From chemistry-request@ccl.net Wed Nov 24 10:55:41 2004 Received: from atom.chem.iupui.edu (atom.chem.iupui.edu [134.68.137.125]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAOFtcrq032262 for ; Wed, 24 Nov 2004 10:55:38 -0500 Received: from atom.chem.iupui.edu:16080 (localhost [127.0.0.1]) by atom.chem.iupui.edu (Postfix) with SMTP id 2F1FDE9FE8B; Wed, 24 Nov 2004 10:12:33 -0600 (CST) Received: from 65.43.84.126 (SquirrelMail authenticated user boyd) by atom.chem.iupui.edu with HTTP; Wed, 24 Nov 2004 10:12:33 -0600 (CST) Message-ID: <51222.65.43.84.126.1101312753.squirrel(at)atom.chem.iupui.edu> Date: Wed, 24 Nov 2004 10:12:33 -0600 (CST) Subject: What software will work? From: boyd(at)chem.iupui.edu To: "CCL" Cc: boyd(at)chem.iupui.edu User-Agent: SquirrelMail/1.4.0 MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 X-Priority: 3 Importance: Normal X-Spam-Status: No, hits=5.7 required=7.5 tests=NO_REAL_NAME,PRIORITY_NO_NAME, RCVD_IN_DSBL,RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net CCLers, We are seeking recommendations on software that can do ALL the following: * run Monte Carlo conformational searches on organic molecules with 200-300 atoms. * use the MMFF force field. * select which torsional angles are free to rotate and set their step size. * fix some torsional angles. * analyze the conformers produced, such as exporting the resulting torsional angles and energies to a spreadsheet. We have tried SYBYL, MacroModel, Spartan, Cerius2, Quanta, and InsightII. In each case, the software was unable to provide a solution. Suggestions? Thankful for your giving recommendations, Don Donald B. Boyd, Ph.D. Department of Chemistry Indiana University-Purdue University at Indianapolis E-mail boyd(at)chem.iupui.edu From chemistry-request@ccl.net Fri Nov 26 04:36:28 2004 Received: from hermes1.cf.ac.uk (hermes1.cf.ac.uk [131.251.0.112]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAQ9aR6A022958 for ; Fri, 26 Nov 2004 04:36:28 -0500 Received: from maincf1p.cf.ac.uk ([131.251.4.20]) by hermes1.cf.ac.uk with esmtp (Exim 4.34) id 1CXcki-0000bg-Pt for chemistry.-at-.ccl.net; Fri, 26 Nov 2004 09:50:56 +0000 Received: from Cardiff_University-MTA by MAINCF1P.cf.ac.uk with Novell_GroupWise; Fri, 26 Nov 2004 09:50:56 +0000 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.5.2 Date: Fri, 26 Nov 2004 09:50:18 +0000 From: "Jamie Platts" To: Subject: X3LYP Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline X-Spam-Status: No, hits=4.0 required=7.5 tests=ALUSSINAN_5,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL'ers, I've been reading with interest Xu and Goddard's recent paper on X3LYP, for which the results look very impressive. Unfortunately, I don't have access to Jaguar, so was thinking about how to implement this in Gaussian, but can't see how to include contributions from two different non-local exchange functionals. Has anybody tried this, or had success with another package? Best regards, Jamie ---------------------------------------------------------- Jamie Platts School of Chemistry Phone: +44 (0) 2920 874950 Cardiff University Email: platts.-at-.cf.ac.uk P.O. Box 912 FAX: +44 (0) 2920 874030 Cardiff CF10 3TB www.cf.ac.uk/chemy From chemistry-request@ccl.net Wed Nov 24 18:56:09 2004 Received: from web53904.mail.yahoo.com (web53904.mail.yahoo.com [206.190.36.214]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iAONu7nw018174 for ; Wed, 24 Nov 2004 18:56:07 -0500 Received: (qmail 74687 invoked by uid 60001); 25 Nov 2004 00:10:31 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=iN2lf2Wrb93YnoLle8ja/TD3S1aDjt3ZZ8GO+nccPmWbX0o/NJdbvRCo1gjwwgYd+J0nZ4/VZEZc2OzRzbwXUqTHPgM1Z3rYJnSqaYtsA1u/AriIinHUMrw7yvAZ1/BV/f+j6/bF/w3mFy3Hw9JRrWPD3sC1FLECHxEgFvZchw8= ; Message-ID: <20041125001031.74681.qmail:at:web53904.mail.yahoo.com> Received: from [129.109.59.107] by web53904.mail.yahoo.com via HTTP; Wed, 24 Nov 2004 16:10:31 PST Date: Wed, 24 Nov 2004 16:10:31 -0800 (PST) From: IEJMD Subject: IECMD 2004 - Conference Program To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=1.1 required=7.5 tests=DRUGS_MUSCLE,FVGT_m_MULTI_ODD2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Internet Electronic Conference of Molecular Design 2004 IECMD 2004, November 29 - December 12 http://www.biochempress.com All accepted papers are posted on the Web and can be downloaded as PDF files from http://www.biochempress.com The complete Conference program is included below. The discussions of the IECMD 2004 papers will take place on the Web, using the Yahoo! group iecmd2004, http://groups.yahoo.com/group/iecmd2004 Please visit the IECMD 2004 discussion site at http://groups.yahoo.com/group/iecmd2004 to sign-up and send comments to the group. Subscribe: iecmd2004-subscribe:at:yahoogroups.com Best regards, IECMD 2004 Organizers ---------------------------------- IECMD 2004, Day 1, November 29 1. IECMD 2004, paper 2 Reaction Rate Assessment of Multiphonon Relaxation Mladen Georgiev and Alexander Gochev 2. IECMD 2004, paper 5 Theoretical Study on the Potential Energy Surface of the CH4-CO complex Nobuaki Tanaka , Hiromasa Nishikiori , and Tsuneo Fujii 3. IECMD 2004, paper 10 Toxicity Analysis of Polychlorinated Dibenzofurans through Global and Local Electrophilicities Utpal Sarkara , Ramakrishnan Parthasarathi , Venkatesan Subramanian , and Pratim Kumar Chattaraj 4. IECMD 2004, paper 40 Aconitum and Delphinium sp. Alkaloids as Antagonist Modulators of Voltage-Gated Na+ Channels: PM3 and QSAR Investigations Malakhat A. Turabekova , Bakhtiyor F. Rasulev , and Mikhail G. Levkovich ----------------------------------------------------------------------- IECMD 2004, Day 2, November 30 1. IECMD 2004, paper 20 Ab initio computations for the ring-opening potential of propylene oxide: roles of a proton and a water molecule Hiroyuki Shinoda , Michio Sayama , Yoshihiro Mori , and Mineyuki Mizuguchi 2. IECMD 2004, paper 21 +Scaly; magnetism of carpet-like polymers of C60 Elena F. Sheka , V. A. Zayets , and I. Ya. Ginzburg 3. IECMD 2004, paper 19 The Structure of I-(H2O)4 Cluster: Ab initio study Masao Masamura 4. IECMD 2004, paper 41 Importance of Alignment in Developing 3-D QSAR Models of 1,5-Diaryl Pyrazoles for Prediction of COX-2 Inhibitory Activity Ramasamy Thilagavathi and Asit K. Chakraborti 5. IECMD 2004, paper 6 A Recalculation of Quantitative Structure Chromatographic Retention Time Relationships on Natural Phenols and Sterols Found in Olive Oil Francisco Hueso-Ureqa , Nuria Illan Cabeza , Sonia B. Jiminez-Pulido , Miguel N. Moreno-Carretero , and Josi M. Martmnez-Martos ----------------------------------------------------------------------- IECMD 2004, Day 3, December 1 1. IECMD 2004, paper 23 Evaluation of 4-Azaindolo[2,1-b]quinazoline-6,12-diones Interaction With Hemin and Hemozoin: A Spectroscopic, Xray Crystallographic and Molecular Modeling Study Rickey P. Hicks , Daniel A. Nichols , Charles A. DiTusa , David J. Sullivan , Mark G. Hartell , Brandon W. Koser , and Apurba K. Bhattacharjee 2. IECMD 2004, paper 26 Unexpected Binding Affinity of [2.2]Paracyclophane to Cations Antonio Frontera , Carolina Garau , David Quiqonero , Pablo Ballester , Antoni Costa , and Pere M. Dey` 3. IECMD 2004, paper 28 Calculation of Ionization Constants of Monoprotic Weak Acids in Aqueous Solutions Sonia E. Blanco and Ferdinando H. Ferretti 4. IECMD 2004, paper 1 A QSAR Approach to Physico-Chemical Data for Organophosphates with Special Focus on Known and Potential Nerve Agents Lars Carlsen ----------------------------------------------------------------------- IECMD 2004, Day 4, December 2 1. IECMD 2004, paper 33 Density Functional Study on the Highest and Lowest Spin States of [Mn2O2(H2O)8]q+ (q = 0, 2, 4) Masaki Mitani , Takeharu Katsurada , Yohei Wakamatsu , and Yasunori Yoshioka 2. IECMD 2004, paper 29 Syn-2,7-disilatetracyclo[6.2.1.13,602,7]dodec-2(7)-ene: Structural Influence of Incorporation of Disilene into Sesquinorbornene Framework: A DFT Study Davor Margetic , Mario Vazdar , and Mirjana Eckert-Maksic 3. IECMD 2004, paper 32 Modeling Structure Property Relationships with Kernel Recursive Least Squares Rajshekhar , Abhijit Kulkarni , Valadi K. Jayaraman , and Bhaskar D. Kulkarni 4. IECMD 2004, paper 44 QSAR Study on 5-N-Substituted-2-(Substituted Benzenesulphonyl) Glutamines as Antitumor Agents through Synthesis and Biological Evaluation: Part III Bikash Debnath , Soma Samanta , Shovanlal Gayen , Anindya Basu , Balaram Ghosh , and Tarun Jha 5. IECMD 2004, paper 14 Property-Based Design Methodology I: Parameters Influencing Solubility R. DeWitte , E. Kolovanov , and F. Gorohov ----------------------------------------------------------------------- IECMD 2004, Day 5, December 3 1. IECMD 2004, paper 35 Computational quantum chemistry study of a self-assembled Zn(II) porphyrin box Fabio Pichierri 2. IECMD 2004, paper 34 Changes in Dipole Moments and Polarization of a Two-Level System with Intramolecular Coupling Josi Luis Paz and Teresa Cusati 3. IECMD 2004, paper 43 On the Inclusion Ability of a Fluorinated Fluorescent Indolizine _-Cyclodextrin Sensor towards Volatile Organic Compounds David Landy , Georgiana G. Surpateanu , Sophie Fourmentin , Philippe Blach , Pirouz Shirali , Patrick Decock , and Gheorghe Surpateanu 4. IECMD 2004, paper 30 Chromatographic Estimation of Apparent Acid Dissociation Constants (pKa) in Physiological Resembling Conditions. A Case Study: Ionisable Non-Steroidal Anti-Inflammatory Drugs Juan Josi Martmnez-Pla , Laura Escuder-Gilabert , Salvador Sagrado , Rosa Marma Villanueva-Camaqas , and Marma Josi Medina-Hernandez 5. IECMD 2004, paper 15 Property-Based Design Methodology II: Assessing Elementary Substituents R. DeWitte , E. Kolovanov , and F. Gorohov ----------------------------------------------------------------------- IECMD 2004, Day 6, December 6 1. IECMD 2004, paper 36 Numerical Evaluation of Two-Center Overlap Integrals Over Slater-Type Orbitals and Convergence Properties Hassan Safouhi and Ahmed Bouferguene 2. IECMD 2004, paper 22 The nano-science of C60 molecule Elena F. Sheka 3. IECMD 2004, paper 25 New Application Design for a 3D Hydropathic Map-Based Search for Potential Water Molecules Bridging between Protein and Ligand Glen E. Kellogg , Micaela Fornabaio , Deliang L. Chen , and Donald J. Abraham 4. IECMD 2004, paper 16 Property-Based Design Methodology III: Identifying Creative Substituents R. DeWitte , E. Kolovanov , and F. Gorohov 5. IECMD 2004, paper 42 General and independent approaches to predict HERG affinity values Elena Fioravanzo , Nicola Cazzolla , Lucia Durando , Cristina Ferrari , Massimo Mabilia , Rosella Ombrato , and Marco Daniele Parenti ----------------------------------------------------------------------- IECMD 2004, Day 7, December 7 1. IECMD 2004, paper 45 Reduced Protein Model as a Tool in the Homology Modeling Andrzej Szymoszek and Martin Zacharias 2. IECMD 2004, paper 38 On the Charge Transfer Between a Toxin and a Biosystem Utpal Sarkar , Ramakrishnan Parthasarathi , Venkatesan Subramanian , and Pratim Kumar Chattaraj 3. IECMD 2004, paper 24 Thermochemistry of Organic and Heteroorganic Species. Part XIV. Application of IR Spectra of the Unsaturated Aliphatic Molecules for Thermochemistry of Vinylic and Allylic Free Radicals D. A. Ponomarev and V. V. Takhistov 4. IECMD 2004, paper 17 Property-Based Design Methodology IV: Heterocycle Replacement R. DeWitte , E. Kolovanov , and F. Gorohov 5. IECMD 2004, paper 3 Conformations of 2-Phenyl-3-Pyridylpropenoic Acid (a-Phenyl Pyridylcinnamic Acid) Dimers A Computational Study Istvan Palinks ----------------------------------------------------------------------- IECMD 2004, Day 8, December 8 1. IECMD 2004, paper 39 Adsorption Models of Bipyrazine on Silver Colloidal Nanoparticles: a Computational Study B. Pergolese , M. Muniz-Miranda , and A. Bigotto 2. IECMD 2004, paper 11 A Theory of the Colossal Van-der-Waals Binding in Soft and Hard Condensed Matter Mladen Georgiev , Alexander Gochev , and Jai Singh 3. IECMD 2004, paper 9 A Predictive Model for Blood-Brain Barrier Penetration Xuchun Fu , Zhifang Song , and Wenquan Liang 4. IECMD 2004, paper 8 Modeling Human Neurokinin-1 Receptor Structure using the Crystal Structure of Bovine Rhodopsin Santosh A. Khedkar , Alpeshkumar K. Malde , and Evans C. Coutinho ----------------------------------------------------------------------- IECMD 2004, Day 9, December 9 1. IECMD 2004, paper 37 Use of Lanczos Tau Method to Derive Polynomial Approximate from the Addition Theorem of Slater Type Orbitals Ahmed Bouferguene and Hassan Safouhi 2. IECMD 2004, paper 7 Study of the Glass Transition Temperatures of Stereoregular PMMAs Using Different Force Fields Armand Soldera and Noureddine Metatla 3. IECMD 2004, paper 18 Numerical characterization of RNA secondary structure Jiaquan Zhan , Bo Liao , and Yusen Zhang 4. IECMD 2004, paper 31 Peptide Potential Energy Surfaces and Protein Folding Francisco Torrens ----------------------------------------------------------------------- IECMD 2004, Day 10, December 10 1. IECMD 2004, paper 4 pH-Dependent Complexation of Methacryloyloxydecyl Dihydrogen Phosphate (MDP) with Dipalmitoylphosphatidylcholine (DPPC) Liposomes: DSC and NMR Measurements Seiichiro Fujisawa , Mariko Ishihara , and Yoshinori Kadoma 2. IECMD 2004, paper 12 Molecular Volume and Density Models for Alkanes and Monoderivatives of Hydrocarbon Chenzhong Cao and Shuo Gao 3. IECMD 2004, paper 27 Qspr Evaluation of Thermodynamic Properties of Acyclic and Aromatic Compounds Pablo R. Duchowicz , Eduardo A. Castro , and Alexei N. Pankratov 4. IECMD 2004, paper 13 Finding Protein Coding Genes in the Yeast Genome Based on the Characteristic Sequences Ping-an He , Chun Li , and Jun Wang __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From chemistry-request@ccl.net Wed Nov 24 08:32:37 2004 Received: from poincare.ciril.fr (medecine.uhp-nancy.fr [194.214.217.19]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAODWZkY019354 for ; Wed, 24 Nov 2004 08:32:36 -0500 Received: from cbt.uhp-nancy.fr (host5.lctn.uhp-nancy.fr [193.50.239.5]) (authenticated bits=0) by poincare.ciril.fr (8.13.1/8.13.1/Guy-23-06-2004) with ESMTP id iAODkYm7018977 (version=TLSv1/SSLv3 cipher=EXP1024-RC4-SHA bits=56 verify=NOT); Wed, 24 Nov 2004 14:46:34 +0100 (MET) Sender: moreau^at^poincare.ciril.fr Message-ID: <41A490D5.D8C5D627^at^cbt.uhp-nancy.fr> Date: Wed, 24 Nov 2004 14:47:02 +0100 From: Yohann Moreau Organization: Equipe de Chimie et Biochimie =?iso-8859-1?Q?Th=E9oriques?= X-Mailer: Mozilla 4.7iC-CCK-MCD [en_US] (X11; I; AIX 4.3) X-Accept-Language: fr, en MIME-Version: 1.0 To: khunter^at^mta.ca CC: chemistry^at^ccl.net Subject: Re: CCL:CCL : question about "Inaccurate quadrature in CalDSu" References: <1101300583.41a48367b9481^at^webmail.mta.ca> Content-Type: multipart/alternative; boundary="------------E9C9AC6D1BBA6D03AAD7D241" X-Spam-Score: -1.424 () BAYES_01,HTML_MESSAGE X-Scanned-By: poincare.ciril.fr on 194.214.217.19 X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_MESSAGE,IMPRONONCABLE_1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --------------E9C9AC6D1BBA6D03AAD7D241 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi Ken, I've already seen this error, especially when using off-atomic basis set (which is your case). I don't exactly know the reason but to avoid it, you can try to use another method than Harris functional to determine your guess wave function. Try for example: guess=INDO which was the default in G98. I hope this will help you, Yohann khunter^at^mta.ca wrote: > I was attempting to run a single point calulation using MP2/aug-cc-pvtz. When > I first tried counterpoise=2 for these calulations, there were problems with > disk space, so I separated the BSSE calculation into the 5 parts. The first > part, with just the single point on the entire system, worked for all of the > complexes, but when used the same procedure with the Bq and added in the basis > set (MP2/gen and then at the end of the com file I placed the basis set from > the .log file from the first part), there seems to be the error that is stated > below... > > " > Leave Link 303 at Tue Nov 23 14:11:29 2004, MaxMem= 196608000 cpu: 1.3 > (Enter /programs/g03/Rev_c02/g03/l401.exe) > Harris functional with IExCor= 205 diagonalized for initial guess. > ExpMin= 2.53D-02 ExpMax= 1.53D+04 ExpMxC= 5.22D+02 IAcc=3 IRadAn= 5 > AccDes= 0.00D+00 > HarFok: IExCor= 205 AccDes= 0.00D+00 IRadAn= 5 IDoV=1 > ScaDFX= 1.000000 1.000000 1.000000 1.000000 > Warning: off-atom basis functions, so minimal bfn integration tests in XC > quadrature. > Spurious integrated density or basis function: > NE= 70 NElCor= 0 El error=1.21D-05 rel=1.73D-07 Tolerance=1.00D-03 > Shell 1 absolute error=9.55D-01 Tolerance=no limit > Shell 52 signed error=8.35D-01 Tolerance=1.00D-01 > Inaccurate quadrature in CalDSu. > Error termination via Lnk1e in /programs/g03/Rev_c02/g03/l401.exe at Tue Nov > 23 > 14:15:06 2004. > Job cpu time: 0 days 0 hours 3 minutes 53.9 seconds. > File lengths (MBytes): RWF= 54 Int= 0 D2E= 0 Chk= 1 Scr= > 1 > " > > Any assistance would be greatly appreaciated. > > Ken Hunter > Mount Allison University > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY^at^ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST^at^ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow^at^nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -- Yohann MOREAU, Doctorant Equipe de Chimie et Biochimie Thioriques UMR CNRS-UHP 7565 "SRMSC" BP 239, F-54506 Vandoeuvre-lhs-Nancy http://www.lctn.uhp-nancy.fr/Etudiants/Yohann.Moreau.html --------------E9C9AC6D1BBA6D03AAD7D241 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Ken,

I've already seen this error, especially when using off-atomic basis set (which is
your case). I don't exactly know the reason but  to avoid it, you can try to use another method
than Harris functional to determine your guess wave function. Try for example: guess=INDO
which  was the default in G98.

I hope this will help you,

Yohann
 

khunter^at^mta.ca wrote:

I was attempting to run a single point calulation using MP2/aug-cc-pvtz. When
I first tried counterpoise=2 for these calulations, there were problems with
disk space, so I separated the BSSE calculation into the 5 parts. The first
part, with just the single point on the entire system, worked for all of the
complexes, but when used the same procedure with the Bq and added in the basis
set (MP2/gen and then at the end of the com file I placed the basis set from
the .log file from the first part), there seems to be the error that is stated
below...

"
Leave Link  303 at Tue Nov 23 14:11:29 2004, MaxMem=  196608000 cpu:       1.3
 (Enter /programs/g03/Rev_c02/g03/l401.exe)
 Harris functional with IExCor=  205 diagonalized for initial guess.
 ExpMin= 2.53D-02 ExpMax= 1.53D+04 ExpMxC= 5.22D+02 IAcc=3 IRadAn=         5
AccDes= 0.00D+00
 HarFok:  IExCor= 205 AccDes= 0.00D+00 IRadAn=         5 IDoV=1
 ScaDFX=  1.000000  1.000000  1.000000  1.000000
 Warning:  off-atom basis functions, so minimal bfn integration tests in XC
quadrature.
 Spurious integrated density or basis function:
 NE=   70 NElCor=    0 El error=1.21D-05 rel=1.73D-07 Tolerance=1.00D-03
 Shell     1     absolute error=9.55D-01              Tolerance=no limit
 Shell    52       signed error=8.35D-01              Tolerance=1.00D-01
 Inaccurate quadrature in CalDSu.
 Error termination via Lnk1e in /programs/g03/Rev_c02/g03/l401.exe at Tue Nov
23
14:15:06 2004.
 Job cpu time:  0 days  0 hours  3 minutes 53.9 seconds.
 File lengths (MBytes):  RWF=     54 Int=      0 D2E=      0 Chk=      1 Scr=
   1
"

Any assistance would be greatly appreaciated.

Ken Hunter
Mount Allison University

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-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

-- 

               Yohann MOREAU, Doctorant                 
       Equipe de Chimie et Biochimie Théoriques   
               UMR CNRS-UHP 7565 "SRMSC"        
          BP 239, F-54506 Vandoeuvre-lès-Nancy  
http://www.lctn.uhp-nancy.fr/Etudiants/Yohann.Moreau.html
  --------------E9C9AC6D1BBA6D03AAD7D241-- From chemistry-request@ccl.net Thu Nov 25 01:40:08 2004 Received: from web42103.mail.yahoo.com (web42103.mail.yahoo.com [66.218.93.196]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iAP6e6Dx012451 for ; Thu, 25 Nov 2004 01:40:07 -0500 Received: (qmail 96957 invoked by uid 60001); 25 Nov 2004 06:54:31 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=lSYlkaTxJ/02egFLCeWlxWIZPBdZ5X4c1ysB4BZg3z4JMXWRASsVfHn/ssHctekYXpLqOir/Hoxuk21U/SED/c/wv2bWCLfvT+HF+xz6USGP8IC6+6zQTV9hDruaqWdLNb4nEhwm7jCeagpS9j294QuTJ4h3rSdFVijBKh14dAo= ; Message-ID: <20041125065431.96955.qmail^at^web42103.mail.yahoo.com> Received: from [146.230.128.29] by web42103.mail.yahoo.com via HTTP; Wed, 24 Nov 2004 22:54:31 PST Date: Wed, 24 Nov 2004 22:54:31 -0800 (PST) From: Sam Gusburg Subject: Gaussian 03 on Linux Clusters To: chemistry^at^ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-2050202607-1101365671=:96915" X-Spam-Status: No, hits=0.3 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-2050202607-1101365671=:96915 Content-Type: text/plain; charset=us-ascii Dear CCL'rs, What bothers me is that NCSA does not yet have a Linux cluster that is able to run Gaussian 03 in parallel? We would like to look at computational software that is running in parallel (non SMP system) on a Linux cluster. Does anyone have more information about successfull clusters (running Gaussian 03)? Cheers Sam --------------------------------- Do you Yahoo!? All your favorites on one personal page Try My Yahoo! --0-2050202607-1101365671=:96915 Content-Type: text/html; charset=us-ascii
Dear CCL'rs,
 
What bothers me is that NCSA does not yet have a Linux cluster that is able to run Gaussian 03 in parallel?  We would like to look at computational software that is running in parallel (non SMP system) on a Linux cluster.
 
Does anyone have more information about successfull clusters (running Gaussian 03)?
 
Cheers
Sam

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All your favorites on one personal page Try My Yahoo! --0-2050202607-1101365671=:96915-- From chemistry-request@ccl.net Wed Nov 24 16:05:42 2004 Received: from mail.monmouth.edu (mail.monmouth.edu [192.100.64.12]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAOL5fGF029707 for ; Wed, 24 Nov 2004 16:05:41 -0500 Received: from monmouth.edu (mu14162.backbone.monmouth.edu [10.1.1.63]) by mail.monmouth.edu (8.12.11/8.12.11) with ESMTP id iAOLK0mN021037; Wed, 24 Nov 2004 16:20:04 -0500 Message-ID: <41A4FAFF.7F0E9574^at^monmouth.edu> Date: Wed, 24 Nov 2004 16:19:59 -0500 From: Robert Topper Organization: Chemistry, Medical Technology and Physics, Monmouth University X-Mailer: Mozilla 4.76 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry^at^ccl.net Subject: ECCC10 April 2004 - Call for Papers Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Scanned-By: MIMEDefang 2.43 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net ECCC10 Announcement Dear colleagues, I am very pleased to invite your participation in the 10th Electronic Computational Chemistry Conference. ECCC10 will be held April 1-30 2005, entirely on the Internet, at http://eccc.monmouth.edu. As with the previous nine ECCCs, ECCC10 has NO registration fee and is a completely virtual, online conference. We are pleased to announce that Dr. Donald G. Truhlar (University of Minnesota) has agreed to present the keynote address to ECCC10. Dr. Truhlar is an internationally respected expert in computational chemistry and chemical physics who to date has co-authored nearly 700 research publications. The proceedings will be published in a special issue of Theoretical Chemistry Accounts. The ECCC is a multidisciplinary, international conference and spans all aspects of computational and theoretical chemistry and materials science, as well as computational molecular biology, computational and theoretical molecular and atomic physics, visualization, cheminformatics, the history of computational chemistry, computational chemistry and education, and all related fields. Participants will be able to view the presentations and discuss them entirely through a web browser. The ECCC was originally developed by Steven Bachrach, who also organized the first five meetings. Abstracts for all contributions to ECCC10 will be peer-reviewed to insure novelty, scientific value, and appopriateness for inclusion in the conference. This peer review is directed by members of the ECCC10 Scientific Organizing Committee, who have volunteered to help with all aspects of the conference. The members of the ECCC10 SOC are: Robert Topper, Monmouth University (Chair) Frederick R. Bennett, CSIRO Minerals David Chatfield, Florida International University Olga Dmitrenko, University of Delaware Guangyu Sun , NCI-Frederick, NIH Mark Tuckerman, New York University Amir Weitz, RAFAEL This year, following peer review of the abstracts we plan to publish a virtual online booklet of the accepted abstracts online sometime after the conference ends. In addition, presenting authors can elect to submit their work for additional peer review and publication in a special ECCC10 Proceedings issue of Theoretical Chemistry Accounts. All presentations must be made in HTML format and ideally will take full advantage of the interactive nature of the World-Wide Web (using animations, hyperactive molecules, etc.) to present their findings and conclusions. Authors may choose to either serve their contributions from their own local web site, or may request us to serve them from our own server. Uploaded contributions will be removed from our server at the end of ECCC10. As in ECCC8 and ECCC9, a single weeklong "interactive" session will be part of the conference. This session will be held via asynchronous posting of questions to the conference site, which authors can choose to receive either at the site, at their personal email account, or both. All authors must commit to having at least one coauthor available to answer questions (i.e. by checking the discussion board at least once daily) during the "interactive" session to provide timely responses (within approximately 24 hours) to any questions that conferees may have about their online presentation. Important dates for ECCC10 are: December 1, 2004 Registration (free) for ECCC10 begins January 28, 2005 - Abstracts must be submitted on the conference website March 24, 2005 - Final presentations of accepted presentations due online April 1, 2005 - ECCC10 begins April 11, 2005 Interactive Session begins April 18, 2005 Interactive Session ends April 30, 2005 ECCC10 ends June 30, 2005 Submissions to the ECCC10 Proceedings due As mentioned above, all ECCC10 presentations must be in HTML format, with their layout and presentation at the discretion of the authors. Authors who wish to submit an article to the ECCC10 Proceedings will need to develop their contribution according to the editorial standards and accepted formats of Theoretical Chemistry Accounts. We greatly look forward to your participation in ECCC10, and ask you to please encourage your colleagues and students to participate in what should be an excellent meeting. -- Robert Q. Topper Chair and Associate Professor Department of Chemistry, Medical Technology and Physics Monmouth University 400 Cedar Avenue West Long Branch, NJ 07764-1898 (732)571-4418 (voice);(732)263-5213 (fax) rtopper^at^monmouth.edu http://www.monmouth.edu/~rtopper From chemistry-request@ccl.net Tue Nov 23 22:33:25 2004 Received: from mx.seanet.com (mx.seanet.com [199.181.164.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAO3XNpV029944 for ; Tue, 23 Nov 2004 22:33:24 -0500 Received: from pepeketua.seanet.com (pepeketua.seanet.com [199.181.164.73]) by milkyway.seanet.com (8.13.1/8.13.1) with ESMTP id iAO3lQLj098835; Tue, 23 Nov 2004 19:47:26 -0800 (PST) (envelope-from mark)at(arguslab.com) Received: from planaria (c-24-18-182-93.client.comcast.net [24.18.182.93]) by pepeketua.seanet.com (Postfix) with ESMTP id E30091143F; Tue, 23 Nov 2004 19:47:43 -0800 (PST) Reply-To: From: "Mark Thompson" To: "Axel Mathieu" , "CCL" Subject: RE: ForceFields for macrocycles Date: Tue, 23 Nov 2004 19:47:42 -0800 Message-ID: <000501c4d1d8$59a47df0$0300a8c0@planaria> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0006_01C4D195.4B813DF0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.6604 (9.0.2911.0) Importance: Normal In-Reply-To: X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=3.7 required=7.5 tests=HTML_60_70,HTML_FONTCOLOR_BLUE, HTML_MESSAGE,RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0006_01C4D195.4B813DF0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Hi Axel, A few years ago I was working on QM/MM methods for MD simulations of macrocycles (18-crown-6, etc.). I combined AM1 with some torsion terms modified from the Amber forcefield. You can get the references from this webpage: http://www.arguslab.com/markthompson.htm Cheers, Mark Thompson Seattle -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request)at(ccl.net]On Behalf Of Axel Mathieu Sent: Tuesday, November 23, 2004 12:39 PM To: CCL Subject: CCL:ForceFields for macrocycles Greetings to all, I ve been having a discussion with some of my colleagues about forcefields and the question came about the use of a proper forcefields for macrocyclic molecules, given our recent NMR developments here. I ve been modeling these types of molecules for about 2 years now and have been using a modified MMFFF94s forcefield for all conformational searches for various reasons but mostly as this in my opinion, is the best forcefield at hand for me right now. Are any of you aware of special forcefields or have developed a specific forcefield for macrocycles? Or then again, what forcefields are you using for macrocyles? Your opinion/experience on this is most valuable to me. Again, many thanks to the CCL community for your never ending help, APM ------=_NextPart_000_0006_01C4D195.4B813DF0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi=20 Axel,
 
A few=20 years ago I was working on QM/MM methods for MD simulations of = macrocycles=20 (18-crown-6, etc.).  I combined AM1 with some torsion terms = modified from=20 the Amber forcefield.  You can get the references from this = webpage: =20 http://www.arguslab.com= /markthompson.htm 
 
Cheers,
Mark Thompson
Seattle
-----Original Message-----
From: Computational = Chemistry List=20 [mailto:chemistry-request)at(ccl.net]On Behalf Of Axel=20 Mathieu
Sent: Tuesday, November 23, 2004 12:39 = PM
To:=20 CCL
Subject: CCL:ForceFields for = macrocycles

Greetings to=20 all,

 

I=92ve been having a = discussion with=20 some of my colleagues about forcefields = and the=20 question came about the use of a proper forcefields=20 for macrocyclic molecules, given our = recent NMR=20 developments here. I=92ve been modeling these types of molecules for = about 2=20 years now and have been using a modified MMFFF94s forcefield for all conformational searches for = various=20 reasons but mostly as this in my opinion, is the best forcefield at hand for me right=20 now.

 

Are any of you aware of = special=20 forcefields or have developed a specific = forcefield for macrocycles? Or=20 then again, what forcefields are you using = for macrocyles? Your opinion/experience on this is = most=20 valuable to me.

 

Again, many thanks to = the=20 CCL community=20 for your never ending=20 help,

 

APM

 

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