From chemistry-request@server.ccl.net Fri May 4 01:05:55 2001 Received: from bioinfo.ernet.in ([202.41.70.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4455rI15973 for ; Fri, 4 May 2001 01:05:54 -0400 Received: from localhost (sangeeta@localhost) by bioinfo.ernet.in (8.8.7/8.8.7) with ESMTP id KAA06961; Fri, 4 May 2001 10:32:46 +0530 Date: Fri, 4 May 2001 10:32:46 +0530 (IST) From: sangeeta@bioinfo.ernet.in To: Fenglou Mao cc: "CHEMISTRY@www.ccl.net" Subject: Re: CCL:Database summary? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Have a look at the January 2001issue of Nucleic Acid Research (NAR) which is dedicated issue for biol. databases. This NAR issue is free for all (full text). You can access it at : http://nar.oupjournals.org/content/vol29/issue1/ In fact, every year, the first issue (in Jan.) of NAR is a database special. Hope this helps. Sangeeta +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Mrs. Sangeeta Sawant Lecturer Bioinformatics Centre University of Pune, Ganeshkhind Pune - 411007 India email: sangeeta@bioinfo.ernet.in phone: +91-20-5655039/5650195 fax: +91-20-5650087 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ On Fri, 4 May 2001, Fenglou Mao wrote: > Dear cclers, > > do anyone know a website or a paper summarized current > biological database? > > -- > Sincerely Yours, > > FengLou Mao > ******************************* > ADD:Mr. FengLou Mao > Institute of Physical Chemistry > Peking University > BeiJing > P.R.China > Tel:86-10-62756833 > Fax:86-10-62751725 > E-mail:mao@mdl.ipc.pku.edu.cn > Homepage:http://mdl.ipc.pku.edu.cn/~mao > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Fri May 4 10:49:30 2001 Received: from pat.ccc.nottingham.ac.uk ([128.243.40.194]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f44EnTI21186 for ; Fri, 4 May 2001 10:49:30 -0400 Received: from www.escalate.nottingham.ac.uk ([128.243.40.50] helo=gotham.ccc.nottingham.ac.uk) by pat.ccc.nottingham.ac.uk with esmtp (Exim 3.20 #2) id 14vgsb-0001nL-00 for chemistry@ccl.net; Fri, 04 May 2001 15:48:25 +0100 Received: from granby ([128.243.40.43] helo=granby.ccc.nottingham.ac.uk) by gotham.ccc.nottingham.ac.uk with esmtp (Exim 3.20 #2) id 14vgtb-0001On-00 for chemistry@ccl.net; Fri, 04 May 2001 15:49:27 +0100 Date: Fri, 4 May 2001 15:49:26 +0100 (BST) From: Simon Cross X-Sender: pcxsc@granby.ccc.nottingham.ac.uk To: ccl list Subject: SYBYL Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I would like to get an idea of the range of software that people use for computational chemistry/drug design - do lots of people use MSI software like InsightII or Tripos software like SYBYL or do most academics use freeware of some kind? Are there any reviews that detail advantages/disadvantages for these packages? Thanks in advance, ----------------------------------------- Simon Cross School of Chemistry University of Nottingham tel. 0115 9514193 Email: pcxsc@nottingham.ac.uk From chemistry-request@server.ccl.net Fri May 4 12:45:23 2001 Received: from deimos.email.Arizona.EDU (IDENT:root@[128.196.133.166]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f44GjNI22063 for ; Fri, 4 May 2001 12:45:23 -0400 Received: from demetrio.ifi.unicamp.br (128.196.86.129) by deimos.email.Arizona.EDU (5.1.056) id 3AD79C96001A5F30 for CHEMISTRY@ccl.net; Fri, 4 May 2001 09:45:21 -0700 Message-Id: <5.0.2.1.0.20010504213956.02f50dc0@deimos.email.arizona.edu> X-Sender: dasf@deimos.email.arizona.edu X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Fri, 04 May 2001 21:43:32 -0700 To: CHEMISTRY@ccl.net From: Demetrio Antonio da Silva Filho Subject: TD-DFT capacities of Gaussian 98 Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_497526==_.ALT" --=====================_497526==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Der CCL'ers, I'm posting a question that a friend asked me to because he sent it to gaussian and he didn't get any answer so far. Thanks, Demetrio Filho I am using the Gaussian version: Gaussian 98: SGI64-G98RevA.7 11-Apr-1999 13-Apr-2001 on an SGI cluster. My problem is the following: I have studied absorption processes in the singlet and triplet manifolds of conjugated oligomers using TD-DFT. The calculations yielded excellent agreement with experimental data considering the energetic positions of the transitions. Also the transition matrix elements from the ground to the one-photon allowed states seemd to be very reasonable. As a next step I tried to study two-photon absotrption processes. Again, the energetic positions of the excited states were very nicely described - to erive the absorption cross-sections I employed a perturbative approach containing the transition matrix elements between a number of excited states. To calculate them I used the option alltransitiondensities with the TD keyword. In the manual this option is, however, mentioned only in the context of HF-SCI calculations and I think I remember that someone at a Gaussian workshop I attended some time ago, told me that it is not possible to calculate transition matrix elemnts between excited states using TD-DFT. The results I obtained were insofar reasonable, as only the two photon allowed states "had" os\cillator strength, but the actual values I obtained for the transition matrix elements were too large (usually by about a factor of around 3. Do you know, wheteher this is due to transition matrix elements between excited states being not yet "fully included" in the TD-DFT capacities of Gaussian 98? thank you, egbert zojer --=====================_497526==_.ALT Content-Type: text/html; charset="us-ascii" Der CCL'ers,

I'm posting a question that a friend asked me to because he sent it to
gaussian and he didn't get any answer so far.

Thanks,

Demetrio Filho



I am using the Gaussian version:
Gaussian 98: SGI64-G98RevA.7 11-Apr-1999
13-Apr-2001
on an SGI cluster.

 My problem is the following:
I have studied absorption processes in the singlet and triplet manifolds of
conjugated oligomers using TD-DFT. The calculations yielded excellent agreement
with experimental data considering the energetic positions of the transitions.
Also the transition matrix elements from the ground to the one-photon allowed
states seemd to be very reasonable. As a next step I tried to study two-photon
absotrption processes. Again, the energetic positions of the excited states
were very nicely described - to erive the absorption cross-sections I employed
a perturbative approach containing the transition matrix elements between a
number of excited states. To calculate them I used the option
alltransitiondensities with the TD keyword. In the manual this option is,
however, mentioned only in the context of HF-SCI calculations and I think I
remember that someone at a Gaussian workshop I attended some time ago, told me
that it is not possible to calculate transition matrix elemnts between excited
states using TD-DFT. The results I obtained were insofar reasonable, as only
the two photon allowed states "had" os\cillator strength, but the actual values
I obtained for the transition matrix elements were too large (usually by about
a factor of around 3. Do you know, wheteher this is due to transition matrix
elements between excited states being not yet "fully included" in the TD-DFT
capacities of Gaussian 98?

thank you, egbert zojer
 --=====================_497526==_.ALT-- From chemistry-request@server.ccl.net Fri May 4 17:50:17 2001 Received: from mr2.wpafb.af.mil ([129.48.104.214]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f44LoHI25462 for ; Fri, 4 May 2001 17:50:17 -0400 Received: from fszhtv02.wpafb.af.mil (fszhtv02.wpafb.af.mil [129.48.26.202]) by mr2.wpafb.af.mil (8.11.3/8.11.3) with ESMTP id f44LoGh26757; Fri, 4 May 2001 17:50:16 -0400 (EDT) Received: by fszhtv02.wpafb.af.mil with Internet Mail Service (5.5.2653.19) id ; Fri, 4 May 2001 17:50:16 -0400 Message-ID: <45EE82EFB176D311815F0000F8CD23546C9C9A@fszhtv48.ml.wpafb.af.mil> From: Nguyen Kiet A Contr AFRL/MLPJ To: CHEMISTRY@ccl.net, "'Demetrio Antonio da Silva Filho'" Subject: RE: TD-DFT capacities of Gaussian 98 Date: Fri, 4 May 2001 17:50:15 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="windows-1252" Here is the message from Doug Fox about transition dipoles between excited states from TDDDFT and RPA for version A.9. Rev. A.9 still does not include code to produce relaxed densities for TD-DFT or RPA. The code to loop over all transition densities in the population analysis not available yet. The densities are written out but there is no current code to process them. You can get any selected transition density used in the population analysis with Density=Transition=(n,m) IOP(6/22=-4) but I am not sure what this your user wants. As you know the ground to excited state dipole moments are printed and these are reasonable although not quantitative. The transitions between excited states have not been studied. > ---------- > From: Demetrio Antonio da Silva Filho > Sent: Saturday, May 5, 2001 12:43 AM > To: CHEMISTRY@ccl.net > Subject: CCL:TD-DFT capacities of Gaussian 98 > > Der CCL'ers, > > I'm posting a question that a friend asked me to because he sent it to > gaussian and he didn't get any answer so far. > > Thanks, > > Demetrio Filho > > > > I am using the Gaussian version: > Gaussian 98: SGI64-G98RevA.7 11-Apr-1999 > 13-Apr-2001 > on an SGI cluster. > > My problem is the following: > I have studied absorption processes in the singlet and triplet manifolds of > conjugated oligomers using TD-DFT. The calculations yielded excellent agreement > with experimental data considering the energetic positions of the transitions. > Also the transition matrix elements from the ground to the one-photon allowed > states seemd to be very reasonable. As a next step I tried to study two-photon > absotrption processes. Again, the energetic positions of the excited states > were very nicely described - to erive the absorption cross-sections I employed > a perturbative approach containing the transition matrix elements between a > number of excited states. To calculate them I used the option > alltransitiondensities with the TD keyword. In the manual this option is, > however, mentioned only in the context of HF-SCI calculations and I think I > remember that someone at a Gaussian workshop I attended some time ago, told me > that it is not possible to calculate transition matrix elemnts between excited > states using TD-DFT. The results I obtained were insofar reasonable, as only > the two photon allowed states "had" os\cillator strength, but the actual values > I obtained for the transition matrix elements were too large (usually by about > a factor of around 3. Do you know, wheteher this is due to transition matrix > elements between excited states being not yet "fully included" in the TD-DFT > capacities of Gaussian 98? > > thank you, egbert zojer > >