From owner-chemistry@ccl.net Thu Jul 21 00:21:21 2005 From: "CCL" To: CCL Subject: CCL: W:molecular orbitals and potential energy scan Message-Id: <-28909-050721002010-7812-eSc6C2yCCSce8pLLLmWjCA[A]server.ccl.net> X-Original-From: "Bryan Wong" Sent to CCL by: "Bryan Wong" Hi! Does anyone know if there is an IOP keyword in Gaussian that will print out the molecular orbital coefficients for every single point in a potential energy scan? Bryan From owner-chemistry@ccl.net Thu Jul 21 04:08:54 2005 From: "CCL" To: CCL Subject: CCL: W:molecular orbitals and potential energy scan Message-Id: <-28910-050721025023-499-eSc6C2yCCSce8pLLLmWjCA%x%server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= Hi, IOp(5/33=2) should print MOs as long as density matrices. CCL a écrit : > Sent to CCL by: "Bryan Wong" > Hi! > > Does anyone know if there is an IOP keyword in Gaussian that will print out the molecular orbital coefficients for every single point in a potential energy scan? > > Bryan> > > > > -- *********** Dr. Nicolas Ferre' *********** Laboratoire de Chimie Theorique et de Modelisation Moleculaire UMR 6517 - CNRS Universites Aix-Marseille Case 521 Centre de Saint-Jerome 13397 - Marseille Cedex 20, France Tel : (+33)4.91.28.27.33 Fax : (+33)4.91.28.87.58 http://www.up.univ-mrs.fr/cbrl/lctmm ************************************************************** From owner-chemistry@ccl.net Thu Jul 21 04:43:04 2005 From: "CCL" To: CCL Subject: CCL: CCSD convergence in g03 Message-Id: <-28911-050721043851-23271-eSc6C2yCCSce8pLLLmWjCA(_)server.ccl.net> X-Original-From: Gert von Helden Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v622) Sent to CCL by: Gert von Helden Dear all, I am trying to do a single point calculation of a molecular complex at the CCSD(T) level using g03 rev C.02, 64 bit on an Opteron. I am using the 6-311++G(2d,p) basis, resulting in 408 BFs. The problem is that the CCSD does not converge. The convergence of the wavefunction ("Norm of the A-vectors") oscillates between 1E-3 and 1E-4 and convergence, even after 50 iterations, is nowhere in sight. Delta E oscillates between 1E-6 and 1E-8. Would a different basis set help? The disk is to small for the aug-cc-pvtz basis. I would appreciate any suggestions. Thanks, Gert von Helden ------------------------------------- Gert von Helden Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 14195 Berlin tel.: +49-30-8413 5615 fax: +49-30-8413 5603 From owner-chemistry@ccl.net Thu Jul 21 06:39:57 2005 From: "CCL" To: CCL Subject: CCL: PCM error termination Gaussian03 Message-Id: <-28912-050721055937-15738-eSc6C2yCCSce8pLLLmWjCA[#]server.ccl.net> X-Original-From: Sofia Godinho Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Mime-Version: 1.0 Sent to CCL by: Sofia Godinho Dear CCL member, while running a PCM calculation with Gaussian03 I got an error message. This happens both when I try to optimise with IEFPCM or to run just a PCM SinglePoint. And not just with one conformation. I tried two different for the same molecule. The last part of one the output files is as follows: --------------------------------------------------------------------------------------------------------------------------- Polarizable Continuum Model (PCM) ================================= Model : PCM. Atomic radii : UAHF (United Atom Topological Model). Polarization charges : Total charges. Charge compensation : None. Solution method : Matrix inversion. Cavity : GePol (RMin=0.200 OFac=0.890). Default sphere list used, NSphG= 13. Tesserae with average area of 0.200 Ang**2. Solvent : Water, Eps = 78.390000 Eps(inf)= 1.776000 RSolv = 1.385000 Ang. ------------------------------------------------------------------------------ AdVTs1: ISph= 648 is engulfed by JSph= 649 but Ae( 648) is not yet zero! Error termination via Lnk1e in /usr/local/chem/g03.C02/g03/l301.exe at Sat Jul 16 17:39:50 2005. ----------------------------------------------------------------------------------------------------------------------------------- What does this means?...How to get around it? Could you kindly help me to solve the problem? Many thanks! Sofia Godinho godinho.sofia at gmail.com From owner-chemistry@ccl.net Thu Jul 21 06:40:39 2005 From: "CCL" To: CCL Subject: CCL: W:All electron basis set for La-Ac Message-Id: <-28913-050721063527-18579-eSc6C2yCCSce8pLLLmWjCA]~[server.ccl.net> X-Original-From: "Jordi Cirera" Sent to CCL by: "Jordi Cirera" We are trying to do calculations in organometallic systems with Lantanide elements,and we want to do it with all electron basis set. We have found the ANO-RCC basis set that is all electron, but is decontracted (and really big), and we are interested in know if someone knows if there is another basis set for those elementes contracted. Thanks in advance to all of you. Jordi Cirera From owner-chemistry@ccl.net Thu Jul 21 07:43:47 2005 From: "CCL" To: CCL Subject: CCL: photoabsorbtion/photodetachment Message-Id: <-28914-050721074215-17742-eSc6C2yCCSce8pLLLmWjCA|*|server.ccl.net> X-Original-From: may abdelghani Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 MIME-Version: 1.0 Sent to CCL by: may abdelghani Hello, CCLers what is the diference between photoabsorbtion and photodetachment, and how we can modelate them theoriticaly? best regards ___________________________________________________________________________ Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! Messenger Téléchargez cette version sur http://fr.messenger.yahoo.com From owner-chemistry@ccl.net Thu Jul 21 14:06:25 2005 From: "CCL" To: CCL Subject: CCL: PMF drug-docking scoring function Message-Id: <-28915-050721132854-24413-eSc6C2yCCSce8pLLLmWjCA[a]server.ccl.net> X-Original-From: Mark Thompson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed MIME-Version: 1.0 Sent to CCL by: Mark Thompson I would like to hear from anyone who has an implementation of Ingo Muegge's PMF scoring function in a commercial or non-commercial product. I am interested in comparing some results. Thanks in advance, Mark Thompson mark[a]arguslab.com http://www.arguslab.com From owner-chemistry@ccl.net Thu Jul 21 16:02:59 2005 From: "CCL" To: CCL Subject: CCL: CCL smiles Message-Id: <-28916-050721151732-10176-eSc6C2yCCSce8pLLLmWjCA^-^server.ccl.net> X-Original-From: "Robinson, James" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Sent to CCL by: "Robinson, James" Smiles are a good choice for storing and sorting textual information. However, ring closure reaction are often stereospecific as one must decide between thermodynamic and kinetic products. Smiles strings may not be the best choice for storing stereoisomers. To find the preferred outcome from a ring closure you might use a script that allows for Baldwins rules of ring closure. It took me a few years with b3lyp to sort out a set of ring closures. Also gas phase calcs may yield stable zwitterions whereas solvated calcs may not indicate stable zwitterions. James -----Original Message----- > From: owner-chemistry^-^ccl.net [mailto:owner-chemistry^-^ccl.net] Sent: 17 July 2005 17:49 To: Robinson, James Subject: CCL: W:SMILES AND MODELLING Sent to CCL by: "Antonio Starcevic" Dear All; We are a academic group working on a bioinformatics application written in Java, that involves certain chemistry solutions. That's the part we need some help solving. We are storing our molecules in SMILES format, and at the end our goal is to turn linear structures into cyclisized. FIRST QUESTION: are SMILES the best choice for database entries and computation of new structres??? SECOND QUESTION: if you model spontaneous cyclization from a linear compound, how can you determine which product out of all possible ones is most likely to be the real thing THIRD QUESTION: is there a software that can help us solve "second question", and could you recomend us some(it should cooperate with SMILES "Daylight toolkit" if possible) P.S. are there any Java libraries for this stuff??? Thanks for all suggestions!