From owner-chemistry@ccl.net Sun Dec 18 10:44:01 2005 From: "Guosheng Wu wu_guosheng2002%yahoo.com" To: CCL Subject: CCL: Free software for smarts substructure search Message-Id: <-30359-051217231627-20104-oa2vGKIodCz/FWPdZTx7Xw]|[server.ccl.net> X-Original-From: Guosheng Wu Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 17 Dec 2005 19:16:20 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Guosheng Wu [wu_guosheng2002^yahoo.com] A friend of mine is a organic chemist, with little software or programming experience. He is looking for some Windows-based free software that can run draw molecules in 2D, and run basic substructure database search using SMARTS. Any information will be appreciated. -Guosheng __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Sun Dec 18 11:19:01 2005 From: "Jinsong Zhao jszhao*|*mail.hzau.edu.cn" To: CCL Subject: CCL:G: adsorption, ab initio study Message-Id: <-30360-051218075732-14026-LDiCxc5tLExStP5g7nfXCQ%x%server.ccl.net> X-Original-From: "Jinsong Zhao" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Sun, 18 Dec 2005 20:37:12 +0800 Mime-Version: 1.0 Sent to CCL by: "Jinsong Zhao" [jszhao..mail.hzau.edu.cn] Thank you very much for your response. Would you like to recommend some introductory readings on this topic? I am a really newcomer to this field. Thanks again for your kindly help. Best wishes, Jinsong Zhao >Sent to CCL by: Yun Wang [wangyun22|yahoo.com] > >It depents on your systems. If you study the >adsorption on solid surface with periodic symmetry, >slab model is better. There are several free software: >CPMD, PWscf,FHI98md etc. If you want to employ cluter >model, you can do calculation with Gaussian, Gamess >etc. Both of them need many computation time. The >computer should be very good. > >Best wishes. > >Yun Wang From owner-chemistry@ccl.net Sun Dec 18 15:09:00 2005 From: "Jeff Nauss jnauss _ accelrys.com" To: CCL Subject: CCL: Force feild of cyclic oligosaccharides Message-Id: <-30361-051218150809-28398-5ntI5CsinuADGjqzj/Ti/Q]=[server.ccl.net> X-Original-From: Jeff Nauss Content-Type: multipart/alternative; boundary="=_alternative 006E9D92882570DB_=" Date: Sun, 18 Dec 2005 12:07:19 -0800 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss+*+accelrys.com] This is a multipart message in MIME format. --=_alternative 006E9D92882570DB_= Content-Type: text/plain; charset="US-ASCII" owner-chemistry_+_ccl.net wrote on 12/17/2005 09:07:45 AM: > I am sudipta an M.sc. student at IIT-KGP, I am doing my final year > project about the dynamics of different non polar solvent around a > cyclic oligosaccharides. Could anyone help me to know, how i get the > force field of different cyclic oligosaccharides. I will appreaciate > your kind help...... You may want to look at the CSFF force field at http://hydrogen.cem.uct.ac.za/compchem/mkuttel/mkuttel.htm. Jeff -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training --=_alternative 006E9D92882570DB_= Content-Type: text/html; charset="US-ASCII"
owner-chemistry_+_ccl.net wrote on 12/17/2005 09:07:45 AM:

> I am sudipta an M.sc. student at IIT-KGP, I am doing my final year
> project about the dynamics of different non polar solvent around a
> cyclic oligosaccharides. Could anyone help me to know, how i get the
> force field of different cyclic oligosaccharides. I will appreaciate
> your kind help......

You may want to look at the CSFF force field at http://hydrogen.cem.uct.ac.za/compchem/mkuttel/mkuttel.htm.
Jeff
--
Jeffrey L. Nauss, Ph.D.
Lead Training Scientist
Accelrys
10188 Telesis Court, Suite 100
San Diego, CA 92121-4779

Phone: +1-858-799-5555
Fax: +1-858-799-5100
http://www.accelrys.com/training
--=_alternative 006E9D92882570DB_=-- From owner-chemistry@ccl.net Sun Dec 18 21:17:00 2005 From: "William F. Polik polik__hope.edu" To: CCL Subject: CCL:G: OT:Fedora Core 3 or 4 and Gaussian - exec problem Message-Id: <-30362-051218200204-16152-PXmJ0aeRfzZTgytXHTxJJA~~server.ccl.net> X-Original-From: "William F. Polik" Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Sun, 18 Dec 2005 19:23:01 -0500 Mime-Version: 1.0 Sent to CCL by: "William F. Polik" [polik~~hope.edu] At 05:55 PM 12/16/2005, you wrote: >Erroneous write during file extend. write 1896 instead of 4096 >Probably out of disk space. This error occurs when g98 or g03 runs on Fedora Core 3 and higher due to a change in the way memory is allocated by the c library and kernel. Briefly, gaussian is requesting memory with the sbrk() function, which not longer allocates memory contiguously. You must tell gaussian to not use sbrk(), but instead to use malloc(). The fix is to add the following line near the top of mdutil.c and recompile: #define NO_SBRK For details and other additional important tips on compiling g03 on FC, see http://forums.fedoraforum.org/archive/index.php/t-1895.html Will Polik ================================ Dr. William F. Polik Hofma Professor of Chemistry Department of Chemistry Hope College 35 East 12th Street Holland, MI 49422-9000 USA polik#,#hope.edu http://www.chem.hope.edu/~polik tel: (616) 395-7639 fax: (616) 395-7118 ================================ From owner-chemistry@ccl.net Sun Dec 18 22:49:00 2005 From: "William F. Polik polik[#]hope.edu" To: CCL Subject: CCL:G: WebMO 6.0 Released Message-Id: <-30363-051218224655-17218-434RaM2qmPPcJqY5UxkYmA^-^server.ccl.net> X-Original-From: "William F. Polik" Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Sun, 18 Dec 2005 22:42:17 -0500 Mime-Version: 1.0 Sent to CCL by: "William F. Polik" [polik**hope.edu] WEBMO 6.0 RELEASED ================== WebMO version 6.0 has been officially released and is available for FREE download at http://www.webmo.net/download Since WebMO is web-based, you can first try it out without installing any software on your computer! Simply go to http://www.webmo.net/demo click the WebMO Demo Server link, login as username="guest" and password="guest" (without the quotes). WEBMO OVERVIEW ============== WebMO is a FREE web-based interface to popular computational chemistry programs including Gamess, Gaussian, Molpro, Mopac, Nwchem, Qchem, and Tinker. WebMO permits users to build 3-D molecular structures, submit multiple jobs, monitor job progress, and view text and graphical results all from within a standard Windows, Mac, or Linux web-browser. To date, over 5,000 copies of WebMO have been downloaded worldwide for teaching and research. NEW FEATURES ============ New features in WebMO version 6.0 include: * New user interface with drop down menus, modern icons, tabbed dialogs, and more efficient screen usage * New graphics engine for greatly enhanced 3D performance and image quality * Editor keyboard shortcuts * Animations of vibrational modes, geometry optimization, and IRC pathways * Updated support for latest versions of computational chemistry programs * New MOViewer for visualization of molecular orbitals, NBO's, and isosurfaces (Pro) * Many user interface enhancements and bug fixes WINDOWS, MAC, & LINUX SUPPORT ============================= The WebMO team has been hard at work expanding the range of supported computer platforms and web browsers. WebMO now supports: * Windows: Internet Explorer, Firefox, Netscape, Opera * Mac OS X: Safari, Firefox, Omniweb, Camino, Opera * Linux: Netscape, Firefox, Opera For details, see http://www.webmo.net/support/browsers.html MOVIEWER ENHANCEMENTS ===================== MOViewer is included with WebMO Pro for visualization of molecular orbitals, NBO's, isosurfaces, electrophilic/nucleophilic frontier densities, and electrostatic potential surfaces. A completely new architecture based on Java Web Start technology is being used for MOViewer which * Installs automatically with no user interaction when viewing orbitals or surfaces * Runs with equal ease on Windows, Mac OS X, and Unix/Linux clients In addition to running on all major platforms, the new MOViewer also supports * Clipping planes, movable contour slices, and semi-transparent surfaces to visualize data in 3-D * Export of publication quality POV-Ray image files (www.povray.org) Enjoy! The WebMO Team ************************************************ WebMO (FREE!): http://www.webmo.net WebMO Pro: http://www.webmo.net/pro Working Demo: http://www.webmo.net/demo Support: http://www.webmo.net/support ************************************************