From owner-chemistry@ccl.net Mon Feb 5 04:32:00 2007 From: "Young Leh youngleh a gmail.com" To: CCL Subject: CCL: Visualization Freeware Message-Id: <-33522-070205043004-11212-bC0iaebMnKWNHgRZX4OMxw(-)server.ccl.net> X-Original-From: "Young Leh" Date: Mon, 5 Feb 2007 04:30:01 -0500 Sent to CCL by: "Young Leh" [youngleh{=}gmail.com] Dear CCLer, I am now looking for a visualization freeware that can be used to produce 3D molecular pictures with publishable quality. Could somebody please give me some hints? Thanks and have a great day. Young Leh From owner-chemistry@ccl.net Mon Feb 5 09:08:01 2007 From: "Bjoern Windshuegel bjorn.windshugel ~~ uku.fi" To: CCL Subject: CCL: Visualization Freeware Message-Id: <-33523-070205070539-15233-Y1mcJdjh87nID/ukXR2+og+*+server.ccl.net> X-Original-From: Bjoern Windshuegel Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Mon, 5 Feb 2007 13:33:45 +0200 MIME-Version: 1.0 Sent to CCL by: Bjoern Windshuegel [bjorn.windshugel*|*uku.fi] Check out VMD and PyMOL. I prefer VMD, you can render pictures with high quality using external renderers like POV-Ray. Best regards, Björn > Sent to CCL by: "Young Leh" [youngleh{=}gmail.com] > Dear CCLer, > > I am now looking for a visualization freeware that can be used to produce > 3D molecular pictures with publishable quality. Could somebody please give > me some hints? > > Thanks and have a great day. > > Young Leh-- Dr. Björn Windshügel Department of Pharmaceutical Chemistry University of Kuopio P.O. Box 1627 70211 Kuopio, FINLAND Email: bjorn.windshugel%x%uku.fi Phone: (+358) 17 162463 Fax: (+358) 17 162456 Web: www.uku.fi/farmasia/fake/modelling/index.shtml From owner-chemistry@ccl.net Mon Feb 5 09:43:00 2007 From: "mike bucholtz bucholtz001---gannon.edu" To: CCL Subject: CCL: autodock Message-Id: <-33524-070203104213-30653-Wb9qQF+T547Z07J+/KPpew-*-server.ccl.net> X-Original-From: "mike bucholtz" Date: Sat, 3 Feb 2007 10:42:09 -0500 Sent to CCL by: "mike bucholtz" [bucholtz001,gannon.edu] I teach at the undergrad level and we are trying to get Autodock(Scripps) to run. Our IT loaded it but the fellow that loaded it left the university. We have Tools, Autogrid and Autodock all loaded on a new PC. We have the tutorial and ran the tutorial pdb files for both protein and ligand(ind.pdb) and saved all the pdb files with the proper pdb file endings and we put them in a folder on the desktop. We reach the step with the widget which provides the path file and we cannot get Autogrid to run the program. This widget has five entries and is at the point where the Autogrid calculation should be started. How can I get the three programs and the stored pdb files for the protein and the ligand to find each other and execute the docking procedure? Thank you. Michael Bucholtz Department of Chemistry Gannon University Erie, Pa bucholtz001-.-gannon.edu From owner-chemistry@ccl.net Mon Feb 5 10:50:00 2007 From: "Jeff Nauss jnauss|accelrys.com" To: CCL Subject: CCL: Visualization Freeware Message-Id: <-33525-070205104818-15590-SzplGWhxhUG0Jo3XEfmawA- -server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Mon, 5 Feb 2007 07:47:16 -0800 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss|a|accelrys.com] "Young Leh" [youngleh{=}gmail.com] wrote on 02/05/2007 01:30:01 AM: > I am now looking for a visualization freeware that can be used to > produce 3D molecular pictures with publishable quality. Could > somebody please give me some hints? You may want to consider Discovery Studio Visualizer. http://www.accelrys.com/products/downloads/ds_visualizer/index.html 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/services/training/ From owner-chemistry@ccl.net Mon Feb 5 11:25:01 2007 From: "Aniko Simon aniko(a)simbiosys.ca" To: CCL Subject: CCL: Visualization Freeware Message-Id: <-33526-070205111805-31191-5QGIKkhQf/0u6MisCydo7g*o*server.ccl.net> X-Original-From: "Aniko Simon" Date: Mon, 5 Feb 2007 11:18:02 -0500 Sent to CCL by: "Aniko Simon" [aniko(a)simbiosys.ca] You could also try : CheVi - that's a new 3D visualization tool free for everyone. http://www.simbiosys.ca/chevi/index.html Produces high quality (high res) images for publishing. There is a setting specifically for choosing the resolution in the export options which could be as high as many mega pixels. Best regards, Aniko From owner-chemistry@ccl.net Mon Feb 5 12:00:00 2007 From: "Shobe, David David.Shobe::sud-chemie.com" To: CCL Subject: CCL:G: Error when writing wfn on gaussian 03 Message-Id: <-33527-070205114202-16736-ShQ4AqgMEs482NVYDkxPDA[#]server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 5 Feb 2007 15:48:18 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe*_*sud-chemie.com] I think the AIM2000 error *is* related. The input routine of AIM2000 would not be able to process the ***'s. Regards, --David Shobe Süd-Chemie, Inc. Attention to detial is essentail. -----Original Message----- > From: owner-chemistry]|[ccl.net [mailto:owner-chemistry]|[ccl.net] Sent: Sunday, February 04, 2007 11:19 AM To: Shobe, David Subject: CCL:G: Error when writing wfn on gaussian 03 Sent to CCL by: "Petrina Kamya" [petrina.k : gmail.com] Hello, I would like to thank you all who responded to my query and summarize some of the replies I got for your information. 1)What you found in Gaussian log file (output file) after the 999th eigen states was not any error or mistakes. In Gaussian program the format statement for the eigen states is only for 3 integers. So if you have more than 999 eigen states, the formatting will not be correct and they print the eigen states for 1000 as only 3 stars (***). The solution is, you can change the formatting statement in Gaussian source file. However, most likely you will not need the 1000th eigen states unless, you are seriously looking for something beyond 1000th eg. states. Anyway, whatever important information (eigen values) will be written on the next column. Only thing, you have to manually check the states beyond 1000 eg. states. 2) Try replacing the *** with appropriate numbers, e.g. 1000, 1001, etc. 3) In the log file, the problem has to do with the integer definition (I believe it can only handle three places). You may have have come across a similar thing in frequency calculations and forces during optimization. As for the AIM2000 error, I'm not sure of they are related - have you checked into the program limitations (i.e., number of atomic centres and number of basis functions, etc.). For example, the demo version is limited to a max of 8 nuclei, 14 orbitals and 128 primitives. Thanks again! Petrinahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Mon Feb 5 12:39:02 2007 From: "Shobe, David David.Shobe*|*sud-chemie.com" To: CCL Subject: CCL: bond lengths and exp data Message-Id: <-33528-070205120153-29767-rkNcuERPBErIcNgvPyaFjg[-]server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 5 Feb 2007 15:41:35 +0100 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe::sud-chemie.com] If by dimers you mean diatomic molecules, there is a web site: DiRef Database http://diref.uwaterloo.ca/admin_login.html This site doesn't give bond lenghts and energies directly, but it will give you a bibliography of papers on the diatomic molecule you specify, which you would then have to consult. Regards, --David Shobe Süd-Chemie, Inc. Attention to detial is essentail. -----Original Message----- > From: owner-chemistry#ccl.net [mailto:owner-chemistry#ccl.net] Sent: Saturday, February 03, 2007 2:42 AM To: Shobe, David Subject: CCL: bond lengths and exp data Sent to CCL by: "soumya s" [soumya_samineni|a|rediff.com] Hi all... Where can i find tabulated experimental data on dimer (homo and hetero) bond lenghts and disassociation energies, with which i can compare my computational data. It will be nice, if some one can provide the table if they have one with them sry for the trouble.. thanx in advance soumyahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Mon Feb 5 13:10:00 2007 From: "Elaine Ching-su Meng meng:_:cgl.ucsf.edu" To: CCL Subject: CCL: Visualization Freeware Message-Id: <-33529-070205123646-24185-4AyahxnjTYweg7qP/3y44w{}server.ccl.net> X-Original-From: "Elaine Ching-su Meng" Date: Mon, 5 Feb 2007 12:36:43 -0500 Sent to CCL by: "Elaine Ching-su Meng" [meng|cgl.ucsf.edu] You could try Chimera (free for noncommercial use): http://www.cgl.ucsf.edu/chimera/ Images can be saved with arbitrarily high resolution, or you can export the scene as a file for POV-ray. Manual page for image-saving: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/print.html "Images for Publication" tutorial: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html From owner-chemistry@ccl.net Mon Feb 5 13:45:00 2007 From: "Jim Harrison jim456harrison- -yahoo.com" To: CCL Subject: CCL:G: Gaussian - memory allocations Message-Id: <-33530-070205131826-19546-k9O1BPVCf1+lObylc3KCPg%server.ccl.net> X-Original-From: Jim Harrison Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1365387081-1170699482=:94932" Date: Mon, 5 Feb 2007 10:18:02 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Jim Harrison [jim456harrison|,|yahoo.com] --0-1365387081-1170699482=:94932 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all My question is on memory allocation for Gaussian B3LYP method. Can I determine before the calculation the right memory allocation of a particular molecule. Many articles on the web specify memory allocation can be determined from "NReg" in the output. I have try them for many molecules especially diatomics and it really works. However, the "Nreg" does not appear for many molecules of more than 4 atoms even when I increase the memory capacity. I have to perform calculations for more than 100 molecules. Can I determine approximately the amount of time such calculations will take. Thanking you all Jim --------------------------------- TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. --0-1365387081-1170699482=:94932 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all
My question is on memory allocation for Gaussian B3LYP method. Can I determine before the calculation the right memory allocation of a particular molecule. Many articles on the web specify memory allocation can be determined from "NReg" in the output. I have try them for many molecules especially diatomics and it really works. However, the "Nreg" does not appear for many molecules of more than 4 atoms even when I increase the memory capacity.
I have to perform calculations for more than 100 molecules. Can I determine approximately the amount of time such calculations will take.

Thanking you all
Jim

TV dinner still cooling?
Check out "Tonight's Picks" on Yahoo! TV. --0-1365387081-1170699482=:94932-- From owner-chemistry@ccl.net Mon Feb 5 14:54:00 2007 From: "Gert Kiss mail++gertkiss.de" To: CCL Subject: CCL: autodock Message-Id: <-33531-070205135809-17998-M5Thqmgj8FqlrQJBYaqvfw*server.ccl.net> X-Original-From: "Gert Kiss" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 5 Feb 2007 10:10:47 -0800 MIME-Version: 1.0 Sent to CCL by: "Gert Kiss" [mail!^!gertkiss.de] Michael, I'm assuming that you're using Windows as an operating system. Make sure that the correct paths to the autogrid and autodock executables are provided to autodock tools (ADT). You can check this by clicking on "Run", "Host Preferences". Let me know if that does the trick, Gert -----Original Message----- > From: owner-chemistry.:.ccl.net [mailto:owner-chemistry.:.ccl.net] Sent: Saturday, February 03, 2007 7:42 AM To: Kiss, Gert Subject: CCL: autodock Sent to CCL by: "mike bucholtz" [bucholtz001,gannon.edu] I teach at the undergrad level and we are trying to get Autodock(Scripps) to run. Our IT loaded it but the fellow that loaded it left the university. We have Tools, Autogrid and Autodock all loaded on a new PC. We have the tutorial and ran the tutorial pdb files for both protein and ligand(ind.pdb) and saved all the pdb files with the proper pdb file endings and we put them in a folder on the desktop. We reach the step with the widget which provides the path file and we cannot get Autogrid to run the program. This widget has five entries and is at the point where the Autogrid calculation should be started. How can I get the three programs and the stored pdb files for the protein and the ligand to find each other and execute the docking procedure? Thank you. Michael Bucholtz Department of Chemistry Gannon University Erie, Pa bucholtz001[#]gannon.eduhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Feb 5 21:19:01 2007 From: "Heidi Klein hklein _ schrodinger.com" To: CCL Subject: CCL: Visualization Freeware Message-Id: <-33532-070205180035-20591-IknmhraDRfwvbOmEBWl+qw||server.ccl.net> X-Original-From: "Heidi Klein" Date: Mon, 5 Feb 2007 18:00:32 -0500 Sent to CCL by: "Heidi Klein" [hklein|schrodinger.com] Hello Young Leh, Schrodinger provides Maestro at no charge to academic users. Maestro is an all-purpose molecular modeling environment that includes a versatile builder with the capabilities you describe and more. Maestro's easy-to-use design is the front end to many other powerful tools. To register and download your own copy, please visit http://www.schrodinger.com/getmaestro. Best Regards, Heidi Klein ****************************** Heidi Klein Schrodinger 101 SW Main Street, Suite 1300 Portland, OR 97204 Phone: 503-299-1150 ext. 113 Cell: 503-803-0494 Fax: 503-299-4532 Email: hklein#,#schrodinger.com ****************************** From owner-chemistry@ccl.net Mon Feb 5 22:50:00 2007 From: "Masahiko Suenaga alohascc#mbox.nc.kyushu-u.ac.jp" To: CCL Subject: CCL:G: Visualization Freeware Message-Id: <-33533-070205224650-5226-PFxl7IkLy+3yiAjOygUEsg%%server.ccl.net> X-Original-From: "Masahiko Suenaga" Date: Mon, 5 Feb 2007 22:46:46 -0500 Sent to CCL by: "Masahiko Suenaga" [alohascc###mbox.nc.kyushu-u.ac.jp] Try Facio. http://www1.bbiq.jp/zzzfelis/Facio.html Facio is a freeware for molecular modeling and vizualization of quantum chemical calculations with Gaussian and GAMESS. Since it's an OpenGL-based graphics software, 3D molecular pictures with publishable quality are easily produced with Facio. Best regards, Masahiko Suenaga, Ph.D. Department of Chemistry, Faculty of Sciences, Kyushu University, Japan