From David.DeVito@chiphy.unige.ch Thu Feb 12 05:11:29 1998 Received: from sc2a.unige.ch for David.DeVito@chiphy.unige.ch by www.ccl.net (8.8.3/950822.1) id FAA24719; Thu, 12 Feb 1998 05:01:43 -0500 (EST) Received: from PCC2340E.unige.ch ([129.194.52.14]) by sc2a.unige.ch (PMDF V5.1-10 #10385) with SMTP id <01ITHNHICTKW000HUN@sc2a.unige.ch> for chemistry@www.ccl.net; Thu, 12 Feb 1998 11:01:26 MET Date: Thu, 12 Feb 1998 11:01:49 +0100 From: David De Vito Subject: Problem with a Gamess input To: chemistry@www.ccl.net Message-id: <004301bd379d$3c716720$0e34c281@PCC2340E.unige.ch> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 4.72.2106.4 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7bit X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 X-Priority: 3 Hello ! I have a problem with my (first) Gamess input. I'd like to do a multiple job: first evaluating an approximate hessian matrix for the formaldehyde decomposition, then trying to find the transition state, reading the hessian from the previous dumpfile. Here is my input; does anyone correct it ? #Evaluate an initial Hessian matrix $CONTRL SCFTYP=RHF RUNTYP=HESSIAN ICHARG=0 MULT=1 COORD=ZMT UNITS=ANGS NZVAR=0 $END $BASIS GBASIS=N31 NGAUSS=6 NPFUNC=2 NDFUNC=2 $END $DATA Transition state for the formaldehyde decomposition CN 1 C1 O2 C1 R1 H3 C1 R2 O2 A1 H4 C1 R3 O2 A2 H3 DHH Variables: R1=1.2 R2=1.3 R3=1.3 A1=100.0 A2=150.0 DHH=0.0 $END #Locate the transition state $CONTRL SCFTYP=RHF RUNTYP=SADPOINT IREST=1 ICHARG=0 MULT=1 COORD=ZMT UNITS=ANGS NZVAR=0 $END $BASIS GBASIS=N31 NGAUSS=6 NPFUNC=2 NDFUNC=2 $END $STATPT HESS=READ METHOD=QA $END $HESS FCM $END $GRAD VECTOR=1 $END $DATA Transition state for the formaldehyde decomposition CN 1 C1 O2 C1 R1 H3 C1 R2 O2 A1 H4 C1 R3 O2 A2 H3 DHH Variables: R1=1.2 R2=1.3 R3=1.3 A1=100.0 A2=150.0 DHH=0.0 $END Thank you very much for the preciously help. D. De Vito. **************************************************************** D. De Vito Department of Physical Chemistry Group of Prof. Weber (Computational Chemistry) University of Geneva Office 106 - Sciences II 30, Quai Ernest-Ansermet 1211 Geneva 4 / Switzerland +4122 / 702.65.35 (Office) +4179 / 310.05.76 (Mobile) +4122 / 733.38.35 (Home) http://lcta/~devito (Personal Page) http://www.unige.ch/sciences/chimie (Web Master) **************************************************************** From richard@tc.cornell.edu Tue Feb 10 09:25:48 1998 Received: from theory.tc.cornell.edu for richard@tc.cornell.edu by www.ccl.net (8.8.3/950822.1) id IAA06372; Tue, 10 Feb 1998 08:34:03 -0500 (EST) Received: from ren.tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.244.22]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id IAA20766; Tue, 10 Feb 1998 08:33:59 -0500 Sender: richard@TC.Cornell.EDU Message-ID: <34E05747.237C@tc.cornell.edu> Date: Tue, 10 Feb 1998 08:33:59 -0500 From: Richard Gillilan X-Mailer: Mozilla 2.02 (X11; I; IRIX 5.3 IP22) To: chemistry@www.ccl.net CC: nc27@cornell.edu Subject: CTC Workshop: Flexible Ligand Docking ***************** CORNELL THEORY CENTER ***************** Flexible Ligand Docking for Drug Design II April 23-25, 1998 *********************** WORKSHOP ************************ http://www.tc.cornell.edu/~richard The Cornell Theory Center will hold a workshop on the use of Monte-Carlo methods for predicting the conformations of small ligands bound to proteins. Class size will be limited to 12 to allow each participant their own SGI workstation. The workshop will be highly practical in nature, focusing on how to run the DockVision docking package, a Monte-Carlo-based docking code created at the University of Alberta. The DockVision algorithm was very successful at the recent CASP2 competition for structure prediction (http://PredictionCenter.llnl.gov/). The format will be short lectures delivered by the authors of DockVision interspersed with periods of laboratory time. Worked examples will be provided for those who do not wish to bring their own data. A huge variety of test ligands will be available via the NCI 3D structural database (see http://epnws1.ncifcrf.gov:2345/dis3d/3Ddatabase/dis3d.html). An experimental virtual reality interface to RESEARCH (part of the DockVision package) will be available for use in the Theory Center's Visual Insight Zone, a state-of-the-art immersive interactive graphics environment. Speakers: Trevor Hart and Steven Ness Department of Medical Microbiology and Immunology University of Alberta, Canada Richard Gillilan Cornell Theory Center Ithaca, NY The workshop will cover o Molecular force fields: a practical guide (including an intro to the CTC's new forcefield assignment and simulation software that uses the Merck Molecular Force Field (MMFF94)) o Introduction to molecular docking o Analysis of data and prediction o Docking with Genetic Algorithms o Database screening o Virtual reality hands on Participants are encouraged to bring their own data sets. Consulting staff will be available to assist researchers in their projects. Licenses for academic or corporate use of the DockVision package may be purchased from the authors. Contact Trevor Hart (trevor.hart@ualberta.ca) for details. Accommodations Attendees are responsible for their own hotel reservations and meals. Paid parking is available on campus, but walking or use of the shuttle or bus service, where available, is recommended. We have reserved a block of rooms at the Best Western. If you want one, tell them you are with the "Theory Center Docking Workshop". Rooms can only be held until April 1 without credit card info. Cancellations must be made before 4pm April 22 to avoid penalty. Best Western University Inn (about 1 mile) East Hill Plaza, Rt. 393 and Judd Falls Road, Ithaca 607/272-6100 FAX: 607/272-1518 Sheraton Inn (3mi) One Sheraton Drive, Ithaca 607/257-2000 FAX: 607/257-3998 Statler Hotel (walking distance) Cornell University Campus 607/257-2500 FAX: 607/257-6432 Collegetown Motor Lodge (walking distance) 312 College Avenue, Ithaca 607/273-3542, 800/745-3542 FAX: 607/272-3542 To Apply Due to restricted space, registration for this workshop is limited. The completed application form, along with payment, must be received by Thurs March 27, 1998. Applications will be accepted after this date if openings still remain. Local researchers may charge the registration fee to the appropriate Cornell University account number. Applications which do not include payment cannot be accepted. Payment checks will be returned promptly to applicants not accepted due to over-enrollment. Payment scale, payable to Cornell University: Academic participants: $250 CTC corporate partners: $450 Corporate participants: $600 Notification will made as soon as possible after we receive your application and payment. ------------------------------------------------------------------------- REGISTRATION FORM Flexible Ligand Docking 98 Name __ Institution __ Address __ Telephone __ Fax __ Preferred electronic mail address __ List special needs: __ (e.g., mobility impaired) Account number to charge: __ (Cornell applicants only) Status (check all that apply): Academic __ Undergraduate Student __ Graduate Student __ Post-doctoral __ Faculty __ Other (explain): __ Corporate/Commercial Research staff __ Other (explain) __ Name of Firm: __ ------------------- This application form and payment must be received by March 27, 1997 Send to: Carol Christofferson Cornell Theory Center Frank H.T. Rhodes Hall Ithaca, NY 14853-3801 (607) 254-8610 carolc@tc.cornell.edu All trade names referenced are trademarks or registered trademarks of their respective companies. From beck@Ba.chem.uh.edu Tue Feb 10 11:22:14 1998 Date: Tue, 10 Feb 1998 02:43:34 -0800 From: "Ricky A. Kendall" Subject: West Coast Theoretical Chemistry Conference 1998 Sender: beck@Ba.chem.uh.edu To: ricky.kendall@pnl.gov Reply-to: ra_kendall@pnl.gov Message-id: <199802101043.CAA04874@cagle.pnl.gov> Hello West Coast Theoretical Chemistry Colleagues, The WCTCC98 meeting will be at Pacific Northwest National Laboratory on June 21-23 (standard 2.5 day format). Registration information and details will appear at the following URL as they become available (soon) :) ::: http://www.emsl.pnl.gov:2080/docs/wctcc98 Note: Don't forget the 2080 or you will run into our firewall! This broadcast email is using an old email distribution list which is likely out of date. Please redistribute this information to all who might be interested!! We would like to have this email list updated. To get your email address on the updated list just send a simple email message to: majordomo@emsl.pnl.gov with "subscribe wctcc" in the body of the message (not in the subject). Thanks for your interest and we hope to see you in June. Regards, Ricky Kendall Rene Corrales Thom H. Dunning, Jr. David A. Dixon Michel Dupuis Administrative Coordinator: Sheri Perkins From jan@Acadia-Pharm.com Wed Feb 11 02:11:13 1998 Received: from rtec01.receptortechnologies.dk for jan@Acadia-Pharm.com by www.ccl.net (8.8.3/950822.1) id BAA12715; Wed, 11 Feb 1998 01:51:17 -0500 (EST) Received: from THC by rtec01.receptortechnologies.dk with SMTP (Microsoft Exchange Internet Mail Service Version 5.0.1458.49) id DA39XMSL; Wed, 11 Feb 1998 07:49:57 +0100 Sender: jan@www.ccl.net Message-ID: <34E1499B.D3B2A439@Acadia-Pharm.com> Date: Wed, 11 Feb 1998 07:47:55 +0100 From: Jan Torleif Pedersen Organization: Acadia Pharmaceuticals (Denmark) X-Mailer: Mozilla 4.03 [en] (X11; I; Linux 2.0.27 i686) To: chemistry@www.ccl.net Subject: pKa calculations Dear CCLers, I am trying to calculate some pKa values for a set of small organic analogs, I would be interested in getting some ideas to what is out there in terms of software that can do this by empirical or semi-empirical methods. I am aware of one such code the PALLAS program from CompuDrug but I would be interested in a number of different methods. -- Jan ----------------------------------------------------------- Dr. Jan T. Pedersen Head of Computational Chemistry Acadia Pharmaceuticals Fabriksparken 58 2600 Glostrup, DENMARK email : jan@Acadia-Pharm.com phone : +45 43 29 30 05 FAX : +45 43 29 30 30 ----------------------------------------------------------- From cdac.ernet.in!gadre@parcom.ernet.in Wed Feb 11 08:11:19 1998 Received: from naveen.ncst.ernet.in for cdac.ernet.in!gadre@parcom.ernet.in by www.ccl.net (8.8.3/950822.1) id HAA14539; Wed, 11 Feb 1998 07:19:11 -0500 (EST) Received: from iucaa (iucaa.ernet.in [202.141.155.1]) by naveen.ncst.ernet.in (8.6.12/8.6.6) with SMTP id RAA22138 for ; Wed, 11 Feb 1998 17:56:12 +0530 Received: from iucaa by iucaa (5.65v3.2/SMI-4.1) id AA10977; Wed, 11 Feb 1998 17:43:27 +0500 Received: by parcom.cdac.ernet.in (4.1/SMI-4.1) id AA18606; Wed Feb 11 17:41:07 1998 (GMT + 0530) Date: Wed Feb 11 17:41:07 1998 (GMT + 0530) From: gadre@cdac.ernet.in Message-Id: <9802111211.AA18606@parcom.cdac.ernet.in> To: CHEMISTRY@www.ccl.net Subject: Hydration of 18 Crown 6 Status: RO Dear Sirs and Madams : Hydration of 18 Crown 6 is of great interest to us. We are aware of a few references on crystallographhic investigations as well as simulations of the crown with 4, 6 and 8 molecules. Please let us know of any recent work (ab initio/semi-empirical theory OR experiments) on these systems. In particular, we are interested in understanding the primitive aptterns (patterns) of the hydration process. Thank you very much...Shridhar gadre From jmolina@goliat.ugr.es Wed Feb 11 12:11:30 1998 Received: from goliat.ugr.es for jmolina@goliat.ugr.es by www.ccl.net (8.8.3/950822.1) id LAA16456; Wed, 11 Feb 1998 11:19:02 -0500 (EST) Received: from goliat.ugr.es (dismol7.ugr.es [150.214.18.186]) by goliat.ugr.es (8.8.5/8.7.3) with ESMTP id RAA18025 for ; Wed, 11 Feb 1998 17:21:08 +0100 (MET) Message-ID: <34E1CF88.A34FEA20@goliat.ugr.es> Date: Wed, 11 Feb 1998 17:19:20 +0100 From: Jose Molina Molina X-Mailer: Mozilla 4.03 [es] (Win95; I) To: "chemistry@www.ccl.net" Subject: 98.04.19-22 3rd Euro Wrkshp Quant Sys in Chem and Phys Second announcement Third European Workshop on QUANTUM SYSTEMS IN CHEMISTRY AND PHYSICS 19-22 APRIL, 1998 Granada, Spain Scientific Organizing Committee: R. McWeeny (Universita di Pisa), J. Maruani (Universite Pierre et Marie Curie), Y.G. Smeyers (C.S.I.C.,Madrid), S. Wilson (Rutherford Appleton Laboratory) Local Organizers: J. Molina (Universidad de Granada) A. Hernandez-Laguna (C.S.I.C., Granada) This Workshop, like the first held at San Miniato in April 1996 and the second held in Oxford in April 1997, will bring together chemists and physicists interested in many-body quantum systems in the molecular sciences. The emphasis will be on innovative theory, its computational realization and applications. The Workshop will include sessions on * Density matrices and density functionals * Electron correlation effects: many-body methods and configuration interaction * Relativistic formulations * Valence theory: chemical bonds and bond breaking * Nuclear motion: vibronic effects, flexible molecules * Response theory: properties and spectra; atoms and molecules in strong electric and magnetic fields * Condensed matter: crystals, clusters, surfaces and interfaces * Reactive collisions and chemical reactions * Computational Chemistry and Physics It is planned to publish the proceedings of the Workshop. The Workshop will be held in the Hotel "Los Alixares" (Av. Alixares del Generalife s/n. E-18009 Granada, Spain, Tlf. +34 58 225575, Fax: +34 58 224102) near the Generalife, which is adjacent to the famous Alhambra. Participants will be expected to arrive on Sunday, 19 April, 1998. Registration will take place from 15:30 - 17:30. The meeting will end after lunch on Wednesday, 22 April, 1998. The number of participants at the Workshop is strictly limited and early application is encouraged. The total cost of participation in the Workshop, including registration, is 55,000 pts. for participants in a single room and 47,000 pts. for participants sharing a room. The cost for accompanying persons, sharing a room with a participant is 27,000 pts. The deadline for paying this amount will be 28th February, 1998. After this date the prices will be increased in 7,000 pts for participants and 4,000 pts. for accompanying persons. Payment should be made by money transfer to "Quantum Systems in Chemistry and Physics" account # 3023 0126 9 5 7000006910 in "Caja Rural de Granada. Urbana 14". Alternatively, payment can be made by Eurocheque (in Spanish currency and made payable to "Quantum Systems in Chemistry and Physics"), which should be sent together with a completed application form, to Dr. Alfonso Hernandez Laguna, Estacion Experimental del Zaidin, C/Profesor Albareda, 1, 18008 Granada, SPAIN The cost includes registration fee, accommodation, and meals. A small number of bursaries will be available. An extra-night in Hotel "Los Alixares" before or after the Workshop will cost 8,500 pts. (+ 7 % IVA) for double room (bed and breakfast 2 persons), or 6,000 pts (+ 7 % IVA) for single room (bed and breakfast). Participants wishes to stay for extra nights should make their arrangements directly with the hotel. The following scientists have indicated that they will probably attend the third workshop:- L. Adamowicz (University of Arizona) G. Aucar (Northeastern University, Corrientes, Argentina) J. Avery (University of Copenhagen) A.A. Bagatur'yants (Russian Academy of Sciences) V. Barone (Universita Federico II, Napoli) M.V. Basilevsky (Karpov Institute of Physical Chemistry, Moscow) R.C. Bochicchio (Universidad de Buenos Aires) I. Borges Jr (University of Rio de Janeiro) F. Borondo (Universidad Autonoma de Madrid) O. Castano (University of Alcala) M. Castella-Ventura (C.N.R.S., Thiais) H. Chojnacki (Institute of Physical and Theoretical Chemistry, Wroclaw) D.L. Cooper (University of Liverpool) G. Delgado-Barrio (C.S.I.C., Madrid) E. Engel (University of Frankfurt) M.B. Ferraro (Universidad de Buenos Aires) F.A. Gianturco (University of Rome) A. Graovac (R. Boskovic Institute, Zagreb) A. Hernandez-Laguna (C.S.I.C.,Granada) K. Hirao (University of Tokyo) I. Hubac (Comenius University, Bratislava) A. Kalemos (University of Athens) U. Kaldor (Tel Aviv University) S. Kotochigova (National Institute of Standards and Technology, Gaithersburg) C. Kozmutza (Technical University of Budapest) L. Lain (Bilbao) J. Maruani (Universite Pierre et Marie Curie) J. Linderberg (Aarhus University) P. Maitre (Universite de Paris-Sud) I. Martin (Universidad de Valladolid) A. Mavridis (University of Athens) R. McWeeny (Universita di Pisa) B. Minaev (Ukraine) R. Moccia (Universita di Pisa) J. Molina (Universidad de Granada) C. Munoz-Caro (Universidad de Castilla-La Mancha) M.A.C. Nascimento (UFRJ, Brazil) C. Nicolaides (National Technical University, Athens) A. Nino (Universidad de Castilla-La Mancha) J.M. Oliva (University of Bristol) A. Papakondylis (University of Athens) D.E. Parry (University of Swansea) R. Pauncz (Technion - Israel Institute of Technology) M. Persico (Universita di Pisa) C. Petrongolo (Universita di Siena) J. Planelles (Universitat Jaume I, Castello) B.T. Pickup (University of Sheffield) J.J. Quirante (Malaga University, Spain) M. Raimondi (Universita di Milan) S. Rettrup (Copenhagen University) G.P. Ripolles (Universitat Jaume I, Castello) A. Rizzo (Universita di Pisa) I. Roeggen (University of Tromso) J. Rychlewski (Poznan Supercomputing and Networking Center) H. Skaane (University of Oxford) A. Sevin (Universite Pierre et Marie Curie) P. Schwerdtfeger (University of Auckland) A. Sgamellotti (Universita di Perugia) Y.G. Smeyers (C.S.I.C.,Madrid) F.M.L.G. Stamato (Universidade Federal de Sao Carlos) B.T. Sutcliffe (University of York) L. Tel (Universidad de Salamanca) A.V. Titov (Petersburg Nuclear Physics Institute) A. Torre (Bilbao) D. Tzeli (University of Athens) C. Valdemoro (C.S.I.C.,Madrid) I. Vandoni (Universita di Milano) S. Varga (University of Kassel) F.T. Vert (Universidad de Valencia) P. Villareal (C.S.I.C.,Madrid) N. Vulliermet (University of Geneva) S. Wilson (Rutherford Appleton Laboratory, Oxon) R.G. Woolley (Nottingham) Y. Yan (Hong Kong University of Science and Technology) TRAVEL TO AND FROM GRANADA: By Air Granada can be reached by domestic flights from Madrid and Barcelona. By train: From Madrid. Time Table: "Chamartin St." 23.00, and "Atocha St." 15.45 From Barcelona: "Sants St." 19.00 Further information Tlf: +34 1 3289020 By bus: From Madrid. The average journey time is 5 hours and the cost is o/w 1,800 pts. The bus depot is in "Continental Auto" c/ Alenza 20, tlf. +34 15330400. The departure times are as follows: Monday to Thursday and Saturday 7.00, 8.30, 10.00, 13.00, 15.00, 17.00, 19.00, 23.00, 1.30 Friday and Sunday: 7.00, 8.30, 10.00, 13.00, 14.00, 15.00, 16.00, 17.00, 19.00, 21.00, 23.00, 1.30 There is a second bus depot in "Estacion Sur de Autobuses", C/ Mendez Alvaro, tlf +34 1 5279927. The departure times are as follows: Monday to Thursday and Saturday 7.30, 9.00, 10.30, 13.30, 15.30, 17.30, 19.30, 23.30, 2.00 Friday and Sunday: 7.30, 9.00, 10.30, 13.30, 14.30, 15.30, 16.30, 17.30, 19.30, 21.30, 23.30, 2.00 From Malaga The average journey time is 2 hours. The bus depot is " T. Alsina Graells Sur S. A." Tlf: +34 5 2318295. Departures to Granada: hourly from 7.00 to 22.00. There is a web page for the workshop. The address is: http://www.eez.csic.es/~quantum/ Please consult this for latest information. If you are interested in attending the Workshop then please return the form below to quantum@rl.ac.uk or reply by regular mail to Dr. Hernandez Laguna at the address given below. -------------------------------------------------------------------------- APPLICATION FORM I would like to attend the Third "Quantum Systems in Chemistry and Physics" Workshop to be held in Granada, Spain, 19 - 22 April 1998. Name ___________________________________________________ Nationality ____________________________________________ Sex M/F Affiliation ____________________________________________ Address ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ Telephone ______________________________________________ Fax ____________________________________________________ e-mail _________________________________________________ Research field _________________________________________ As numbers will be strictly limited, an early response is desirable. Please indicate your accommodation requirements I would like a single room @ Yes/No I would like a shared room @ Yes/No (Please indicate who you would like to share with) I shall be accompanied Yes/No Please indicate any special dietary requirements If you would like to make a presentation at the Workshop then please complete the following:- I would like to give a talk entitled ________________________________________________ in the session on ________________________________________________ Author(s) ______________________________________ (Please underline the speaker.) I would like to give a poster entitled ________________________________________________ Author(s) Any comments and suggestions that you may have at this stage would be most welcome. ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ Accommodation and meals will be provided in Hotel "Los Alixares", and the total cost, including registration fee, is 55,000 pts. for participants in a single room, and 47,000 pts. for participants sharing a room. The cost for accompanying persons, sharing a room with a participant is 27,000 pts. Payment should be made by money transfer to "Quantum Systems in Chemistry and Physics" account # 3023 0126 9 5 7000006910 on "Caja Rural de Granada. Urbana 14". The deadline for paying this amount will be 28th February, 1998. After this date the prices will be increased in 7,000 pts for participants and 4,000 pts. for accompanying persons. Alternatively, payment can be made by Eurocheque, which should be sent together with a completed application form, to Dr. Alfonso Hernandez Laguna, Estacion Experimental del Zaidin, C/Profesor Albareda, 1, 18008 Granada, SPAIN From elewars@alchemy.chem.utoronto.ca Wed Feb 11 16:11:21 1998 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id PAA19190; Wed, 11 Feb 1998 15:11:19 -0500 (EST) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id PAA26989 for chemistry@www.ccl.net; Wed, 11 Feb 1998 15:11:12 -0500 (EST) Date: Wed, 11 Feb 1998 15:11:12 -0500 (EST) From: "E. Lewars" Message-Id: <199802112011.PAA26989@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: OXIDATION POTENTIAL Status: RO Content-Length: 2270 11 Feb 1998 Hello, Zhang X-D posed the question: ------ 11-FEB-1998 09:55:37.66 >From: IN%"zhangxd@xx1.icas.ac.cn" "zhang" To: IN%"PAUL_MATHIAS@aspentec.com" "PAUL_MATHIAS.ASPENTECH.COM" CC: IN%"chemistry@www.ccl.net", IN%"kumar@plmsc.psu.edu", IN%"clive@ msi.com" Subj: CCL:help Hi,netters I have an question as follows: how to calculate the oxidated electric potential of a large molecule, such as polymer, protein etc with quantum chemical methods such as GS ? Thanks in advances! zhangxd ----------------- How to calc the oxidation potential of a protien or polymer using a QM method: The oxidation potential is essentially the solution ionization potential. There are references in the literature to the calc of oxidation potential, but my ideas are: Ox pot correlates with ionization pot; In both cases we are removing an electron from the molecule. The IP is just the E needed to remove an electron in the gas phase, but the oxidation potential is more complicated,describing a process occurring in solution, often at a surface, and it is defined relative to an arbitrary reference, H2. However, IP and OP should be at least approximately correlated. To calculate _relative_ OP's, _approximately_, you can you Koopmans' theorem and equate the negative of the highest occupied MO with the IP. For a protein or other polymer an ab initio calc is not possible on the whole molecule. So : (1) Try a semiempirical cal. You may not be able to do a SE geometry optimizaytion, and may have to do a SE single-point calc on a molecular mechanics geom. (2) Even a single-pt. SE calc may be to big a job; if so, look at the molecule, decide which regions are likely to be the ones of lowest IP, and do calcs on small model compounds with the same structure (e.g. a di- tri- or tetrapepetide for a protein). (3) Ab initio single-pt or even optimization jobs may be possible on model compounds (i.e. on small regions of the polymer). ------------ A plot of calc IP' (done by you) vs. experimental oxidation potentials (find some compounds of your kind whose ox pot's are known) will show you how good your chosen procedure is. E. Lewars ======================= From darrena@chem.leeds.ac.uk Thu Feb 12 10:13:10 1998 Received: from chemistry.leeds.ac.uk for darrena@chem.leeds.ac.uk by www.ccl.net (8.8.3/950822.1) id JAA26110; Thu, 12 Feb 1998 09:19:12 -0500 (EST) Received: from [129.11.12.138] (chmmac37.leeds.ac.uk [129.11.12.138]) by chemistry.leeds.ac.uk (8.8.8/8.8.8) with ESMTP id OAA08091 for ; Thu, 12 Feb 1998 14:18:50 GMT Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 12 Feb 1998 14:13:03 +0000 To: chemistry@www.ccl.net From: Darren Andrews Subject: Scratch space limitation Dear all, I sent a message the other day about Gaussian 92 scratch space limitation. Basically I was trying to get around the 2Gig file size limitation imposed by some operating systems. It seemed that short of upgrading to G94 or IRIX 6.3 I am out of luck. Somebody suggested using MAXDISK but I'm not sure how to make this work; certainly putting the option MAXDISK=100000000 in the route card didn't have any effect. I am now trying the same job using GAMESS US and having (of course) the same problem. Is there a work around in GAMESS US/UK or CADPAC 6.1? Darren Andrews. PostGraduate Student, School of Chemistry, University of Leeds, Leeds. LS2 9JT. England. Darrena@chem.leeds.ac.uk Tel: 0113 233 6594. Fax: 0113 233 6565. From mariusz@qc.chem.ualberta.ca Thu Feb 12 13:11:33 1998 Received: from quartz.ucs.ualberta.ca for mariusz@qc.chem.ualberta.ca by www.ccl.net (8.8.3/950822.1) id MAA27792; Thu, 12 Feb 1998 12:12:47 -0500 (EST) Received: from qc.chem.ualberta.ca (qc.chem.ualberta.ca [129.128.2.12]) by quartz.ucs.ualberta.ca (8.8.7/8.8.7) with ESMTP id KAA25124 for ; Thu, 12 Feb 1998 10:12:46 -0700 Received: (from mariusz@localhost) by qc.chem.ualberta.ca (8.6.12/8.6.10) id KAA05279 for CHEMISTRY@www.ccl.net; Thu, 12 Feb 1998 10:12:37 -0700 Date: Thu, 12 Feb 1998 10:12:37 -0700 From: Mariusz Klobukowski Message-Id: <199802121712.KAA05279@qc.chem.ualberta.ca> To: CHEMISTRY@www.ccl.net Subject: HPCS'98 X-Sun-Charset: US-ASCII 12th Annual International Symposium on ====================================== High Performance Computing Systems and Applications =================================================== Call for Participation ====================== May 20-22, 1998 Edmonton, Alberta http://www.cs.ualberta.ca/~hpcs98 Computational Biology, Chemistry, and Physics ============================================= In the past the HPCS series of conferences have been targeted towards the computing scientists. This year, the conference has changed directions, trying to get computer scientists together with users who need high performance computing. The program features three new streams: o Computational biology, o Computational chemistry, and o Computational physics. All this in an atmosphere which promotes conversation and collaboration. Program Highlights ================== The conference features: o at least six internationally recognized keynote speak- ers, o three streams of invited papers (computational biology, chemistry, and physics), o refereed papers, o posters, and o a vendor exhibit. All papers will be published in the book "High Performance Computing Systems and Applications" (Kluwer Academic Press). Poster Session ============== The conference includes a poster session. We want your submission! Please fill out the form available on our web page. The deadline for poster submissions is April 16. All poster abstracts will be printed in the conference proceed- ings. A Unique Conference Venue! ========================== The conference is being held at the Fantasyland Hotel at the world-famous West Edmonton Mall (http://www.westedmall.com). This is a unique venue for the conference; one that will appeal to the entire family. Be decadent and book the "Polynesian" room; be Canadian and book the "Igloo". Enjoy the world's largest indoor amuse- ment center, the indoor golfing, water park, and many other unusual attractions. Register Now! ============= Conference registration includes lunch each day, a conference banquet, a wine and cheese poster session, as well as the usual amenities. There is a special rate for students. For more information, see www.cs.ualberta.ca/~hpcs98, send e-mail to hpcs98@cs.ualberta.ca, or call (403) 492-5185. From chas@alinga.newcastle.edu.au Thu Feb 12 14:11:34 1998 Received: from alinga.newcastle.edu.au for chas@alinga.newcastle.edu.au by www.ccl.net (8.8.3/950822.1) id NAA28170; Thu, 12 Feb 1998 13:47:28 -0500 (EST) Received: from localhost (chas@localhost) by alinga.newcastle.edu.au (8.8.5/8.8.5) with SMTP id FAA13830 for ; Fri, 13 Feb 1998 05:47:07 +1100 (EST) Date: Fri, 13 Feb 1998 05:47:06 +1100 (EST) From: SUDARKO A Reply-To: SUDARKO A To: chemistry@www.ccl.net Subject: dipole moment calculation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I sent this message the other day to molpro-support@tc.bham.ac.uk. Basically I was trying to determine dipole moment functions of several non linear triatomic molecules. I need to have the dipole moment in the center-of-mass coordinate system instead of the center-of-charge system. I noticed that MOLPRO can be used to calculate the dipole moment in the center-of-mass system. However,the magnitude of the total dipole moment using the center-of-mass system calculated with the PROPERTIES program is now different from the expectation value of the dipole moment (which is given as a default value). Can you refer me to a publication which would explain why these two values are different. Or is there any program that can be used to convert the dipole moment calculated with G94(using center-of-charge coordinate system) to the dipole moment with center-of-mass coordinate system. Thank you for your assistance in this matter. *************************************************************************** Sudarko 4/19 Gamack ST Chemistry Department Mayfield NSW 2304 The University of Newcastle Tel : (H) (+)61-2-49688382 Callaghan NSW 2308 (O) (+)61-2-49215467 From nglover@sfu.ca Thu Feb 12 15:11:34 1998 Received: from gremlin.chem.sfu.ca for nglover@sfu.ca by www.ccl.net (8.8.3/950822.1) id OAA28360; Thu, 12 Feb 1998 14:39:02 -0500 (EST) Received: from gremlin (localhost [127.0.0.1]) by gremlin.chem.sfu.ca (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id LAA20000; Thu, 12 Feb 1998 11:33:41 -0800 Sender: nick@sfu.ca Message-ID: <34E34E94.167E@sfu.ca> Date: Thu, 12 Feb 1998 11:33:40 -0800 From: Nick Glover X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@www.ccl.net CC: nglover@sfu.ca Subject: CCL: Salt bridges, H-bonds, aromatic stacking in MD? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit CCLers: I am looking at the interaction of a bound peptide and a target enzyme with EM and MD simulations. The peptide is docked into the active site, and lies, extended, across the protein, plugging a 'hole' on the surface of the protein. I have three queries: --------------- Q1: Salt bridge... My major concern is that I have noticed that a salt-bridge between a surface Arg on the protein and a bound peptide Asp residue lengthens from ~4.0 ang. when docked to > 6.0 ang. during the MD portion of an EM/MD run. It seems to fluctuate by about 1 ang., but over 100 ps doesn't shorten to ~4.0 ang. again. The system is in a large solvated sphere, and calculations are run on Discover 95 with CVFF using the default water model. As per advice from MSI, the cutoffs are set thus (i.e. double cutoffs, no switching function): cutoff=13.00 cutdis=12.00 swtdis=0 cutof2=15.00 cutds2=14.00 swtds2=0 Is this observation considered 'normal' given the conditions of the calculations, or should I be concerned? ------------- Q2: Intermolecular hydrogen bonds... Similar to Q1, I also see certain intermolecular H-bonds lengthen to > 4.0 ang. (acceptor - donor) during MD simulations, and fluctuate about this longer distance (i.e. 3.5 - 4.5 ang). Again, is this considered 'normal' given the conditions of the calculation, or should I be concerned? ------------- Q3: Aromatic stacking... Can anybody indicate how successful the CVFF forcefield is at simulating aromatic-aromatic stacking interactions? I notice that phenyl rings in the active site pocket of the enzyme re-orient with respect to ligand, and appear to adopt 'favourable' edge-on, tilted-T, etc. orientations, depending on the ligand. How 'realistic' (within context) are these observations likely to be? ------------- Can anybody offer any insights into these phenomena? Thanks in advance, Nick ____ Nick Glover Department of Chemistry Simon Fraser University 8888 University Drive Burnaby, BC V5A 1S6 Canada Tel: (604) 291-4531 Fax: (604) 291-3765 email: nglover@sfu.ca