 08:52:43 -0700 (PDT) From: topper@magnum.cooper.edu To: CHEMISTRY@ccl.net Cc: topper@cooper.edu Subject: ECCC9 - March 2003 - Call for Papers ECCC9 MARCH 2003 - Announcement and Call for Papers Dear colleagues, We are very pleased to notify you that the Ninth Electronic Computational Chemistry Conference (ECCC9) will be held March 1 - March 31, 2003, entirely on the Internet, at http://eccc9.cooper.edu . ECCC9 is sponsored by the Cooper Union for the Advancement of Science and Art's Albert Nerken School of Engineering ( http://www.cooper.edu ). As in previous years, the conference is multidisciplinary and covers all aspects of computational and theoretical chemistry, as well as computational molecular biology, computational and theoretical molecular and atomic physics, visualization, cheminformatics and the history of computational chemistry. Participants will be able to view the presentations and discuss them entirely through a web browser. As with the previous eight ECCCs, ECCC9 has NO registration fee and is a completely virtual, online conference. There were 230 registered participants in ECCC8, who perused and discussed 36 presentations by scientists from all around the world (19 nations and 5 continents were represented by the presenting authors alone). The ECCC was originally developed by Steven Bachrach, who also organized the first five meetings. Abstracts for all contributions to ECCC9 will be reviewed by the Scientific Organizing Committee (SOC) to insure novelty, scientific value, and appropriateness for inclusion in the conference. The members of the SOC will be announced shortly. All abstracts will be submitted electronically to the ECCC9 web site. All presentations must be made in HTML format (no PDB or DOC files) and ideally will take full advantage of the interactive nature of the World-Wide Web to present their findings and conclusions. In addition to completed work, work in progress is also acceptable for an ECCC9 presentation. Authors may choose to either serve their contributions from their own local web site, or may request us to serve them from our own server. Uploaded contributions will be removed from our server at the end of ECCC9. As in ECCC8, a single week-long "interactive" session will be part of the conference. This session will be held via asynchronous posting of questions to the conference site, which authors can choose to receive either at the site, at their personal email account, or both. All authors must commit to having at least one coauthor available to answer questions (i.e. by checking the discussion board at least once daily) during the "interactive" session to provide timely responses (within approximately 24 hours) to any questions that conferees may have about their online presentation. Failure to participate fully in the interactive session may result in a presentation being withdrawn from the conference. Important dates for ECCC9 are: November 11, 2002 - Registration opens; abstracts of papers accepted December 13, 2002 - Abstracts of presentations due February 24, 2003 - Final presentations due online March 1, 2003 - Conference begins March 17, 2003 - Interactive Session begins March 24, 2003 - Interactive Session ends April 1, 2003 - ECCC9 ends Please note that the deadline for receipt of an abstract for the conference is December 13, 2003. Please also note that "posters" which are not completely ready by the beginning of the conference may be considered to be withdrawn. We invite all interested parties to contribute to ECCC9 and participate! Please share this announcement with your colleagues and post it wherever appropriate so that ECCC can continue to thrive and be a vital meeting for the international computational chemistry community. Also, please feel free to email us with your questions or comments. Robert Topper Cooper Union Department of Chemistry ECCC9 Principal Organizer topper@cooper.edu Christopher Lent and Robert Hopkins Cooper Union Computer Center and the Brooks Engineering Design Center School of Engineering The Cooper Union for the Advancement of Science and Art 51 Astor Place New York, NY 10003