From sxr224@anugpo.anu.edu.au Wed Jun 7 01:47:40 1995 Received: from anugpo.anu.edu.au for sxr224@anugpo.anu.edu.au by www.ccl.net (8.6.10/930601.1506) id BAA29591; Wed, 7 Jun 1995 01:36:43 -0400 Received: from surya (surya.anu.edu.au [150.203.7.194]) by anugpo.anu.edu.au (8.6.12/8.6.12) with SMTP id PAA27989 for ; Wed, 7 Jun 1995 15:29:50 +1000 Message-Id: <199506070529.PAA27989@anugpo.anu.edu.au> Comments: Authenticated sender is From: "Shoba Ranganathan" To: CHEMISTRY@ccl.net Date: Wed, 7 Jun 1995 15:36:26 +0000 Subject: CCL: Protein Domain Prediction Reply-to: Shoba.Ranganathan@anu.edu.au Priority: normal X-mailer: Pegasus Mail for Windows (v2.0-WB3) Hi, Is there any method/program that can successfully identify domain boundaries from the amino acid sequence of a protein? This will be a first step towards inverted protein structure prediction, I believe. Shoba =========================================================== Dr. Shoba RANGANATHAN Tel: +616-279-8301 Div. of Biochemistry & Mol. Biology Fax: +616-249-0415 JCSMR, Australian National University Canberra ACT 2002 Australia. email:Shoba.Ranganathan@anu.edu.au ---------------------------------------------------------- From toukie@zui.unizh.ch Wed Jun 7 03:02:41 1995 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.10/930601.1506) id CAA00258; Wed, 7 Jun 1995 02:49:41 -0400 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA21419; Wed, 7 Jun 95 08:49:38 +0200 X-Nupop-Charset: Swiss Date: Wed, 7 Jun 1995 08:49:33 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <31773.toukie@zui.unizh.ch> To: chemistry@ccl.net Subject: Conformation of aq. alkyls Dear Colleagues; I am seeking information re the conformation of long-chain alkanes, alkylbenzenes, or alkoxybenzenes in aqueous solution. I imagine that in an aqueous milieu the alkyl moieties should curl up into a sort of ball to minimise contact with water. Does anyone know of any nmr or theoretical analyses of long-chain alkanes, alkylbenzenes, or alkoxybenzenes in water? Kindly send details to me directly at toukie@zui.unizh.ch Thanks in advance to all responders. Sincerely, S. Shapiro ZH toukie@zui.unizh.ch From JeanLuc.Verschelde@rug.ac.be Wed Jun 7 03:17:42 1995 Received: from mserv.rug.ac.be for JeanLuc.Verschelde@rug.ac.be by www.ccl.net (8.6.10/930601.1506) id DAA00382; Wed, 7 Jun 1995 03:04:28 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA14723 (5.67b/IDA-1.5 for ); Wed, 7 Jun 1995 09:03:01 +0200 Received: by allserv.rug.ac.be (5.x/SMI-SVR4) id AA27123; Wed, 7 Jun 1995 09:03:54 +0200 Date: Wed, 7 Jun 1995 09:03:54 +0200 (MET DST) From: Jean-Luc Verschelde To: OHIO SUPER Subject: GRASP Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, Can someone tell where I can find GRASP. Thanks, Jean-Luc =================================================================================== Verschelde Jean-Luc University of Ghent Lab. of Physiological Chemistry K.L. Ledeganckstraat 35 9000 Ghent Belgium. Tel.:09/264 53 06 Fax:09/264 53 37 Email:Jeanluc.Verschelde@rug.ac.be =================================================================================== From sanja@indigo.irb.hr Wed Jun 7 04:32:42 1995 Received: from indigo.irb.hr for sanja@indigo.irb.hr by www.ccl.net (8.6.10/930601.1506) id EAA00751; Wed, 7 Jun 1995 04:24:43 -0400 Received: by indigo.irb.hr (940816.SGI.8.6.9/930416.SGI.AUTO) for CHEMISTRY@ccl.net id KAA05375; Wed, 7 Jun 1995 10:26:14 -0700 From: "sanja" Message-Id: <9506071026.ZM5373@indigo.irb.hr> Date: Wed, 7 Jun 1995 10:26:02 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@ccl.net Subject: scaling MP2 freq. Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, I am interested in scaling vibration frequencies calculated at the MP2/6-31G** level. Should I use the scaling factor of 0.9427, proposed by J.A. Pople et.al for the MP2/6-31G* calculated frequencies. I am not sure how much this scaling factor is sensitive to the difference in the basis sets. Every comment is wellcome. Thanx, Sanja -- *~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* Sanja Sekusak e-mail: sanja@indigo.irb.hr Rudjer Boskovic Institute phone: (385-1) 46 10 89 HR-41001 Zagreb, CROATIA fax: (385-1) 27 26 48 *~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* From Don_Gregory@msi.com Wed Jun 7 08:50:02 1995 Received: from msi.com for Don_Gregory@msi.com by www.ccl.net (8.6.10/930601.1506) id IAA05367; Wed, 7 Jun 1995 08:41:34 -0400 Received: from qmail-gw.msi.com by msi.com (4.1/SMI-4.1) id AA25421; Wed, 7 Jun 95 08:38:48 EDT Message-Id: Date: 7 Jun 1995 08:40:38 -0400 From: "Don Gregory" Subject: Structural Domain Analysis To: "Comp. Chem. Listserver" X-Mailer: Mail*Link SMTP-QM 3.0.2 Subject: Time:8:18 AM OFFICE MEMO Structural Domain Analysis Date:6/7/95 Dr. Shoba Ranganathan asked: "Is there any method/program that can successfully identify domain boundaries from the amino acid sequence of a protein?" Quanta has had this capability for some time; but I must stress that the "domains" that Quanta determines are *structural* domains, and not functional domains. I would love it if I were to be soon proven wrong, but I believe it is clear that the ability to 'predict' functional domains quite a way into the future. This does not mean, however, that knowledge of structural domains is not useful, as often the organization of the structure of a protein system exists for the very purpose of facilitating the functionality of the enzyme, receptor, etc. Don Gregory MSI From mk34+@andrew.cmu.edu Wed Jun 7 11:02:56 1995 Received: from po2.andrew.cmu.edu for mk34+@andrew.cmu.edu by www.ccl.net (8.6.10/930601.1506) id KAA17429; Wed, 7 Jun 1995 10:50:16 -0400 Received: (from postman@localhost) by po2.andrew.cmu.edu (8.6.12/8.6.12) id KAA07479; Wed, 7 Jun 1995 10:50:09 -0400 Received: via switchmail; Wed, 7 Jun 1995 10:50:08 -0400 (EDT) Received: from unix14.andrew.cmu.edu via qmail ID ; Wed, 7 Jun 1995 10:49:41 -0400 (EDT) Received: from unix14.andrew.cmu.edu via qmail ID ; Wed, 7 Jun 1995 10:49:39 -0400 (EDT) Received: from mms.4.60.Jan.26.1995.18.43.47.sun4c.411.EzMail.2.0.CUILIB.3.45.SNAP.NOT.LINKED.unix14.andrew.cmu.edu.sun4c.411 via MS.5.6.unix14.andrew.cmu.edu.sun4c_411; Wed, 7 Jun 1995 10:49:38 -0400 (EDT) Message-ID: <4jpPm2W00YUqI6gbJ_@andrew.cmu.edu> Date: Wed, 7 Jun 1995 10:49:38 -0400 (EDT) From: Michael Tor Klawansky To: Outbound News Subject: CCL:METHODS OF MOLECULAR MECHANICS WORKSHOP Cc: Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , Outbound News , rna@net.bio.net, chemistry@ccl.net ***** NOTE:When replying please reply to ropelews@slave.psc.edu ***** "METHODS OF MOLECULAR MECHANICS AND DYNAMICS OF BIOPOLYMERS" WORKSHOP Pittsburgh Supercomputing Center August 16-19, 1995 The Pittsburgh Supercomputing Center (PSC) is hosting a workshop on "Methods of Molecular Mechanics and Dynamics of Biopolymers," August 16-19, 1995. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in molecular mechanics. Practical experience on our supercomputers will be gained in the application to: (1) the theory and practice of molecular mechanics and dynamics; (2) the development and refinement of molecular mechanics force fields; (3) the problem of conformation mapping and analysis of polypeptide structures, including the refinement of structure from measured NMR data; and (4) computation of interaction energies and free energies for protein-drug interactions and conformational thermodynamics. Workshop leaders are Dr. Charles L. Brooks III, The Scripps Research Institute and Dr. Alexander D. MacKerell Jr., University of Maryland at Baltimore. The worskhop will consist of lectures and extensive hands-on sessions. General aspects of molecular mechanics software will be discussed and a number of packages are available for use at the PSC. However, the programs CHARMM and QUANTA will be utilized most extensively in demonstrations. Hands-on sessions will be emphasized. Participants will be able to work on the examples provided or on their own experimental data. No prior supercomputing experience is necessary. This workshop is funded by a grant from the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. TRAVEL, MEALS AND HOTEL ACCOMMODATIONS FOR RESEARCHERS AFFILIATED WITH U.S. ACADEMIC INSTITUTIONS ARE SUPPORTED BY THIS GRANT. Enrollment is limited to 20. An application form is included. Deadline for applications is: June 22, 1995. Please direct inquires or send the following application form to blankens@psc.edu. Additional information about this workshop can be found in http://pscinfo.psc.edu/biomed/workshops95.html PITTSBURGH SUPERCOMPUTING CENTER BIOMEDICAL INITIATIVE ************************************** August 16-19, 1995 APPLICATION Name:________________________________________________________________________ Affiliation:_________________________________________________________________ Address:_____________________________________________________________________ (Business) _____________________________________________________________________________ ____________________________________________________________________________ (Home) ____________________________________________________________________________ Telephone: ____________________ ______________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship: ____________ Electronic Mail Address:____________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: _______________________________________________ How did you learn about this workshop? _____________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, your current research and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials by June 22, 1995 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From raman@bioc01.uthscsa.edu Wed Jun 7 12:47:54 1995 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.10/930601.1506) id MAA20531; Wed, 7 Jun 1995 12:32:45 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Wed, 7 Jun 1995 11:36:45 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA06475; Wed, 7 Jun 95 11:32:35 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9506071632.AA06475@bioc01.uthscsa.edu> Subject: Re: CCL:Protein Domain Prediction To: Shoba.Ranganathan@anu.edu.au Date: Wed, 7 Jun 1995 11:32:34 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <199506070529.PAA27989@anugpo.anu.edu.au> from "Shoba Ranganathan" at Jun 7, 95 03:36:26 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 2462 Shoba: > > Is there any method/program that can successfully identify domain > boundaries from the amino acid sequence of a protein? This will be a > first step towards inverted protein structure prediction, I believe. You might want to take a look at the following paper from Kahn's group in Toulouse. It provides a method for identifying domains in proteins Sonnhammer EL; Kahn D. Modular arrangement of proteins as inferred from analysis of homology. Protein Science, 1994 Mar, 3(3):482-92. In addition, you can use the database used in this study to evaluate the domain structure of your protein, by sending an email to: prodom@toulouse.inra.fr To get a help file, send the message "help" in the body of your message. Also, see the recent paper by Sowdhamini and Blundell in Protein Science [1995] 4, 506-520 "An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins". Regards -raman -- _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ C.S.RAMAN _/ _/ Department of Biochemistry _/ _/ University of Texas Health Science Center _/ _/ 7703 Floyd Curl Drive _/ _/ San Antonio, TX 78284-7760 _/ _/ USA _/ _/ _/ _/ Tel: (210) 567-6623 _/ _/ Fax: (210) 567-6595 _/ _/ E-mail: raman@bioc01.uthscsa.edu _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ How can it be that mathematics, a product of human thought _/ _/ independent of experience, is so admirably adapted to the _/ _/ objects of reality? -Albert Einstein _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ From angel@hobbit.quimica.uniovi.es Wed Jun 7 14:47:50 1995 Received: from opalo.etsiig.uniovi.es for angel@hobbit.quimica.uniovi.es by www.ccl.net (8.6.10/930601.1506) id OAA24359; Wed, 7 Jun 1995 14:41:46 -0400 Received: from hobbit.quimica.uniovi.es by etsiig.uniovi.es (PMDF V5.0-3 #4541) id <01HRFN93U2GG95MZWJ@etsiig.uniovi.es> for chemistry@ccl.net; Wed, 07 Jun 1995 18:29:26 +0100 (GMT) Received: by hobbit.quimica.uniovi.es (5.64/7.0) id AA05177; Wed, 07 Jun 1995 18:27:20 +0200 Date: Wed, 07 Jun 1995 18:27:20 +0200 From: angel@hobbit.quimica.uniovi.es (Angel Martin Pendas) Subject: Symmetry coupling coef. under finite groups? To: chemistry@ccl.net Cc: angel@etsiig.uniovi.es Message-id: <9506071627.AA05177@hobbit.quimica.uniovi.es> Content-transfer-encoding: 7BIT Dear Netters, I would very much appreciate any kind of information (bibliography, computational codes, etc) regarding the efficient automatic calculation of symmetry coupling coefficients under finite groups . Our aim is to build a code in order to perform general symmetry (crystal field-like) restricted Hartree-Fock (RHF) ATOMIC calculations. It would also be very interesting for me to obtain a computational source code to construct the character tables (or irreducible matrix representations) of finite groups from the group symbol. I will be posting a summary of the answers. ---------------------------------------------------------------------------- Angel Martin Pendas Quantum Chemistry group University of Oviedo. SPAIN e-mail: angel@hobbit.quimica.uniovi.es ---------------------------------------------------------------------------- From sherm@ccl.net Wed Jun 7 16:47:52 1995 Received: from coh.Coh.ORG for sherm@ccl.net by www.ccl.net (8.6.10/930601.1506) id QAA26748; Wed, 7 Jun 1995 16:43:08 -0400 Received: from iris.coh.org by coh.Coh.ORG (5.0/SMI-SVR4) id AA13589; Wed, 7 Jun 1995 13:43:03 +0800 Received: by iris.coh.org (920330.SGI/911001.SGI) for @coh.coh.org:chemistry@ccl.net id AA02583; Wed, 7 Jun 95 13:39:27 -0700 Date: Wed, 7 Jun 95 13:39:27 -0700 From: sherm@ccl.net (Mark A. Sherman) Message-Id: <9506072039.AA02583@iris.coh.org> To: chemistry@ccl.net Subject: Molecular modeling core facilities Reply-To: sherm@coh.Coh.ORG content-length: 604 I'm interested in finding out: (1) how many universities/institutes/companies maintain molecular modeling core facilities, and (2) how much they charge their users (both internal and external) for use of the facility. You need not state your affiliation if you wish to keep pricing information confidential. I simply need to know how our facility compares to others. Thanks for taking time to respond. I will deposit the data I gather in the archives. Mark A. Sherman, Ph.D. Director, Molecular Modeling Core Facility Beckman Research Institute of the City of Hope, Duarte, California sherm@coh.org From aps501@anugpo.anu.edu.au Wed Jun 7 20:17:55 1995 Received: from anugpo.anu.edu.au for aps501@anugpo.anu.edu.au by www.ccl.net (8.6.10/930601.1506) id UAA29740; Wed, 7 Jun 1995 20:06:05 -0400 Received: from huxley.anu.edu.au (aps501@huxley.anu.edu.au [150.203.2.12]) by anugpo.anu.edu.au (8.6.12/8.6.12) with ESMTP id JAA12718; Thu, 8 Jun 1995 09:58:21 +1000 From: Anthony P Scott Received: (aps501@localhost) by huxley.anu.edu.au (8.6.12/8.6.12) id KAA07312; Thu, 8 Jun 1995 10:04:40 +1000 Date: Thu, 8 Jun 1995 10:04:40 +1000 Message-Id: <199506080004.KAA07312@huxley.anu.edu.au> To: CHEMISTRY@ccl.net, sanja@indigo.irb.hr Subject: Re: CCL:scaling MP2 freq. The original poster asked about scaling factors to be applied to mp2/6-31g** calculated frequencies. He asked if our mp2/6-31g* scaling factor is applicable and if the scalinf factor varies with basis set. Our worl in this area, which is nearing completion, indicates that the mp2 level of theory is not particularly sensitive to basis set in predicting frequencies. While the 6-31g** basis set was not studied, we have data for the 6-311g** basis set. The appropriate scaling factor for the mp2 level of theory with this basis set is 0.9496 (with about the same overall RMS error as wefound for the mp2/6-31g* level of theory). We have actually studied a very extensive range of methods (including DFT) with various basis sets. If readers would like further information then please contact me. Hope this is of some assistance, Kind Regards, Anthony P. Scott Research Officer Computational Chemistry Group Research School of Chemistry Australian National University Canberra, ACT, Australia From zhy@ailab.ia.ac.cn Wed Jun 7 20:47:55 1995 Received: from ailab.ia.ac.cn for zhy@ailab.ia.ac.cn by www.ccl.net (8.6.10/930601.1506) id UAA00177; Wed, 7 Jun 1995 20:47:02 -0400 Received: by ailab.ia.ac.cn id AA00221 (5.67b/IDA-1.5 for CHEMISTRY@ccl.net); Thu, 8 Jun 1995 09:48:30 +0900 Date: Thu, 8 Jun 1995 09:48:30 +0900 From: Zhang HongYu Message-Id: <199506080048.AA00221@ailab.ia.ac.cn> To: CHEMISTRY@ccl.net Subject: re: CHARMM Charges Dear CHarles, CHARMM has its data file of atom type, MASSES.RT, while the atom charge is depend on different residue environment, so in different RTF(residue topology file), such as AMINO.RTF and POLYSACCHARIDESH.RTF et al, same atom type will take different charges, thus you need to open different RTF for different molecule. You have to consult with your system manager for CHARMM data file's location. hope this helps Hongyu Zhang ---------------------------------------------------------------------- Henry Hongyu Zhang, Ph.D. student | email: zhy@ailab.ia.ac.cn Molecular Design Laboratory | zhy@pchsgi25.ipc.pku.edu.cn Institute of Physical Chemistry | Tel: 861-2501490 Peking University | Fax: 861-2501725 Peking 100871 , China | ----------- Too stiff, easily broken Too soft, easily crashed ------------ old Chinese Saying From mw@crystal.uwa.edu.au Wed Jun 7 23:03:07 1995 Received: from uniwa.uwa.edu.au for mw@crystal.uwa.edu.au by www.ccl.net (8.6.10/930601.1506) id XAA01140; Wed, 7 Jun 1995 23:02:11 -0400 Received: from graf.crystal.uwa.edu.au (graf.crystal.uwa.edu.au [130.95.232.1]) by uniwa.uwa.edu.au (8.6.10/8.6.9) with SMTP id LAA06876 for ; Thu, 8 Jun 1995 11:02:02 +0800 Received: from pack.crystal.uwa.edu.au by graf.crystal.uwa.edu.au with SMTP (5.61+IDA+MU) id AA02850; Thu, 8 Jun 1995 11:43:38 +0800 From: mw@crystal.uwa.edu.au (Magda Wajrak) Message-Id: <9506080256.AA03028@pack> Subject: Singlet-Triplet Replies To: CHEMISTRY@ccl.net Date: Thu, 8 Jun 95 10:56:42 "WST Mailer: Elm [revision: 70.85] Dear Netters Thank you to all those who replied to my question on singlet-triplet splitting. I also wanted to ask if anyone knows of some references or knows off hand the value of singlet-triplet energy gap for Sulfur atom and S2 molecule, experimental and/or theoretical values. Thank you for your help. Magda Wajrak (email: mw@crystal.uwa.edu.au)