From chemistry-request@server.ccl.net Wed Jan 29 04:12:21 2003 Received: from suncom.rz.hu-berlin.de ([141.20.1.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0T9CKP22224 for ; Wed, 29 Jan 2003 04:12:20 -0500 Received: from impact1.chemie.hu-berlin.de (impact1.chemie.hu-berlin.de [141.20.72.25]) by suncom.rz.hu-berlin.de (8.9.3/8.9.3) with ESMTP id KAA00671 for ; Wed, 29 Jan 2003 10:12:16 +0100 (MET) Received: (from ah@localhost) by impact1.chemie.hu-berlin.de (SGI-8.9.3/8.9.3) id KAA75902 for chemistry@ccl.net; Wed, 29 Jan 2003 10:12:15 +0100 (MEZ) Date: Wed, 29 Jan 2003 10:12:15 +0100 From: "Dr. Alexander Hofmann" To: chemistry@ccl.net Subject: Benchmarks for NEC SX6i? Message-ID: <20030129101215.J173727@chemie.hu-berlin.de> Reply-To: ah@chemie.hu-berlin.de Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i Hello alltogether, is there somebody who did benchmark calculations on a NEC SX6i? My special interest is MP4 or CCSD(T) in comparison to the new IBM Power4 cpu ... GFlop-Rating shows approx. 3 times better for NEC (rough estimate by some top500-list values). Thanks in advance Alex -- Dr. Alexander Hofmann Humboldt-Universitaet zu Berlin Institut fuer Chemie Arbeitsgruppe Quantenchemie Brook-Taylor-Strasse 2 12489 Berlin ah@chemie.hu-berlin.de Tel.: +49-30-2093-7138 Fax.: +49-30-2093-7136 http://www.chemie.hu-berlin.de/ag_sauer/index.html PGP-Key: wwwkeys.de.pgp.net ID: D9D62D35 From chemistry-request@server.ccl.net Wed Jan 29 05:34:50 2003 Received: from darius.ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0TAYoP02986 for ; Wed, 29 Jan 2003 05:34:50 -0500 Received: from echo.ribotargets.com (echo [194.129.39.91]) by darius.ribotargets.com (SGI-8.9.3/8.9.3) with ESMTP id KAA37515; Wed, 29 Jan 2003 10:44:20 GMT Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 18dpUR-0004RJ-00; Wed, 29 Jan 2003 10:30:43 +0000 Date: Wed, 29 Jan 2003 10:30:43 +0000 (GMT) From: Szilveszter Juhos To: james.metz@abbott.com cc: chemistry@ccl.net Subject: Re: CCL:X-ray or NMR structures of weakly bound complexes In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 28 Jan 2003 james.metz@abbott.com wrote: > I am looking for X-ray or NMR structures of weakly bound ligands > (Ki > 50 uM) to proteins. The structures should include ordered > water. Hello, I doubt you will find water in NMR structures but still there should be some structures at Abbott since this paper below refers to weakly bound ligands: Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein. Muegge I, Martin YC, Hajduk PJ, Fesik SW J Med Chem 1999 Jul 15 42:14 2498-503 http://reviews.bmn.com/medline/jbrowse/record?uid=MDLN.99340121&rendertype=full There are some K_D values in the paper itself, but not structures. Szilva From chemistry-request@server.ccl.net Wed Jan 29 09:55:34 2003 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0TEtWP08151 for ; Wed, 29 Jan 2003 09:55:34 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h0TEtTj07945; Wed, 29 Jan 2003 09:55:29 -0500 (EST) Date: Wed, 29 Jan 2003 09:55:28 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net, mel@asdn.net cc: Jan Labanowski , anatoli.korkin@motorola.com, matt.stoker@motorola.com Subject: Workshop - KHIMERA - 1st principles mechanism/kinetics soft Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII KHIMERA: Universal software program for first principles mechanism and chemical kinetics studies March 18, 2003 9 AM to 5 PM, Tempe, Arizona WORKSHOP When: March 18, 2003 9 AM to 5 PM Where: Motorola, Semiconductor Products Sector, Bldg 99 2100 E Elliot Rd, Tempe, Arizona 85284 Fee: No fee Sponsors: DigitalDNA Labs, Kinetic Technologies, LtD (Kintech), US Department of Energy We are pleased to announce a one-day workshop to introduce the KHIMERA software. KHIMERA allows engineers and researchers to efficiently calculate the thermodynamics and kinetics of elementary chemical reactions from the results of quantum chemistry calculations and analyze these results using a variety of simple reactor models. Based on Transition State and RRKM theories, KHIMERA provides an important link between quantum chemistry, reaction kinetics and reactor modeling. In addition, KHIMERA includes a database containing thermodynamic and kinetic data for various materials and processes. KHIMERA is a valuable new software tool for the study and development of models of chemical reactions and mechanisms. Further description of this code can be found at http://kintech.ru The workshop will include a detailed description of the existing code capabilities, a roadmap for the addition of new features, and time for hands-on evaluation. To register and obtain further information, please fill in the form below and send it to Matt Stoker at matt.stoker@motorola.com Registration form ================= Name: ____________________________________ Organization: ______________________________ Address: __________________________________ City: ________________State:______Zip:________ Country: __________________________________ Phone____________________________________ Fax______________________________________ Email: ____________________________________ Web site: _______________________________ Area of research: _________________________ Accommodations: Recommended: Best Western Dobson Ranch in Mesa (480) 831-7000 cost (with Motorola discount) ~ $115/night Directions: Sky Harbor Airport Phoenix to the workshop site. MapQuest: http://www.mapquest.com/directions/main.adp?2a=2100%20E%20Elliot%20Rd&1z=85034%2d4403&2pn=Motorola&1a=3400%20E%20Sky%20Harbor%20Blvd&2z=85284%2d1806&go=1&1np=18&1pn=Airport%20Ground%20Trans Sky Harbor Airport to the Best Western Dobson Ranch. MapQuest: http://www.mapquest.com/directions/main.adp?2a=1666%20S%20Dobson%20Rd&1z=85034%2d4403&1a=3400%20E%20Sky%20Harbor%20Blvd&2z=85202%2d5610&go=1&1np=18&1pn=Airport%20Ground%20Transportation&2pn=Best%20Western Best Western Dobson Ranch to the workshop site MapQuest: http://www.mapquest.com/directions/main.adp?2a=2100%20E%20Elliot%20Rd&1z=85202%2d5610&1a=1666%20S%20Dobson%20Rd&2z=85284%2d1806&go=1&1pn=Best%20Western&2pn=Motorola Contact: Matt Stoker Email: matt.stoker@motorola.com Motorola, SPS EL722 Phone: (480) 413-2744 2100 E Elliot Road Fax: (480) 413-4511 Tempe, AZ 85284 From chemistry-request@server.ccl.net Wed Jan 29 10:37:15 2003 Received: from igor.urz.unibas.ch ([131.152.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0TFbFP08859 for ; Wed, 29 Jan 2003 10:37:15 -0500 Received: from [131.152.94.93] by igor.urz.unibas.ch (PMDF V6.1-1 #40761) with ESMTP id <0H9H00BNAFE2PM@igor.urz.unibas.ch> for chemistry@ccl.net; Wed, 29 Jan 2003 16:37:14 +0100 (MET) Date: Wed, 29 Jan 2003 16:37:16 +0100 From: Michele Porro Subject: Re: CCL:AutoDock Tools+charges (2nd response) In-reply-to: <3E36E664.1EFF4E15@uci.edu> To: sheffron@uci.edu Cc: CCL Message-id: MIME-version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.0.4 Hi Susan and all other CCL'members, i tested ADT with practical all the values (different Metals, Halogens, ...) Susan sended to me (lj4.py) and i found out the follow : if you insert rij and epsij when asked by ADT, the program write you a correct *.gpf file with in addition to the usual parameters also those for your metal or else. For example for Ca in the C.map section: nbp_r_eps 4.00 0.0222750 12 6 # C-C lj nbp_r_eps 3.75 0.0230026 12 6 # C-N lj nbp_r_eps 3.60 0.0257202 12 6 # C-O lj nbp_r_eps 4.00 0.0257202 12 6 # C-S lj nbp_r_eps 3.00 0.0081378 12 6 # C-H lj nbp_r_eps 3.00 0.0081378 12 6 # C-H lj nbp_r_eps 2.99 0.0575000 12 6 # C-M lj (C-Ca) By starting then Autogrid (from ADT) the software also use the correct 12-6 or 12-10 parameters that are needed for generating the different grids and in the end you get the maps you were looking for...GREAT! I really would like to thank you Susan for your precious help. Best regards mike ******************************** Michele Porro Institute of Molecular Pharmacy Pharmacenter University of Basel Klingelbergstrasse 50 CH-4056 Basel Phone : +41 61 267 15 63 FAX : +41 61 267 15 52 e-mail: michele.porro@unibas.ch http://www.pharma.unibas.ch http://www.pharmacenter.ch ******************************** on 28.1.2003 21:21 Uhr, Susan Heffron at sheffron@uci.edu wrote: > Hi again, Mike. > > It just occurred to me that if you're using autodock tools, you just need to > provide Rij and epsij when it asks for them. I believe the values needed are > the ones listed for Calcium-Calcium in the (long) list that I previously sent. > So, that would be: > rij = 1.98 > epsij= 0.550 * 0.1485 = 0.081675 > > Best regards, > Susan > From chemistry-request@server.ccl.net Wed Jan 29 13:30:52 2003 Received: from cardinal3.Stanford.EDU ([171.64.15.251]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0TIUpP14628 for ; Wed, 29 Jan 2003 13:30:52 -0500 Received: (from liviu@localhost) by cardinal3.Stanford.EDU (8.11.6/8.11.6) id h0TIUc207316; Wed, 29 Jan 2003 10:30:38 -0800 Date: Wed, 29 Jan 2003 10:30:38 -0800 (PST) From: Liviu Mihail Mirica To: chemistry@ccl.net Subject: Optimizing to a local minimum in Gaussian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am trying to geometry optimize two isoelectronic isomers of a copper complex using Gaussian 98. I know that one of the isomers is more stable than the other, and that there is a small barrier between them. When i try to optimize the less stable isomer, the optimization in Gaussian takes it all the way to the more stable isomer. I was wondering how can i modify the optimization procedure so that it stops to the local minimum of that particular isomer. should i make the optimization loose or tight, should i increase the vshift value? any advice will be greatly appreciated. Thank you. Liviu Mirica Stanford Univ. ************************** Liviu Mihail Mirica tel: 650-497-3188 Escondido Village, 35 B email: liviu@leland.stanford.edu Stanford, CA 94305, USA From chemistry-request@server.ccl.net Wed Jan 29 14:56:07 2003 Received: from qtp.ufl.edu ([128.227.89.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0TJu7P16509 for ; Wed, 29 Jan 2003 14:56:07 -0500 Received: from pc1 (ntred1 [128.227.192.113]) by qtp.ufl.edu (8.9.1a/8.9.1/deumens) with SMTP id OAA07435; Wed, 29 Jan 2003 14:56:16 -0500 (EST) Message-ID: <08a301c2c7d1$d5aecc10$71c0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Liviu Mihail Mirica" Cc: "CCL - all" References: Subject: Re: Optimizing to a local minimum in Gaussian Date: Wed, 29 Jan 2003 15:05:51 -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 Hi Liviu, if you know of some geometrical difference between the isomers (e.g. a longer bond or a different angle), then you might try to do a partial optimization with the most different parameter frozen. It might be best to choose the frozen parameter as the optimized value of the global minimum plus the experimental difference. If the difference is in electronic state, (e.g. a second singlet state), you can use the following sequence: 1) # scf/basis ... pop(minimal) ... to get the orbital energies and symmetries. Keep the checkpoint file. 2) scf(symm)/basis ... guess(check,alter) ... to calculate the energy of the new electronic state. The symm option to SCF keeps the number of electrons per irrep as in the initial guess (new, read-in or altered). Delta_SCF excitation energies may be off by maybe 30 kcal/mol. If it is off by more than 100 kcal/mol, try a different set of alterations. Keep in mind that the wavefunction is constrained to D2h and subgroups. This may give rise to problems with molecules that are linear or have rotational symmetry elements larger than C2. Hope this helps, Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@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@server.ccl.net Wed Jan 29 15:13:46 2003 Received: from venus.phpwebhosting.com ([64.29.16.27]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h0TKDjP16844 for ; Wed, 29 Jan 2003 15:13:45 -0500 Received: (qmail 1804 invoked from network); 29 Jan 2003 20:13:37 -0000 Received: from unknown (HELO localhost.leitl.org) (62.155.144.87) by venus.phpwebhosting.com with SMTP; 29 Jan 2003 20:13:37 -0000 Received: from localhost (eugen@localhost) by localhost.leitl.org (8.11.6/8.11.6) with ESMTP id h0TKDRc21690; Wed, 29 Jan 2003 21:13:29 +0100 X-Authentication-Warning: localhost.localdomain: eugen owned process doing -bs Date: Wed, 29 Jan 2003 21:13:27 +0100 (CET) From: Eugen Leitl X-X-Sender: To: cc: nano Subject: [PyMOL] parallel em code (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Wed, 29 Jan 2003 14:37:28 -0500 (EST) From: Nat Echols To: PyMOL list Subject: [PyMOL] parallel em code Hi-- This sounds a bit offtopic, but it's related to a project that would probably be built off of PyMOL. Does anyone have any experience with protein dynamics software that runs on clusters and performs energy minimization? I've seen all sorts of pure MD packages that run on clusters (GROMACS, NAMD, etc.) but all I want to do is adiabatic mapping. None of these programs seem to be designed for this. I've been using CNS for everything and as far as I know this does not come in an MPI-based flavor. I've seen reference to an MPI version of CHARMm, but I'm not sure how to get ahold of it (we have a Harvard CHARMm license, at least). thanks, Nat ---------------------------------------------------------------------------- Nathaniel Echols Programmer nat@bioinfo.mbb.yale.edu Gerstein Lab 203-589-6765 Yale University ---------------------------------------------------------------------------- ------------------------------------------------------- This SF.NET email is sponsored by: SourceForge Enterprise Edition + IBM + LinuxWorld = Something 2 See! http://www.vasoftware.com _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users From chemistry-request@server.ccl.net Wed Jan 29 11:00:37 2003 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0TG0bP09581 for ; Wed, 29 Jan 2003 11:00:37 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h0TG0bj12911; Wed, 29 Jan 2003 11:00:37 -0500 (EST) Date: Wed, 29 Jan 2003 11:00:37 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: Summer Undergraduate research opportunities at IBM Almaden Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Tue, 28 Jan 2003 14:57:39 -0800 From: Jed W Pitera To: jkl@ccl.net Subject: CCL question -- posting undergraduate research opportunities? Hello, We have a number of possible summer research opportunities for undergraduates here at IBM Almaden. The projects this summer are primarily focused on analyzing some of the initial data from protein folding simulations carried out as part of the Blue Gene science program. If you know of any promising undergraduates who are interested in protein folding, computational chemistry, or molecular simulation, please encourage them to apply to the following programs: http://www.stanford.edu/group/CPIMA/education/index.htm -- For this they need to have 3 letters of reference, a transcript and a completed application -- ALL received by Stanford by FEB 7. Details on the web site. Our project is number 23.5 -- Protein Folding Simulation and Analysis. http://www.almaden.ibm.com/st/studentopps/NSFopps/ For this they need to submit a one page resume, a one page essay, and send an official transcript, as well as have two letters of recommendation sent -- again by FEBRUARY 7. Details on the web site. Here they should mention interest in the work in our group (Protein folding/computational chemistry) -- and any of our names (Julia Rice, William Swope, Jed Pitera). Application deadlines for both programs are February 7, and we apologize for the short notice. Please feel free to contact me if any questions arise. Thank you, Jed Pitera IBM Almaden Research Center San Jose, CA USA pitera@us.ibm.com (408) 927-2084 From chemistry-request@server.ccl.net Wed Jan 29 16:12:37 2003 Received: from uni-kl.de ([131.246.137.52]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0TLCbP18739 for ; Wed, 29 Jan 2003 16:12:37 -0500 Received: from mailgate1.uni-kl.de (mailgate1.uni-kl.de [131.246.120.5]) by uni-kl.de (8.12.4/8.12.4) with ESMTP id h0TLCaES024183 for ; Wed, 29 Jan 2003 22:12:37 +0100 (MET) Received: from service.chemie.uni-kl.de (service.chemie.uni-kl.de [131.246.58.77]) by mailgate1.uni-kl.de (8.12.6/8.12.6) with ESMTP id h0TLCatu011076 for ; Wed, 29 Jan 2003 22:12:36 +0100 Received: from localhost (unknown [127.0.0.1]) by service.chemie.uni-kl.de (Postfix on SuSE Linux 7.1 (ppc)) with ESMTP id D92D336E05 for ; Wed, 29 Jan 2003 21:07:58 +0000 (UTC) Received: from pc1.chemie.uni-kl.de (pc1.chemie.uni-kl.de [131.246.58.1]) by service.chemie.uni-kl.de (Postfix on SuSE Linux 7.1 (ppc)) with ESMTP id C147F36D5E for ; Wed, 29 Jan 2003 22:07:57 +0100 (CET) Received: from pc3 (pc3.chemie.uni-kl.de [131.246.58.3]) by pc1.chemie.uni-kl.de (Postfix on SuSE Linux 7.0 (i386)) with ESMTP id 7697D140E8 for ; Wed, 29 Jan 2003 22:12:35 +0100 (CET) Content-Type: text/plain; charset="us-ascii" From: Elmar Gerwalin Reply-To: elg@chemie.uni-kl.de To: chemistry@ccl.net Subject: G98: gdiis and POpt ? Date: Wed, 29 Jan 2003 22:12:34 +0100 User-Agent: KMail/1.4.3 MIME-Version: 1.0 Message-Id: <200301292212.34664.elg@chemie.uni-kl.de> X-Virus-Scanned: by AMaViS perl-11 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h0TLCbP18740 Hello, I'm trying to partially optimize a medium sized molecule using g98, ( # b3lyp popt) and guess the pot.energy surface is very flat. So, I tried to use the option "gdiis" that should help in that cases.... but Popt(gdiis) fails: all variables are active, internal coordinates are generated, my Z-Matrix coordinates (and fixations) are ignored : it is like using "opt" , not "popt". Is this a bug or a feature of g98? For the specialists: here's the output from a diff over the IOp-Section: diff good bad 1,2c1,2 < is "good" < 1/10=7,14=-1,26=3,38=1/1,3; > 1/10=7,14=-1,18=40,26=3,38=1/1,3; < 1/10=7,14=-1/3(1); > 1/10=7,14=-1,18=40/3(1); < 1/14=-1/3(-5); > 1/14=-1,18=40/3(-5); I'd be glad if you could help me . By Elmar -- ======================================================== Elmar Gerwalin , University of Kaiserslautern,Germany Dept. of Theoretical Chemistry and IT Service Team elg@chemie.uni-kl.de 0631-205-2749 ======================================================== From chemistry-request@server.ccl.net Wed Jan 29 16:03:08 2003 Received: from sciences.sdsu.edu ([130.191.226.112]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0TL37P18479 for ; Wed, 29 Jan 2003 16:03:08 -0500 Received: from localhost (jcuervo@localhost) by sciences.sdsu.edu (8.10.2+Sun/8.8.8/SCEC-8.8.8-AS.AR.S5) with ESMTP id h0TL38K21097 for ; Wed, 29 Jan 2003 13:03:08 -0800 (PST) Date: Wed, 29 Jan 2003 13:03:08 -0800 (PST) From: Javier Cuervo To: chemistry@ccl.net Subject: Force Field question Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, We are thinking in obtain a program for doing energy calculation of proteins. We would like to be able of have the energy profile given as a "contribution per atom" to the total energy, and this contribution split in the differents terms (van Der Walls, electrostatic,H-bond, etc). We are considering AMBER as an option but we don't now if this package has this feature (or if there is any program that can do what we want). It would be helpful for us to hear your advise in this matter. Regards Javier Cuervo Graduate Student Computational Science Program SDSU