From owner-chemistry@ccl.net Tue Oct 30 04:21:00 2007 From: "Dr. Niharendu Choudhury nihcho/./barc.gov.in" To: CCL Subject: CCL: The xyz of fullerenes Message-Id: <-35523-071030012130-16519-PQpIwvNQopYT19nGeOWqnQ,,server.ccl.net> X-Original-From: "Dr. Niharendu Choudhury" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 30 Oct 2007 10:04:43 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Dr. Niharendu Choudhury" [nihcho*|*barc.gov.in] There are many modeler for CNTs such as nanotube modeler and tubegen online. Please perform a google search and reach the related websites. Niharendu Choudhury Quoting "John W Daily john.daily]-[colorado.edu" : > Check out > > http://www.personal.rdg.ac.uk/~scsharip/tubes.htm > > http://www.jcrystal.com/products/wincnt/ > > > On Oct 28, 2007, at 9:19 AM, yorth kos yortama2003^_^yahoo.ca wrote: > > > > > > > Note: forwarded message attached. > > > > Ask a question on any topic and get answers from real people. Go to > > Yahoo! Answers. > > > > Date: October 21, 2007 7:36:28 AM MDT > > > > > > Subject: The caretesian coordintes of fullerenes > > To: CCL Subscribers > > MIME-Version: 1.0 > > Content-Type: multipart/alternative; > > boundary="0-1024001970-1192973788=:19196" > > Content-Transfer-Encoding: 8bit > > Content-Length: 512 > > > > --0-1024001970-1192973788=:19196 > > Content-Type: text/plain; charset=iso-8859-1 > > Content-Transfer-Encoding: 8bit > > > > Dear Folks > > > > I'm interested to have a full information regarding to the > > Cartesian coordinates(xyz) of different carbon nanotubes and their > > derivatives.It is appreciated if anyone could kindly give me a > > clear address about them . > > > > Thanks so much in advance > > Best wishes > > Hossein > > > > > > --------------------------------- > > All new Yahoo! Mail - > > --------------------------------- > > Get a sneak peak at messages with a handy reading pane. > > --0-1024001970-1192973788=:19196 > > Content-Type: text/html; charset=iso-8859-1 > > Content-Transfer-Encoding: 8bit > > > >
Dear Folks
 
I'm interested to > > have a full information regarding to the Cartesian coordinates(xyz) > > of different carbon nanotubes and their derivatives.It is > > appreciated if anyone could kindly give me a clear address about > > them .
 
Thanks so much in advance > DIV>
Best wishes
Hossein

> >

All new Yahoo! Mail - > b> > >
Get a sneak peak at messages with a handy reading pane. > > --0-1024001970-1192973788=:19196-- > > > > > > ************************************************************************* * * * Dr. Niharendu Choudhury Tel: 91-22-2559 5089 * * Theoretical Chemistry Section, Fax: 91-22-2550 5151 * * RC & CD Division, Chemistry Group, 91-22-2551-9613 * * Mod. Lab, Email: nihcho-.-barc.gov.in * * Trombay, Mumbai-400 085 * * INDIA * * * * Residence Tel. No. 91-22-2552 7832 * ************************************************************************* ------------------------------------------------- From owner-chemistry@ccl.net Tue Oct 30 05:47:01 2007 From: "Raji Raji raji%a%anal.chem.tohoku.ac.jp" To: CCL Subject: CCL: TDDFT and Charge Transfer Transitions Message-Id: <-35524-071030052521-10821-oj7Mg8XXulgAHnqT96mKKw[]server.ccl.net> X-Original-From: "Raji Raji" Date: Tue, 30 Oct 2007 05:25:16 -0400 Sent to CCL by: "Raji Raji" [raji~!~anal.chem.tohoku.ac.jp] Dear CCL Members, I know that TDDFT may underestimate the energy of charge transfer transitions. But i wonder whether it can underestimte the energy of charge transfer transition which is about 120 nm (TDDFT calculated) below than the transition of interest? This is equal to about 1eV. If it is so, then is there any way to rectify this? At present I am not interested in other methods like CIS. I want to investigate the charge transfer transitions using TDDFT. Just qualitative results are enough. Please give me your comments and suggestions on this. Thank you very much in advance. Raji. From owner-chemistry@ccl.net Tue Oct 30 07:51:00 2007 From: "Naser Eltaher eltayeb nasertaha90 ~ yahoo.co.uk" To: CCL Subject: CCL: Molecular Orbital Composition Message-Id: <-35525-071030074717-14201-il5EBQOqVw1sT4HuppQ+RQ[-]server.ccl.net> X-Original-From: "Naser Eltaher eltayeb" Date: Tue, 30 Oct 2007 07:47:14 -0400 Sent to CCL by: "Naser Eltaher eltayeb" [nasertaha90]=[yahoo.co.uk] Dear CCl members I am looking for free software can give me the molecular orbital composition in table (e.g. Cl% 4.2%, C% 54%..). It shall be better if it can transfer Gaussia output to table. Thank you Naser Eltaher From owner-chemistry@ccl.net Tue Oct 30 08:43:01 2007 From: "Chong Hak Chae chchae(~)krict.re.kr" To: CCL Subject: CCL:G: Q optimal configuration for G03 running? Message-Id: <-35526-071030025404-10260-VGJTCyeh4OrfszRPSnIOFQ * server.ccl.net> X-Original-From: "Chong Hak Chae" Date: Tue, 30 Oct 2007 02:54:00 -0400 Sent to CCL by: "Chong Hak Chae" [chchae a krict.re.kr] I was wondering what is the optimal configuration (Default.Route file) for my PC to run gaussian03. I have two identical computers running Windows2003 32-bit and Redhat linux 32-bit. CPU : 4-core = 2 x dual-core Zeon Mem : 8GB HDD : 300GB My ultimate goal is to calculate the pKa of small molecules : about 300 basis set, G2/CBS calculations and solvation. But when I try with mem=2GB or more, the program halts. Only under 1.5 GB memory can be used by g03, and endless disk-read/write for electron integral calculations. How can I make use of all the 8GB memory and minimize the disk I/O? Thanks in advance. ~Chchae From owner-chemistry@ccl.net Tue Oct 30 10:25:00 2007 From: "Andrew Turner andrew.turner]*[ed.ac.uk" To: CCL Subject: CCL:G: Molecular Orbital Composition Message-Id: <-35527-071030102309-11275-qqHXYKBQ6c4gMdSaXqlvww^server.ccl.net> X-Original-From: Andrew Turner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 30 Oct 2007 14:23:04 +0000 MIME-Version: 1.0 Sent to CCL by: Andrew Turner [andrew.turner---ed.ac.uk] We have a set of Linux tools that can do this as part of the EaStCHEM Submission package. It can read the MO cfs from either G03 or GAMESS-UK output and compute occupancies by basis function and atom. The output can be easily imported into OO Calc (for example). You can download the package from: http://www.edikt.org/edikt2/ComputationalChemistryActivity/SupportPages/EaStCHEMSub Unfortunately there is not much support available yet but once it is installed you should just be able to edit the eastchem-sub/bash/setsubenv.bash file to reflect your installation and then source it to have access to all the tools. The utility you are looking for is called 'getocc' Hope this helps Andy Naser Eltaher eltayeb nasertaha90 ~ yahoo.co.uk wrote: > Sent to CCL by: "Naser Eltaher eltayeb" [nasertaha90]=[yahoo.co.uk] > Dear CCl members > > I am looking for free software can give me the molecular orbital composition > in table (e.g. Cl% 4.2%, C% 54%..). It shall be better if it can transfer > Gaussia output to table. > > Thank you > > Naser Eltaher> > > > -- ================================== Dr Andrew R. Turner Research Computing Officer e: andrew.turner..ed.ac.uk t: +44 (0)131 650 7748 w: http://www.eastchem.ac.uk/rcf icq: 370-899-715 p: School of Chemistry University of Edinburgh EH9 3JJ ================================== From owner-chemistry@ccl.net Tue Oct 30 13:05:01 2007 From: "Pedro D. Vaz pmvaz-.-fc.ul.pt" To: CCL Subject: CCL: Molecular Orbital Composition Message-Id: <-35528-071030115721-8148-pWuOQY6hNzcEJYDSBVGa7g=server.ccl.net> X-Original-From: "Pedro D. Vaz" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Tue, 30 Oct 2007 15:21:29 -0000 MIME-Version: 1.0 Sent to CCL by: "Pedro D. Vaz" [pmvaz]_[fc.ul.pt] There is also Pymolyze2.0 which can do that and is free. Just google around for it ----- Original Message ----- > From: "Naser Eltaher eltayeb nasertaha90 ~ yahoo.co.uk" To: "Vaz, Pedro D " Sent: Tuesday, October 30, 2007 11:47 AM Subject: CCL: Molecular Orbital Composition > > Sent to CCL by: "Naser Eltaher eltayeb" [nasertaha90]=[yahoo.co.uk] > Dear CCl members > > I am looking for free software can give me the molecular orbital > composition > in table (e.g. Cl% 4.2%, C% 54%..). It shall be better if it can transfer > Gaussia output to table. > > Thank you > > Naser Eltaher> > > From owner-chemistry@ccl.net Tue Oct 30 14:08:01 2007 From: "Victor Nemykin victor_nemykin*yahoo.com" To: CCL Subject: CCL:G: Molecular Orbital Composition Message-Id: <-35529-071030135129-9625-Pta1e2IITl73tnqPI1HRBg^server.ccl.net> X-Original-From: Victor Nemykin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 30 Oct 2007 09:51:18 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Victor Nemykin [victor_nemykin[a]yahoo.com] Hello Naser: VMOdes available at: http://www.d.umn.edu/~vnemykin/VMOdes/VMOdes.htm can do this using output files generated by Gaussian, GAMESS, and HyperChem. Best, Victor --- "Naser Eltaher eltayeb nasertaha90 ~ yahoo.co.uk" wrote: > > Sent to CCL by: "Naser Eltaher eltayeb" [nasertaha90]=[yahoo.co.uk] > Dear CCl members > > I am looking for free software can give me the molecular orbital > composition > in table (e.g. Cl% 4.2%, C% 54%..). It shall be better if it can > transfer > Gaussia output to table. > > Thank you > > Naser Eltaher > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > > > ***** Dr. Victor N.Nemykin e-mail: victor_nemykin|,|yahoo.com ***** __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Tue Oct 30 14:50:00 2007 From: "Frank Neese neese++thch.uni-bonn.de" To: CCL Subject: CCL: Molecular Orbital Composition Message-Id: <-35530-071030144725-14670-NXVUFQMkJxJrZAOhMO38ng%a%server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 30 Oct 2007 19:46:24 +0100 MIME-Version: 1.0 Sent to CCL by: Frank Neese [neese,,thch.uni-bonn.de] >> >> I am looking for free software can give me the molecular orbital >> composition >> in table (e.g. Cl% 4.2%, C% 54%..). ... the ORCA program will also do that for you (http://www.thch.uni-bonn.de/tc/orca/). best regards, Frank -- --------------------------------------------------------------- Prof. Dr. Frank Neese Lehrstuhl fuer Theoretische Chemie Universitaet Bonn Wegelerstr. 12 D-53115 Bonn, Germany neese*o*thch.uni-bonn.de Phone: +49-28-732351 FAX: +49-(0)228-739064 --------------------------------------------------------------- From owner-chemistry@ccl.net Tue Oct 30 16:50:00 2007 From: "David Hose anthrax_brothers-$-hotmail.com" To: CCL Subject: CCL:G: Q optimal configuration for G03 running? Message-Id: <-35531-071030164704-12608-48I3mMBZGFFlBr2hE6JfTA:_:server.ccl.net> X-Original-From: "David Hose" Date: Tue, 30 Oct 2007 16:47:00 -0400 Sent to CCL by: "David Hose" [anthrax_brothers]-[hotmail.com] Chchae, Your problem is the 32 bit operating system. Although your BIOS will see 8 Gb of RAM on boot up, Windows can only access about 3 Gb to due the 32 bit addressing. You'll have to upgrade to XP 64 or a Linux equivalent to use all 8 Gb. Regards, Dave. _________________ Sent to CCL by: "Chong Hak Chae" [chchae a krict.re.kr] I was wondering what is the optimal configuration (Default.Route file) for my PC to run gaussian03. I have two identical computers running Windows2003 32-bit and Redhat linux 32-bit. CPU : 4-core = 2 x dual-core Zeon Mem : 8GB HDD : 300GB My ultimate goal is to calculate the pKa of small molecules : about 300 basis set, G2/CBS calculations and solvation. But when I try with mem=2GB or more, the program halts. Only under 1.5 GB memory can be used by g03, and endless disk-read/write for electron integral calculations. How can I make use of all the 8GB memory and minimize the disk I/O? Thanks in advance. ~Chchaehttp://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 Tue Oct 30 17:45:00 2007 From: "Adam Tenderholt atenderholt%x%gmail.com" To: CCL Subject: CCL:G: Molecular Orbital Composition Message-Id: <-35532-071030173028-10149-4kBjG/p0FA1nNy/TX2mVSw%x%server.ccl.net> X-Original-From: "Adam Tenderholt" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 30 Oct 2007 13:29:47 -0700 MIME-Version: 1.0 Sent to CCL by: "Adam Tenderholt" [atenderholt(-)gmail.com] There's also my QMForge program (http://qmforge.sourceforge.net). It was recently renamed from PyMOlyze, and I have yet to formally announce it on this list. But on to topics more critical to this thread.... QMForge is cross-platform, and has binary packages for Windows and Mac OS X. The source code is available, and should run easily on Linux, but I haven't tested it. QMForge allows you to assign various parts of a molecule to "fragments", which can be made up of as many atoms/basis functions as you choose, using a graphical interface. I often create fragments based on metal d orbitals, metal s/p orbitals, S atoms, and C/H atoms. Once fragments have been assigned, you can run Mulliken or C-squared analyses to get the composition of MOs. The results can then be saved as a text file, and with a bit of tweaking, read into a spreadsheet program. Adam On 10/30/07, Andrew Turner andrew.turner]*[ed.ac.uk wrote: > > Sent to CCL by: Andrew Turner [andrew.turner---ed.ac.uk] > We have a set of Linux tools that can do this as part of the EaStCHEM > Submission package. It can read the MO cfs from either G03 or GAMESS-UK > output and compute occupancies by basis function and atom. The output > can be easily imported into OO Calc (for example). > > You can download the package from: > > http://www.edikt.org/edikt2/ComputationalChemistryActivity/SupportPages/EaStCHEMSub > > Unfortunately there is not much support available yet but once it is > installed you should just be able to edit the > eastchem-sub/bash/setsubenv.bash file to reflect your installation and > then source it to have access to all the tools. The utility you are > looking for is called 'getocc' > > Hope this helps > > Andy > > Naser Eltaher eltayeb nasertaha90 ~ yahoo.co.uk wrote: > > Sent to CCL by: "Naser Eltaher eltayeb" [nasertaha90]=[yahoo.co.uk] > > Dear CCl members > > > > I am looking for free software can give me the molecular orbital composition > > in table (e.g. Cl% 4.2%, C% 54%..). It shall be better if it can transfer > > Gaussia output to table. > > > > Thank you > > > > Naser Eltaher> > > > > > > > > -- > ================================== > Dr Andrew R. Turner > Research Computing Officer > e: andrew.turner_+_ed.ac.uk > t: +44 (0)131 650 7748 > w: http://www.eastchem.ac.uk/rcf > icq: 370-899-715 > p: School of Chemistry > University of Edinburgh > EH9 3JJ > ==================================> > > > From owner-chemistry@ccl.net Tue Oct 30 23:08:01 2007 From: "Andrew D. Fant fant{=}pobox.com" To: CCL Subject: CCL: Yet another software recommendation request Message-Id: <-35533-071030230616-12893-o7KS2wZGxnoXTqeCarACbA^^server.ccl.net> X-Original-From: "Andrew D. Fant" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 30 Oct 2007 22:19:53 -0400 MIME-Version: 1.0 Sent to CCL by: "Andrew D. Fant" [fant]|[pobox.com] Greetings all, Having reached that point of my life where I want to spend time less time being my own systems administrator, I've decided to replace my (deceased) notebook with a shiny new mac (at least after macworld when the prices drop). Given this, would people please share their favorite 3d capable molecular editor that runs natively in MacOSX and Carbon. I know that there are free options if I use parallels to run something under Windows, or the X server, but I have had nothing but hassles with that approach on the lab workstation (nasty cut and paste errors and random crashes). I was apparently the last to discover that ChemDraw doesn't do any real 3D functionality on the Mac after buying a copy. What I want is something that will let me sketch a small molecule with a reasonably simple interface, convert it to a 3D form, and do enough of a structural minimization to get the geometry cleaned up enough that a real MM/MD or quantum program won't choke on it. Oh, and it needs to be within the budget of a self-funded graduate student, which is to say that I am not eager to drop several hundred dollars for it. Any nominees? Thanks, Andy