From owner-chemistry@ccl.net Wed Nov 1 03:13:00 2006 From: "M Meno mahesh_menon71###yahoo.com" To: CCL Subject: CCL:G: Raman polarizability Message-Id: <-32919-061101031058-27657-d13bc3mUg8HuskBwXZnnXQ.@.server.ccl.net> X-Original-From: "M Meno" Date: Wed, 1 Nov 2006 03:10:57 -0500 Sent to CCL by: "M Meno" [mahesh_menon71:-:yahoo.com] Hi all, I wanna post the following question for my friend. I would really appreciate your reply. Regards, Menon The question is: How do one gets a Raman Polarizability of a particular normal mode in Gaussian (G98/G03) ? Thanks, Timur. From owner-chemistry@ccl.net Wed Nov 1 04:57:00 2006 From: "Val Gillet v.gillet|-|sheffield.ac.uk" To: CCL Subject: CCL: Fourth Joint Sheffield Conference on Chemoinformatics: Call for Papers Message-Id: <-32920-061101045430-30960-gxIXHjLJ+AkdkT3+BChMdQ^server.ccl.net> X-Original-From: "Val Gillet" Date: Wed, 1 Nov 2006 04:54:30 -0500 Sent to CCL by: "Val Gillet" [v.gillet!=!sheffield.ac.uk] Fourth Joint Sheffield Conference on Chemoinformatics: Call for Papers The Chemical Structure Association Trust and the Molecular Graphics and Modelling Society announce their Fourth Joint Sheffield Conference on Chemoinformatics. The conference will be held in The Octagon Centre and the Stephenson and Tapton Halls of Residence, University of Sheffield, UK, from 18th-20th June 2007. Offers of papers are welcomed in all aspects of chemoinformatics. Possible topics include (but are not limited to): * High-Throughput Screening, including: assay quality control; design of screening collections; systems based design * Virtual Screening including, including: docking and pharmacophore analysis, similarity and clustering methods; machine learning * Computational Methods for Lead Identification and Optimisation including: modelling and structure-activity methods; structure-based design; ADMET prediction * New Algorithms and Technologies including: data mining; searching methods; distributed processing; data handling and visualisation; * Case Histories, incorporating practical experience of any of the above The programme will have space for ca. two dozen oral presentations, and there will also be extensive opportunities for poster presentations. Authors wishing to submit a paper should send a title and abstract (minimum 500 words) by 31st January 2007 to cheminf2007.^.sheffield.ac.uk, stating whether they wish to be considered for an oral or for a poster presentation. Submissions will be selected as either oral contributions or posters by the Organising Committee, with notification of acceptance by 28th February 2007. In selecting papers for oral presentation, the Committee will seek to achieve a balance between the various areas of the subject and between new methodologies and successful applications of existing techniques. Further details of the conference, including registration information and opportunities for sponsorship and participation in the conference exhibition will follow later in the year, and will be posted at the conference website http://cisrg.shef.ac.uk/shef2007/ From owner-chemistry@ccl.net Wed Nov 1 08:49:01 2006 From: "Sergio Emanuel Galembeck segalemb]-[usp.br" To: CCL Subject: CCL: theoretical study of pi-pi stacking Message-Id: <-32921-061101084750-32019-hfNEbzp4J8iTNKFVL93lwg[a]server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 01 Nov 2006 10:47:39 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb---usp.br] Dear Jay, I recomend that you search between the papers of Pavel Hobza. He published a lot on pi-pi interaction. Best regards, Sergio Citando "jun tie cheng ccl]=[mail.sioc.ac.cn" : > Sent to CCL by: "jun tie cheng" [ccl++mail.sioc.ac.cn] > Hi all, > > Can anyone suggest some articles on the theoretical study of pi-pi > stacking? > > thanks in advance! > > sincerely, > > JAY> > > > From owner-chemistry@ccl.net Wed Nov 1 09:24:00 2006 From: "Sergio Emanuel Galembeck segalemb[A]usp.br" To: CCL Subject: CCL:G: UV Spectra Calculation using Gaussian03 Message-Id: <-32922-061101090216-20631-22zHL3MSjrNfJkxsgQsWzw++server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 01 Nov 2006 11:02:07 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb|,|usp.br] Dear Yuong, The Gxx input is almost always the same: # keywords comments charge multiplicity geometry blank line As an example: # B3LYP/6-31+G(d,p) TD electronic vertical excitation of CH4 0 1 C H 1 1.09 H 1 1.09 2 109.45 H 1 1.09 2 109.45 3 120.0 H 1 1.09 2 109.45 3 -120.0 The output gives the wavelength of the exitation and the oscillator strength. In order to simulate the spectra you will need to use a software that fit the data to a gaussian. Best regards, Sergio Citando "Young Leh youngleh~~gmail.com" : > Sent to CCL by: "Young Leh" [youngleh_+_gmail.com] > I am planing to calculate UV spectra using Gaussian03. I found "TD" is > keyword to go from the manual but it does not state clearly how to use it. > > B3LYP/6-31G* TD > > UV Spectra > > molecular specification > > > Can I extract the info Absorbance vs. Lamda and compare with exeprimental > spectra? > > Thanks> > > > From owner-chemistry@ccl.net Wed Nov 1 10:53:01 2006 From: "Alvyn Liang alvyn.liang^^^gmail.com" To: CCL Subject: CCL:G: Bond breaking and bond distance Message-Id: <-32923-061101104857-26594-G70m0fRkG6UJDx42vmxCbA%%server.ccl.net> X-Original-From: "Alvyn Liang" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 1 Nov 2006 14:51:12 +0000 MIME-Version: 1.0 Sent to CCL by: "Alvyn Liang" [alvyn.liang(~)gmail.com] Has anybody got any experience of simulating the bond breaking energy using Gaussian package? I tried to use 6-311++G(3d,2p) B3LYP method by UHF mix LUMO and HOMO, but I found when the HF bond distance is greater then about 7.5 Bohr, there is a gap where the energy is not smooth. Is there a better way to simulate a better and more reasonable bond breaking behavior? Many thanks. Alvyn From owner-chemistry@ccl.net Wed Nov 1 11:37:00 2006 From: "Dr. N. SUKUMAR nagams()rpi.edu" To: CCL Subject: CCL:G: UV Spectra Calculation using Gaussian03 Message-Id: <-32924-061101112545-5045-e0/5l0UIGlHJLBeuEbaxLQ[#]server.ccl.net> X-Original-From: "Dr. N. SUKUMAR" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Wed, 01 Nov 2006 11:25:37 -0500 MIME-Version: 1.0 Sent to CCL by: "Dr. N. SUKUMAR" [nagams||rpi.edu] Let's try this again to get it formatted correctly (apologies for double posting): GaussSum http://gausssum.sourceforge.net/ SWizard http://www.sg-chem.net/swizard/ WebMO http://www.webmo.net/features.html GaussView 3.0 http://www.gaussian.com/gv_plat.htm Origin 7.5 http://www.originlab.com/ Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute ==============Original message text=============== On Tue, 31 Oct 2006 22:08:10 EST "Dr. N. SUKUMAR nagams*rpi.edu" wrote: Sent to CCL by: "Dr. N. SUKUMAR" [nagams-#-rpi.edu] Lots of programs do this: GaussSum http://gausssum.sourceforge.net/SWizard http://www.sg-chem.net/swizard/WebMO http://www.webmo.net/features.htmlDr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute ==============Original message text=============== On Tue, 31 Oct 2006 13:49:57 EST "Shobe, David David.Shobe()sud-chemie.com" wrote: Sent to CCL by: "Shobe, David" [David.Shobe-x-sud-chemie.com] Unfortunately, none of the methods in Gaussian will give you an actual spectrum (i.e. a continuous graph of absorbance v. wavelength). All you will get are energy levels and transition moments. To the list: is there a program that will calculate actual spectra? Nothing was available when I last asked (about five years ago) but maybe that's changed. --David Shobe -----Original Message----- > From: owner-chemistry!A!ccl.net [mailto:owner-chemistry!A!ccl.net] Sent: Tuesday, October 31, 2006 2:22 AM To: Shobe, David Subject: CCL:G: UV Spectra Calculation using Gaussian03 Sent to CCL by: "Young Leh" [youngleh_+_gmail.com] I am planing to calculate UV spectra using Gaussian03. I found "TD" is keyword to go > from the manual but it does not state clearly how to use it. B3LYP/6-31G* TD UV Spectra molecular specification Can I extract the info Absorbance vs. Lamda and compare with exeprimental spectra? Thankshttp://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.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text===========http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Wed Nov 1 12:18:00 2006 From: "matthew tassell mjt22*sussex.ac.uk" To: CCL Subject: CCL: TDDFT-populations Message-Id: <-32925-061101121542-8836-+cTVjn++Y9EWoRNvyJjFpw{}server.ccl.net> X-Original-From: "matthew tassell" Date: Wed, 1 Nov 2006 12:15:41 -0500 Sent to CCL by: "matthew tassell" [mjt22{=}sussex.ac.uk] Dear All, when using Gaussain 03 to perform TDDFT calculations i noticed that in the output you get excitation energies and oscillator strengths and no other information. I was wondering if perhaps anybody knew of a way to get information about the excited state electron configuration? so that i would be able work out which electron has performed the transition. Any insight gratefully recieved, matt From owner-chemistry@ccl.net Wed Nov 1 12:58:00 2006 From: "me00109,cc.uoi.gr" To: CCL Subject: CCL:G: GO3 W vs GO3 Linux Message-Id: <-32926-061031194130-24520-kGaR/Fv2pE/MQxpk5Tg5iw]=[server.ccl.net> X-Original-From: me00109_-_cc.uoi.gr Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-7 Date: Wed, 1 Nov 2006 01:40:47 +0200 MIME-Version: 1.0 Sent to CCL by: me00109||cc.uoi.gr Try to run G03W in dos mode. It will be faster than the GUI interface. George Papamokos > Sent to CCL by: "Gustavo Seabra" [gustavo.seabra**gmail.com] > Definetely, the linux version will be faster. (I'm yet to hear about a > scientific application that runs faster in Windows.;-) > > Also, there was a problem with the windows version being unable to > generate the orbitals, which I don't know if it has been solved. > > HTH. > > Gustavo. > > On 10/29/06, neeraj misra misraneeraj|,|gmail.com > wrote: > > Sent to CCL by: "neeraj misra" [misraneeraj%a%gmail.com] > > > > DEAR CCL'ERS > > I WOULD BE GRATEFUL IF SOMEONE COULD TELL ME WHICH ONE > WOULD BE FASTER/BETTER ON COMPARISON. > > > > GAUSSIAN 03 FOR WINDOWS VERSUS GAUSSIAN 03 FOR LINUX. > > IS A CALCULATION ON AS LINUX PLATEFORM FASTER. > > THANKS IN ADVANCE> > > From owner-chemistry@ccl.net Wed Nov 1 13:32:00 2006 From: "Markus Weingarth m.weingarth,,web.de" To: CCL Subject: CCL: Chirality.c - Amber - Fatal Error Message-Id: <-32927-061101124712-30818-gooNh6Y/y61u4w2TbrRNoQ^_^server.ccl.net> X-Original-From: "Markus Weingarth" Date: Wed, 1 Nov 2006 12:47:11 -0500 Sent to CCL by: "Markus Weingarth" [m.weingarth[A]web.de] Hello, I have a little problem in loading in my .pdb files of a certain molecule. Building the .lib file worked and the UNIT looks good (think so). But as soon as I try to load the .pdb file, XLeap is aborted. Message : !FATAL ERROR---------------------------------------- !FATAL: In file [chirality.c], line 116 !FATAL: Message: No C4 in aaOrig list ! !ABORTING. I took a look at the C4, and exactly there I have a stereo-center. I found that chirality.c file, but I'm not able to get the clue, sorry. Would anyone be so kind to help me? Markus From owner-chemistry@ccl.net Wed Nov 1 14:08:00 2006 From: "Lauren O Neil lhunter2*_*nd.edu" To: CCL Subject: CCL: Chirality.c - Amber - Fatal Error Message-Id: <-32928-061101140623-19906-oqEwjiEV4zsx98DZWEnpBg|a|server.ccl.net> X-Original-From: "Lauren O'Neil" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 01 Nov 2006 12:52:15 -0500 MIME-Version: 1.0 Sent to CCL by: "Lauren O'Neil" [lhunter2{=}nd.edu] Markus, In my very limited experience this error has to do with the head and tail atoms of the UNIT. So, try desc UNIT in xleap and see what the head and tail are set as and then fix them if needed. Hope this helps. Lauren O'Neil University of Notre Dame Markus Weingarth m.weingarth,,web.de wrote: >Sent to CCL by: "Markus Weingarth" [m.weingarth[A]web.de] >Hello, > >I have a little problem in loading in my .pdb files of a certain molecule. >Building the .lib file worked and the UNIT looks good (think so). But as >soon as I try to load the .pdb file, XLeap is aborted. > >Message : > >!FATAL ERROR---------------------------------------- >!FATAL: In file [chirality.c], line 116 >!FATAL: Message: No C4 in aaOrig list >! >!ABORTING. > > >I took a look at the C4, and exactly there I have a stereo-center. I found >that chirality.c file, but I'm not able to get the clue, sorry. > >Would anyone be so kind to help me? > >Markus> > > > > From owner-chemistry@ccl.net Wed Nov 1 14:43:00 2006 From: "Atilio I Anzellotti/O/VCU aanzellotti_-_vcu.edu" To: CCL Subject: CCL:G: UV Spectra Calculation using Gaussian03 Message-Id: <-32929-061101112950-11744-J+nfq/vOWC9qpbSXXB8DZA###server.ccl.net> X-Original-From: Atilio I Anzellotti/O/VCU Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Wed, 1 Nov 2006 10:44:06 -0500 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: Atilio I Anzellotti/O/VCU [aanzellotti~~vcu.edu]
Dear All,
 
   Regarding calcu= lation of UV spectra with gaussian 03, I have used DFT to optimize the geom= etry of some free and platinated nucleobases, the energy HOMO/LUMO gap = ;is showing a smaller separation for the platinated compared to the fr= ee ones. I can see this shift in the UV absorption maxima. Could I proposed= a direct correlation between calculated HOMO/LUMO gaps and experimental re= sults?
 
Many Thanks.
 
A= tilio.
-----owner-chemistry**ccl.net wrote: -= ----

To= : "Anzellotti, Atilio " <aanzellotti**vcu.edu>
From: "Shobe= , David David.Shobe()sud-chemie.com" <owner-chemistry**ccl.net>
Sen= t by: owner-chemistry**ccl.net
Date: 10/31/2006 02:45PM
Subject: CCL:G= : UV Spectra Calculation using Gaussian03

Sent to CCL by: "Shobe, David= " [David.Shobe-x-sud-chemie.com]

Unfortunately, none of the methods = in Gaussian will give you an actual
spectrum (i.e. a continuous graph of= absorbance v. wavelength).  All you
will get are energy levels and= transition moments.  

To the list: is there a program that wil= l calculate actual spectra?
Nothing was available when I last asked (abo= ut five years ago) but maybe
that's changed.

--David Shobe

-----Original Message-----
> From: owner-chemistry!A!ccl.net [mailto:owner-chem= istry!A!ccl.net]
Sent: Tuesday, October 31, 2006 2:22 AM
To: Sho= be, David
Subject: CCL:G: UV Spectra Calculation using Gaussian03
Sent to CCL by: "Young  Leh" [youngleh=5F+=5Fgmail.com] I am planing = to
calculate UV spectra using Gaussian03.  I found "TD" is keyword = to go
> from the manual but it does not state clearly how to use it.<= BR>
B3LYP/6-31G* TD

UV Spectra

molecular specification

Can I extract the info Absorbance vs. Lamda and compare with
ex= eprimental spectra?

Thankshttp://www.ccl.net/cgi-bin/ccl/send=5Fccl= =5Fmessagehttp://www.ccl.net/chemistry/sub=5Funsub.shtmlhttp://www.ccl.net/= spammers.txtThis e-mail message may contain confidential and / or privilege= d information. If you are not an addressee or otherwise authorized to recei= ve this message, you should not use, copy, disclose or take any action base= d on this e-mail or any information contained in the message. If you have r= eceived this material in error, please advise the sender immediately by rep= ly e-mail and delete this message.
Thank you.



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