From chemistry-request@server.ccl.net Tue Mar 27 09:43:17 2001 Received: from host240.abbott.com ([63.77.7.240]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f2REhHD24101 for ; Tue, 27 Mar 2001 09:43:17 -0500 Received: by host240.abbott.com id AA11465 (InterLock SMTP Gateway 3.0 for CHEMISTRY@ccl.net); Tue, 27 Mar 2001 08:12:27 -0600 Received: by host240.abbott.com (Internal Mail Agent-2); Tue, 27 Mar 2001 08:12:27 -0600 Received: by host240.abbott.com (Internal Mail Agent-1); Tue, 27 Mar 2001 08:12:27 -0600 From: Yvonne Martin To: Cc: Jerry DeLazzer Subject: Displaying 100's of structures on a web page Message-Id: <0055600005757414000002L042*@MHS> Date: Tue, 27 Mar 2001 08:42:08 -0600 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f2REhID24102 What is your favorite program for doing this? We are happy to supply the program a list of smiles or an sdf file. Plug-ins are not the answer for such a large number of structures. Please answer to me and to Jerry DeLazzer. yvonne.c.martin@abbott.com jerry.delazzer@abbott.com Thanks! Yvonne From chemistry-request@server.ccl.net Tue Mar 27 09:53:11 2001 Received: from bom2.vsnl.net.in ([202.54.1.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2RErAD24152 for ; Tue, 27 Mar 2001 09:53:11 -0500 Received: from bom2.vsnl.net.in (unknown [203.199.88.33]) by bom2.vsnl.net.in (Postfix) with ESMTP id A92891069D for ; Tue, 27 Mar 2001 20:23:04 +0530 (GMT+5:30) Message-ID: <3AC0A814.5040307@bom2.vsnl.net.in> Date: Tue, 27 Mar 2001 20:17:48 +0530 From: meenatul User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; m18) Gecko/20001108 Netscape6/6.0 X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: about FT Dock Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit I would like to know about FT Dock (fourirer transformed) programme. I have heard that this program is usefull to find the favourable binding site very efficiently on the receptor, whose binding site is not known. Can you throw more light on this. thank you Meena From chemistry-request@server.ccl.net Tue Mar 27 11:41:00 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2RGf0D24820 for ; Tue, 27 Mar 2001 11:41:00 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id LAA02820; Tue, 27 Mar 2001 11:40:58 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Tue, 27 Mar 2001 11:40:12 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GAV00JJE7HEAV@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Tue, 27 Mar 2001 11:36:50 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Tue, 27 Mar 2001 11:40:58 -0500 Content-return: allowed Date: Tue, 27 Mar 2001 11:40:57 -0500 From: "Shobe, Dave" Subject: RE: CCL:spin-orbit coupling To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAADA9@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f2RGf0D24821 Related question: how does spin-orbit coupling work for nonlinear molecules? I don't think of them as having orbital angular momentum quantum numbers, but OTOH I have trouble believing that an energy split that occurs for a linear triatomic suddenly disappears when the molecule is bent to 179.9 degrees. (And does it matter if the bending is the result of vibrational motion as opposed to some external force breaking the symmetry?) > How do I calculate the splitting of the ground electronic state due to spin-orbit coupling? > Does this have a noticeable effect on the heat capacity or entropy? --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com From chemistry-request@server.ccl.net Tue Mar 27 11:47:13 2001 Received: from aquarius.ime.eb.br ([200.20.120.44]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2RGl9D24836 for ; Tue, 27 Mar 2001 11:47:12 -0500 Received: from epq.ime.eb.br (epq.ime.eb.br [200.20.120.217]) by aquarius.ime.eb.br (8.9.1a/8.9.1) with ESMTP id NAA14673 for ; Tue, 27 Mar 2001 13:50:12 -0300 Received: from EPQ/SpoolDir by epq.ime.eb.br (Mercury 1.47); 27 Mar 01 13:47:34 -0300 Received: from SpoolDir by EPQ (Mercury 1.47); 27 Mar 01 13:47:07 -0300 Received: from sdio.ime.eb.br (200.20.123.210) by epq.ime.eb.br (Mercury 1.47); 27 Mar 01 13:46:46 -0300 Message-ID: <003a01c0b6dd$81cb8400$LocalHost@ime.eb.br> From: "Teodorico Ramalho" To: Subject: Calcule of the thermodynamics properties. Date: Tue, 27 Mar 2001 13:46:43 -0300 Dear all, There are diferences between thermodynamics properties calculated > from vibracional frequencies and thermodynamics properties calculates > from Monte Carlo method or DM of complexs? Thank you very much for all, Teodorico C. Ramalho From chemistry-request@server.ccl.net Tue Mar 27 13:15:34 2001 Received: from quim.iq.usp.br ([143.107.46.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2RIFTD25628 for ; Tue, 27 Mar 2001 13:15:29 -0500 Received: (from jacksong@localhost) by quim.iq.usp.br (8.9.3/8.9.3) id PAA24557; Tue, 27 Mar 2001 15:12:48 -0300 (EST) Date: Tue, 27 Mar 2001 15:12:48 -0300 (EST) From: Jackson Gois X-Sender: jacksong@quim To: chemistry@ccl.net Subject: Minimization with Thor In-Reply-To: <003a01c0b6dd$81cb8400$LocalHost@ime.eb.br> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CClers I am a graduate student working with MHC proteins. We intend to use Thor program to minimize the structures. Is there a manual or something about it ? If not, does anybody in this list work with this program that could give us some hints ? Thanks in advance. Jackson Gois jacksong@iq.usp.br jacksons@iae-sp.br From chemistry-request@server.ccl.net Tue Mar 27 12:33:26 2001 Received: from hartree.chem.kuleuven.ac.be ([134.58.49.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2RHXPD25344 for ; Tue, 27 Mar 2001 12:33:25 -0500 Received: from localhost (kiran@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with ESMTP id TAA46988 for ; Tue, 27 Mar 2001 19:33:26 +0100 Date: Tue, 27 Mar 2001 19:33:26 +0100 (NFT) From: Kiran Boggavarapu To: chemistry@ccl.net Subject: counter ions and DFT Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I would like to know how to include counter ions in an ab initio calculation (DFT) using propular packages like Gaussian or Turbomole etc. And also I would like to hear from experienced people, how good are these methods (if any!) in predicting the relative energies of a large system (say porphyrin like). Thanks in advance! -kiran kiran.boggavarapu@chem.kuleuven.ac.be From chemistry-request@server.ccl.net Tue Mar 27 21:36:02 2001 Received: from blakey.sci.ccny.cuny.edu (IDENT:root@[134.74.52.245]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2S2a1D28429 for ; Tue, 27 Mar 2001 21:36:01 -0500 Received: from localhost (amasunov@localhost) by blakey.sci.ccny.cuny.edu (8.11.0/8.11.0) with ESMTP id f2S2cnR15445 for ; Tue, 27 Mar 2001 21:38:49 -0500 Date: Tue, 27 Mar 2001 21:38:49 -0500 (EST) From: Artem Masunov To: Subject: DFT is over !/? (expert opinion SUMMARY) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Many thanks to Drs. Grimme, Rassolov and Lewars for making it clear. Nothing is perfect, including Coulomb-hole. Although the difference between 3 parameters in B3LYP and 12 parameters in Coulomb-hole approach does not seem that drastic to me.. Artem The original question was: > I just became aware of the recent paper by Clementi et al. (see the > relevant abstracts below). It seems to me that the quest for > correlation functional is over: Clementi just did it (without any > density, but with many empirical parameters). He...He, water trimer, and > atomization energies to +/- 0.05 kcal/mol sound pretty convincing. ---------------------------------------- From: E. Lewars It seems to me that if this work refers to an *empirical* functional then the quest is not over. We want a *theoretically derived* functional with no empirical parameters. ---------------------------------------- From: Vitaly Rassolov I'm a bit familiar with the Clementi approach, and I don't like it (admittedly, without knowing some of the details). One can parametrize almost anything. The physics behind the parameters is pretty murky (if it exist). To me, scientists should simplify things, if possible. 16 parameters don't do that. And this ridiculous accuracy of .05 kcal is a proof that it is data fitting, not interaction description. ---------------------------------------- From: Stefan Grimme I recently had the opportunity to talk with Clementi about his approach and I also read a recent preprint (I think the one you mentioned). I'm not really convinced that the Coulomb-hole approach with a lot of parameters represents a reasonable quantum chemical approch. The main points of my criticism are as follows: 1. The dispersive interactions are modelled by an empirical formula which means that the approach is not more than a combination of force field technology and QM in that respect, i.e. its a new version of QM/MM. 2. The Coulomb-hole (CH) improves on the HF atomization energies but does NOT improve the relative energies which we are most interested in (Clementi strongly emphasizes on atomisation energies but forgot to look to the relative energies!). Simple organic reaction energies are even WORSE with the CH-HF method compared to HF. Even the simplest DFT's perform better in that respect. 3. An important part of the new CH-HF formalism is based on Mulliken charges and bond orders. We all know the problems associated with this approach (strong basis set dependence) and I therefore expect that each basis set would need its own parametrization (this problem has not been discussed in the paper I know). 4. Some time ago we tested a simpler (meaning a smaller number of parameters) version of CH-HF for He and H-. The result was that the radial densities were even worse than those from HF when compared with almost exact densities. My impression was that the basic correlation effects are NOT included accurately, even not in a qualitative manner. Again, DFT improves upon HF, at least qualitatively. Thus, I don't expect any improvement for properties with the CH-HF method (I think this question is important and Clementi has to investiagte this. We know that DFT does not only improve energies but also properties like dipole moments etc.; the reason is simply that the DFT densities are on the whole better than HF densities). In summary I think the approach is worth while testing it but I don't think that "the quest for correlation functional is over". -- __ ___________ Artem.Masunov@USA.net; Tel 212-650-7792 / \ / __ __ \ Computational Biophysical Chemistry Group / \/\ \ \ \ \ \ Chemistry Dept, City College, CUNY / /\ \ \ \ \ \ \ \ J-1325, Convent Ave, New York, NY 10031 / ____ \ \ \ \ \ \ \ -------http://www.biosys.net/artem---------- /__/\ _/\ _\ \ _\ \ _\ \ _\ FORGIVE MY NONSENSE AS I ALSO FORGIVE THOSE \ _\/ \/__/\ __/\ __/\ __/ WHO THINK THEY TALK SENSE -- ROBERT FROST