From chemistry-request@ccl.net Mon Oct 27 05:00:06 2003 Received: from mailbox.univie.ac.at (mail.univie.ac.at [131.130.1.27]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9R9xYch007437 for ; Mon, 27 Oct 2003 04:59:35 -0500 Received: from univie.ac.at (nt.itc.univie.ac.at [131.130.39.37]) by mailbox.univie.ac.at (8.12.10/8.12.10) with ESMTP id h9R9xOD2022724 for ; Mon, 27 Oct 2003 10:59:27 +0100 Message-ID: <3F9CEC7D.1030304~at~univie.ac.at> Date: Mon, 27 Oct 2003 10:59:25 +0100 From: Daniel Tunega Organization: Institute for Theoretical Chemistry and Structural Biology, University of Vienna User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020830 X-Accept-Language: de, sk, en MIME-Version: 1.0 To: CHEMISTRY~at~ccl.net Subject: CCL:cif to pdb Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-DCC-ZID-Univie-Metrics: imap 4245; Body=0 Fuz1=0 Fuz2=0 X-Spam-Status: No, hits=-0.3 required=7.0 tests=SIGNATURE_LONG_DENSE,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, I want to use crystal structure to calculate some molecular properties. Can anyone suggest a software that can convert cif file to pdb (or ent) file? Thanks Yi Try http://www.ccdc.cam.ac.uk/prods/mercury/ Daniel -- ****************************************************************** Daniel Tunega Institute for Theoretical Chemistry and Structural Biology University of Vienna Waehringerstrasse 17 A-1090 Vienna, Austria Phone: +43-1-4277-52749 Fax : +43-1-4277-9527 Email: Daniel.Tunega~at~univie.ac.at ****************************************************************** From jkl@ccl.net Mon Oct 27 03:33:36 2003 -0500 Message-Id: <200310270837.QAA28695<>ns.ciac.jl.cn> Date: Mon, 27 Oct 2003 16:36:40 +0800 From: zhijian WU >ns.ciac.jl.cn> Reply-To: zjwu<>ns.ciac.jl.cn To: "jkl<>ccl.net" >ccl.net> Subject: CCL: How to run CASSCF/TDDFT in Gaussian Organization: ciac ----------message------- Hi, CCLers, I am going to calculate the geometry (ground and excited states) of a transition metal dimer using CASSCF. But it seems it doesnot work. Does anybody know how to make a calculation using CASSCF? Is it possible to use CASSCF or TDDFT to optimize the structure? The keywords I used is: ************************ #HF/Lanl2dz guess=only pop=reg ..... --Link1-- #CASSCF(4,6)/Lanl2dz guess=read pop=reg ... ************************* The program exits with the following message: ********************* The smallest eigenvalue of the overlap matrix is 1.872D-03 NBasis= 44 RedAO= F NBF= 10 2 5 5 2 10 5 5 NBsUse= 44 1.00D-04 NBFU= 10 2 5 5 2 10 5 5 RdChkP: Unable to locate IRWF=0 Number= 522. Error termination via Lnk1e in d:\G98W\l401.exe. Job cpu time: 0 days 0 hours 0 minutes 7.0 seconds. File lengths (MBytes): RWF= 15 Int= 0 D2E= 0 Chk= 1 Scr= 1 ********************* Any message is welcomed. Best wishes, Zhijian WU Changchun Institute of Applied Chemistry Chinese Academy of Sciences ------------------------------------------------ From chemistry-request@ccl.net Sun Oct 26 15:25:27 2003 Received: from no-spam.it.helsinki.fi (NO-SPAM.it.helsinki.fi [128.214.205.34]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9QKOnch017709 for ; Sun, 26 Oct 2003 15:24:56 -0500 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by no-spam.it.helsinki.fi (8.12.10/8.12.10) with ESMTP id h9QKOmeY010139 for ; Sun, 26 Oct 2003 22:24:49 +0200 (EET) Received: from soul.helsinki.fi (localhost [127.0.0.1]) by soul.helsinki.fi (8.12.10/8.12.10) with ESMTP id h9QKOmDd142545 for ; Sun, 26 Oct 2003 22:24:48 +0200 (EET) Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.12.10/8.12.10/Submit) with ESMTP id h9QKOmts142546 for ; Sun, 26 Oct 2003 22:24:48 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Sun, 26 Oct 2003 22:24:48 +0200 (EET) From: Mikael Johansson X-X-Sender: mpjohans.-at-.soul.helsinki.fi To: chemistry.-at-.ccl.net Subject: CCL:Excited state optimisation with DFT In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-1.4 required=7.0 tests=IN_REP_TO,REFERENCES,USER_AGENT_PINE,X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello All! I need to do a geometry optimisation for the first excited triplet state for a molecule with a singlet ground state. Is there any principal difference in doing a "proper" geometry optimisation, with excited state gradients, compared with simply specifying the molecule to have two excess alpha electrons and doing a normal, "ground state", optimization on that? As I understand, there could be some "wave-function" flexibility differences in favour of using the exc-gradients, but apart from these more or less numerical issues, are there any other approximations involved? Or does a normal optimisation (both SCF and geometry) caveatlessly provide the lowest triplet state when using DFT? Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ From chemistry-request@ccl.net Mon Oct 27 02:27:35 2003 Received: from tigris.unideb.hu (tigris.unideb.hu [193.6.138.33]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9R7R2ch001101 for ; Mon, 27 Oct 2003 02:27:02 -0500 Received: from Cthulhu (193.6.133.108) by tigris.unideb.hu (MX V5.1-A Vn6f) with SMTP for ; Mon, 27 Oct 2003 08:25:26 +0100 Message-ID: <001e01c39c5b$b954df50$6c8506c1@Cthulhu> From: "Tamas E. Gunda" To: Subject: CCL: Mol2Mol 5.2 Date: Mon, 27 Oct 2003 08:27:05 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL Members, The new 5.2.0 version of the molecule file conversion, manipulation and utility program Mol2Mol is now available > from http://web.interware.hu/frenzy/mol2mol as trial or shareware version. The current version of Mol2Mol recognizes, and interconverts about 50 different file formats (including subtypes). It can slice multiple structural files to single ones (such as PDB models or MDL SD files to single ones) and vice versa in several variations. Support for PDB Chime subformat (with 1-2-3 bonds). Many molecular utilities. New in Mol2Mol 5.2: New file format: Hyperchem HCS [conformation search] (read only) New utility: - Superimposing and rms comparison of two molecules; use of all atoms or only selected ones, optionally with different weight factors; it can be done automatically for all structures in multiple files; fitted molecules can be outputted to multiple files. New in POV-Ray format: - bond types are supported in vector mode too; - stereo bond types are supported; - support for rendering elemental symbols in vector mode; - support for rendering atom aliases, linear substituents in 2D sketch files in vector mode; and several bug fixes. Mol2Mol is a very handy set of tools for everybody dealing with molecular modelling. It is impossible to write here all of the features of Mol2Mol, but have a look at its home page: http://web.interware.hu/frenzy/mol2mol POV-Ray fans may also have a look at: http://dragon.klte.hu/~gundat/povraya.htm The program is available as 30 days unrestricted trial version or as shareware version. From chemistry-request@ccl.net Mon Oct 27 10:05:31 2003 Received: from mailhost.ens-lyon.fr (pluvier.ens-lyon.fr [140.77.167.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9RF50ch020043 for ; Mon, 27 Oct 2003 10:05:00 -0500 Received: by mailhost.ens-lyon.fr with scanned-ok (Exim 3.35 #1 (Debian)) id 1AE8vS-0008VN-00 for ; Mon, 27 Oct 2003 16:04:58 +0100 Received: from mailhost.ens-lyon.fr ([127.0.0.1]) by localhost (pluvier [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 31568-07 for ; Mon, 27 Oct 2003 16:04:57 +0100 (CET) Received: from [140.77.2.15] (helo=140.77.2.15) by mailhost.ens-lyon.fr with esmtp (Exim 3.35 #1 (Debian)) id 1AE8vP-0008TR-00 for ; Mon, 27 Oct 2003 16:04:55 +0100 From: Paul Fleurat-Lessard Organization: Laboratoire de Chimie / ENS Lyon To: chemistry[at]ccl.net Subject: Replacement for Cerius2 ? Date: Mon, 27 Oct 2003 16:16:32 +0100 User-Agent: KMail/1.5 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Disposition: inline Message-Id: <200310271616.32349.Paul.Fleurat-Lessard[at]ens-lyon.fr> X-Virus-Scanned: by amavisd-new-20030616-p5 (Debian) at ens-lyon.fr X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h9RF5Vch020063 Dear all, We are working in theoretical study of surface catalysis. Up to now, we were using Cerius2 to prepare our input files and to visualize the results of our calculations. We are planning to move, and we will not have access anymore to Cerius2. Do you know some software to replace it ? Up to now, I have found only Material Studio (sold by Accelrys, same company as Cerius2). In particular, do you know software running under Linux ? Thanks in advance, Paul. -- Dr Fleurat-Lessard Paul e-mail: Paul.Fleurat-Lessard[at]ens-lyon.fr Laboratoire de Chimie Ecole Normale Supirieure de Lyon Tel: + 33 (0)4 72 72 81 54 46, Allie d'Italie Fax: + 33 (0)4 72 72 84 83 69364 Lyon Cedex 07 From chemistry-request@ccl.net Mon Oct 27 10:21:22 2003 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9RFKpch020893 for ; Mon, 27 Oct 2003 10:20:51 -0500 Received: from gollum.unb.ca (gollum.unb.ca [131.202.3.51]) by mailserv.unb.ca (8.12.10/8.12.6) with ESMTP id h9RFKnmc005200 for ; Mon, 27 Oct 2003 11:20:49 -0400 Received: from gollum.unb.ca (localhost.localdomain [127.0.0.1]) by gollum.unb.ca (8.12.8/8.12.8) with ESMTP id h9RFKnjS011728 for ; Mon, 27 Oct 2003 11:20:49 -0400 Received: (from apache@localhost) by gollum.unb.ca (8.12.8/8.12.8/Submit) id h9RFKmgO011722 for chemistry~at~ccl.net; Mon, 27 Oct 2003 11:20:48 -0400 Received: from athlon2.chem.unb.ca (athlon2.chem.unb.ca [131.202.171.176]) by webmail.unb.ca (IMP) with HTTP for ; Mon, 27 Oct 2003 11:20:48 -0400 Message-ID: <1067268048.3f9d37d0be439~at~webmail.unb.ca> Date: Mon, 27 Oct 2003 11:20:48 -0400 From: Joey Harriman To: CCL posting Subject: Implicit MD simulations in Amber MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 131.202.171.176 X-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: not spam (whitelisted), SpamAssassin (score=-0.6, required 5, SPAM_PHRASE_02_03, USER_AGENT, USER_AGENT_IMP) X-Spam-Status: No, hits=-0.3 required=7.0 tests=USER_AGENT_IMP version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi everyone, I am currently in the process of running some implicit MD simulations in Amber7. As far as I can tell the only flags that need to be included in the MD input file are: gbsa=1 igb=1 extdiel=*** Can anyone confirm this? In addition, I am trying to do a MD simulation on a ligand in Toluene (extdiel=2.4)...are there any suggestions to make this calculation faster? I am currently usine SHAKE 2 for the calculations. Thanks in advance for your response, Joey Harriman ---------------------------------- Joey Harriman MSc Computational Chemistry University of New Brunswick Room 228 Toole Hall s808o~at~unb.ca 476-6543 ---------------------------------- From chemistry-request@ccl.net Mon Oct 27 12:05:40 2003 Received: from mxout2.cac.washington.edu (mxout2.cac.washington.edu [140.142.33.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9RH58ch031443 for >ccl.net>; Mon, 27 Oct 2003 12:05:08 -0500 Received: from hymn17.u.washington.edu (hymn17.u.washington.edu [140.142.15.131]) by mxout2.cac.washington.edu (8.12.10+UW03.09/8.12.10+UW03.09) with ESMTP id h9RH56hu010328 for >ccl.net>; Mon, 27 Oct 2003 09:05:07 -0800 Received: from localhost (localhost [127.0.0.1]) by hymn17.u.washington.edu (8.12.10+UW03.09/8.12.10+UW03.09) with ESMTP id h9RH56ki028371 for >ccl.net>; Mon, 27 Oct 2003 09:05:06 -0800 Date: Mon, 27 Oct 2003 09:05:06 -0800 (PST) From: liaoyi<>u.washington.edu To: chemistry<>ccl.net Subject: Thanks a lot and a summary about cif to pdb Message-ID: >hymn17.u.washington.edu> Received: from [128.95.173.122] by hymn17.u.washington.edu via HTTP; Mon, 27 Oct 2003 09:05:05 PST MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII X-Spam-Status: No, hits=1.2 required=7.0 tests=MSG_ID_ADDED_BY_MTA_2,NO_REAL_NAME,USER_AGENT_PINE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, Thanks a lot for all the replys of my question about cif to pdb. To those who are also interested, here are the summary of all the answers. Mercury, freeware provided by CCDC (Cambridge Crystallographic Data Centre), was recommended by several people. www.ccdc.cam.ac.uk/mercury http://www.ccdc.cam.ac.uk/prods/mercury Others are: Mol2Mol http://web.interware.hu/frenzy/mol2mol platon www.cryst.chem.uu.nl/platon/ EnCIFer (http://www.ccdc.cam.ac.uk/prods/encifer/) related webpages: http://www.bernstein-plus-sons.com/software/cif2pdb/ http://pdb.rutgers.edu/mmcif/CIFTr/index.html Thanks again. Yi From chemistry-request@ccl.net Mon Oct 27 14:21:06 2003 Received: from qtp.ufl.edu (entry.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9RJKYch004093 for ; Mon, 27 Oct 2003 14:20:34 -0500 Received: from pc1 (dred1 [192.168.4.129]) by qtp.ufl.edu (8.12.8p1/8.12.8/Server/deumens) with SMTP id h9RJKFWo010970; Mon, 27 Oct 2003 14:20:32 -0500 (EST) Message-ID: <017201c39cc1$22ed8b00$8104a8c0_at_qtp.ufl.edu> From: "Stefan Fau" To: "Mikael Johansson" Cc: "CCL - all" References: Subject: CCL:Re: Excited state optimisation with DFT Date: Mon, 27 Oct 2003 14:32:42 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 X-Scanned-By: MIMEDefang 2.36 X-Spam-Status: No, hits=-0.5 required=7.0 tests=REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Mikael, a "ground state" method uses the variational principle to find the best wavefunction for a given spatial and electronic symmetry. Therefore, it can be used whenever there are no lower-lying states of the same (nuclear and electronic) symmetry and multiplicity. In contrast, excited state methods find wavefunctions that are orthogonal to all lower-lying wavefunctions of the same symmetry and multiplicity. The results of regular ground-state methods for symmetry-restricted calculations should always be checked to see if there are imaginary frequencies. Similarly, a different multiplicity may have a lower energy solution. Stefan ______________________________________________________________________ Dr. Stefan Fau | fau_at_qtp.ufl.edu University of Florida | (352) 392-6714 Quantum Theory Project 2319 NPB #92, P.O.Box 118435 Gainesville, FL 32611-8435 From chemistry-request@ccl.net Mon Oct 27 15:02:41 2003 Received: from uni-kl.de (mail.uni-kl.de [131.246.137.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9RK29ch005467 for ; Mon, 27 Oct 2003 15:02:10 -0500 Received: from mailgate1.uni-kl.de (mailgate1.uni-kl.de [131.246.120.5]) by uni-kl.de (8.12.8/8.12.8) with ESMTP id h9RK28rO024446 for ; Mon, 27 Oct 2003 21:02:08 +0100 (MET) Received: from aixs1.rhrk.uni-kl.de (aixs1.rhrk.uni-kl.de [131.246.137.3]) by mailgate1.uni-kl.de (8.12.10/8.12.10) with ESMTP id h9RK28s4030929 for ; Mon, 27 Oct 2003 21:02:08 +0100 Received: from aixd1.rhrk.uni-kl.de ([131.246.137.210]) by aixs1.rhrk.uni-kl.de with esmtp (Exim 4.20) id 1AEDZ1-000G9s-Vj for chemistry:at:ccl.net; Mon, 27 Oct 2003 21:02:07 +0100 Received: from mwalter (helo=localhost) by aixd1.rhrk.uni-kl.de with local-esmtp (Exim 3.03 #5) id 1AEDZ1-000Qyk-00 for chemistry:at:ccl.net; Mon, 27 Oct 2003 21:02:07 +0100 Date: Mon, 27 Oct 2003 21:02:07 +0100 (MEZ) From: Marc Walter To: chemistry:at:ccl.net Subject: ECPp`s for Ba and Sr In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-0.5 required=7.0 tests=IN_REP_TO version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi CCLers, I want to calculate a few organometallic compounds containing Ba and Sr. I was therefore looking for ECP`s on both elements to implement them into my G98 inputs. As far as I know the Stuttgart ECP`s for Barium in G98 contain the wrong contraction factors. Can anybody point me to a source of these corrected basis sets in the correct Gaussian input format ? And furthermore I would appreciate any suggestions how to implement the ECP`s in the input file ? Thanks in advance. Marc Walter From chemistry-request@ccl.net Mon Oct 27 14:32:14 2003 Received: from juju1er.dyndns.org (AMarseille-202-1-1-231.w217-128.abo.wanadoo.fr [217.128.57.231]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9RJVgch004432 for ; Mon, 27 Oct 2003 14:31:43 -0500 Received: from free.fr (localhost [127.0.0.1]) by juju1er.dyndns.org (Postfix) with ESMTP id C036A24EB63 for ; Mon, 27 Oct 2003 20:31:40 +0100 (CET) Date: Mon, 27 Oct 2003 20:31:37 +0100 Mime-Version: 1.0 (Apple Message framework v552) Content-Type: text/plain; charset=ISO-8859-1; format=flowed Subject: Atom contribution From: Julien Chiron To: chemistry:at:ccl.net Message-Id: <2E59652A-08B4-11D8-98B4-003065F5988C:at:free.fr> X-Mailer: Apple Mail (2.552) X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_APPLEMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h9RJWEch004464 Hi, I did some energy minimization calculation with GAMESS and I would like to get the atomic contribution for some MO. The MO calculation of GAMESS give the each AO contribution of each atom for each MO, but I didn't find how to get the global contribution of each atom in each MO. Is there a particular parameter to set in order to get these values ? As I'm not a theorician, is there an easy method to calculate these value "by hand" or with a home-made software ? Thanks Best regards Julien Chiron Laboratoire de Valorisation de la Chimie Fine Service 552 Faculti des Sciences de Saint Jirtme 13397 Marseille CEDEX 20 FRANCE Tel: 33 (0)4 91 28 81 92 Fax : 33 (0)4 91 28 83 23