From chemistry-request@server.ccl.net Thu Feb 7 04:25:28 2002 Received: from web13608.mail.yahoo.com ([216.136.175.119]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g179PSc27238 for ; Thu, 7 Feb 2002 04:25:28 -0500 Message-ID: <20020207092512.58654.qmail@web13608.mail.yahoo.com> Received: from [129.215.220.29] by web13608.mail.yahoo.com via HTTP; Thu, 07 Feb 2002 09:25:12 GMT Date: Thu, 7 Feb 2002 09:25:12 +0000 (GMT) From: =?iso-8859-1?q?tj=20su?= Subject: The Z-matrix of C60 To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, Can anyone give us the Z-matrix of C60 as well as that of carbon nanotubes? Any suggestions will be appreciated. David P. Rickover __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page > from News and Sport to Email and Music Charts http://uk.my.yahoo.com From chemistry-request@server.ccl.net Wed Feb 6 22:59:28 2002 Received: from mercury.sunesis.com ([64.240.200.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g173xSc17492 for ; Wed, 6 Feb 2002 22:59:28 -0500 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: Announce: PyMOL v0.78 X-MimeOLE: Produced By Microsoft Exchange V6.0.4712.0 Date: Wed, 6 Feb 2002 19:59:09 -0800 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Announce: VMD 1.7.2 (Windows-only GUI update) is available Thread-Index: AcGveU2KwescmfQ6RMe8GEXtKc0evwAABbng From: "DeLano, Warren" To: Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g173xSc17493 PyMOL version 0.78 is now released for download from http://pymol.sf.net . RPM packages are available for quick installation under Linux RedHat 7.x, and Windows and IRIX binaries are provided along with source code. PyMOL is the most powerful free molecular graphics system currently available as unrestricted open-source software. PyMOL works great as a stand-alone viewer but is also well suited for infrastructure given its robust Python API and its ability to run as an anonymous module. Unlike other popular free graphics programs, (such as VMD, RasMOL, SwissPDBViewer, Chime, and the Accelrys Viewer), you can use PyMOL for any purpose, and you are permitted to modify and redistribute derivates of PyMOL without cost or without being required to release derivative source code (though it is encouraged). Thus, PyMOL is ideally suited for corporate applications where license restrictions are of paramount concern. Software companies, start-ups, biotech, and big-pharma can all benefit from using PyMOL for 3D molecular visualization on low-cost hardware. Of particular note, version 0.78 contains an early release of PyMOL's remarkable "sculpting" capability. With "auto-sculpting" enabled in Editing Mode, you can simply CTRL-Click-and-Drag atoms to where you want them to be, and then PyMOL will do its best to make sure that bonds, angles, planarity, chirality, and van der Waals radii are maintained. It is not particularly realistic, but it sure looks cool -- as if your molecules were made of "gummy worms" candy! With its built-in molecular building and manipulation features, PyMOL can now serve as a reasonable front-end to your favorite mechanics and minimization engine (i.e. BatchMin). Alternatively, you can just use PyMOL to view trajectories, docking runs, or to make exceptional figures and animations. In the long run, PyMOL aims to match the molecular graphics quality of Molscript/Raster3D, the molecular editing capabilities of MacroModel, the animations and performance of VMD, the electrostatic surfaces of Grasp, the macromolecular crystallography of O, the interactivity of Sculpt, and the programmability of M.O.E. (but using Python instead of SVL), all in one FREE & UNRESTRICTED OPEN-SOURCE package. If you haven't yet seen PyMOL in action recently, you will be surprised how far it has progressed toward this goal... Cheers, Warren L. DeLano, Ph.D. PyMOL Creator DeLano Scientific PS. If you try PyMOL and like it, then please consider helping out! While the PyMOL open-source community is growing rapidly, more involvement is needed in order to help the project achieve longevity. From chemistry-request@server.ccl.net Thu Feb 7 12:46:57 2002 Received: from email03.aon.at ([195.3.96.115]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g17Hkvc07088 for ; Thu, 7 Feb 2002 12:46:57 -0500 Received: (qmail 637844 invoked from network); 7 Feb 2002 17:46:36 -0000 Received: from n769p007.adsl.highway.telekom.at (HELO pc1) ([62.47.40.7]) (envelope-sender ) by qmail3.highway.telekom.at (qmail-ldap-1.03) with SMTP for ; 7 Feb 2002 17:46:36 -0000 To: chemistry@ccl.net Subject: QM program calculating forces exerted on point charges? From: Hannes Loeffler Date: 07 Feb 2002 18:46:35 +0100 Message-ID: <87wuxpi3r8.fsf@uibk.ac.at> Lines: 20 User-Agent: Gnus/5.0808 (Gnus v5.8.8) XEmacs/21.4 (Common Lisp) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, many QM programs allow to calculate energy and gradients of a molecule under the influence of point charges. For typical QM/MM calculations (coupling term) it would be necessary to also calculate the gradients/forces exerted _on_ these point charges. Currently I'm not aware of many programs (maybe I'm missing something?) doing that: GAMESS-US for example has been interfaced to CHARMM, but obviously the calculation of point charge gradients is a special extension for CHARMM (the GAMESS source code has to be prepared for that and requires CHARMM to do proper setup). This makes it somewhat difficult to adapt the program for our own purposes. Now I wonder if there are any QM programs which output these additional gradients by default (or probably by user request). Since many QM programs already allow the calculation of energy/gradients with point charges, would it be difficult to enhance the program to compute these additional gradient? Thanks for any help, Hannes. From chemistry-request@server.ccl.net Thu Feb 7 10:29:37 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g17FTbc21647 for ; Thu, 7 Feb 2002 10:29:37 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id KAA00963; Thu, 7 Feb 2002 10:29:37 -0500 (EST) Date: Thu, 7 Feb 2002 10:29:34 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: 2002.08.04 Drug Discovery Technology (TM) 2002, Boston Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8BIT ---------- Forwarded message ---------- Date: Thu, 7 Feb 2002 09:30:19 -0500 From: "Prudhomme, James" To: jkl@ccl.net Subject: Suggested Conference Posting: Drug Discovery Technology (TM) 2002 Conference Title: IBC’s 7th Annual World Congress: Drug Discovery Technology (TM) 2002 Organizer: IBC USA Conferences, Inc. Conference Dates: August 4-9, 2002 Exhibition Dates: August 5-7, 2002 Location: Boston, MA Venue: The Hynes Convention Center Event’s Website: http://www.drugdisc.com/?source=us2-44 Event Description: Drug Discovery Technology ™ is the world’s leading conference and exposition to provide information about the newest drug discovery technologies and applications of these technologies. In 2001, there were more than 5,200 attendees. Over 100 speakers will discuss new scientific data, and how they are implementing new technologies and techniques in actual drug discovery research projects. In addition, these one day sessions will be offered: “Creative Partnering and Deal-Making in Drug Discovery” and “Information Technology for Drug Discovery and the Life Sciences.” The expanded exhibit hall will include more than 350 booths. Contact information: Client Services Dept. IBC USA Conferences, Inc. 1 Research Drive, Suite 400A Westborough, MA 01581-5195 Tel: (508) 616-5550 X1004 Fax: (508) 616-5522 E-mail: reg@ibcusa.com Sincerely, Jim Prudhomme IBC USA Conferences, Inc. From chemistry-request@server.ccl.net Thu Feb 7 14:47:04 2002 Received: from web13403.mail.yahoo.com ([216.136.175.61]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g17Jl3c22290 for ; Thu, 7 Feb 2002 14:47:03 -0500 Message-ID: <20020207194643.11265.qmail@web13403.mail.yahoo.com> Received: from [67.17.165.2] by web13403.mail.yahoo.com via HTTP; Thu, 07 Feb 2002 11:46:43 PST Date: Thu, 7 Feb 2002 11:46:43 -0800 (PST) From: quch quch Subject: compile AMBER on cygwin? To: amber@heimdal.compchem.ucsf.edu Cc: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii hello, has anyone tried to compile AMBER on Cygwin successfully? I would appreciate it if you could share your knowledge. thanks. qc __________________________________________________ Do You Yahoo!? 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Greetings! http://greetings.yahoo.com From chemistry-request@server.ccl.net Thu Feb 7 10:13:47 2002 Received: from smtp2.libero.it ([193.70.192.52]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g17FDlc21326 for ; Thu, 7 Feb 2002 10:13:47 -0500 Received: from k7 (151.29.218.99) by smtp2.libero.it (6.0.040) id 3C5840440053BB8E for chemistry@ccl.net; Thu, 7 Feb 2002 16:13:17 +0100 From: "Elena Fioravanzo" To: "CCL" Subject: exclusion volume Date: Thu, 7 Feb 2002 16:16:31 +0100 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0006_01C1AFF2.CDCB8C60" 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 This is a multi-part message in MIME format. ------=_NextPart_000_0006_01C1AFF2.CDCB8C60 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Dear CCLers, is there any freeware software which is able to calculate molecular volume and exclusion volume? I thank you all in advance for your help Elena Fioravanzo ------------------------------------------------------ dott. Elena Fioravanzo - Consultant S.IN - Soluzioni Informatiche S.a.s. ------=_NextPart_000_0006_01C1AFF2.CDCB8C60 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear=20 CCLers,
 
is = there any=20 freeware software which is able to calculate molecular volume and = exclusion=20 volume?
I = thank you all in=20 advance for your help
 
Elena=20 Fioravanzo
 
------------------------------------------------------
dott. Elena Fioravanzo - = Consultant
S.IN -=20 Soluzioni Informatiche S.a.s.
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