From sumiya@translell.tutkie.tut.ac.jp Wed Jan 25 07:39:35 1995 Received: from translell.translell.tutkie.tut.ac.jp for sumiya@translell.tutkie.tut.ac.jp by www.ccl.net (8.6.9/930601.1506) id HAA06683; Wed, 25 Jan 1995 07:32:12 -0500 Received: (from sumiya@localhost) by translell.translell.tutkie.tut.ac.jp (8.6.9+2.4Wb3/3.3Wb) id VAA22953 for CHEMISTRY@ccl.net; Wed, 25 Jan 1995 21:33:16 +0900 Date: Wed, 25 Jan 1995 21:33:16 +0900 From: Tsuyoshi Sumiya Message-Id: <199501251233.VAA22953@translell.translell.tutkie.tut.ac.jp> To: CHEMISTRY@ccl.net Subject: Help Dear Netters: Has anyone here performed energy calculations on proteins? I would like to know the order of magnitude of the energy for proteins in the crystal state, i.e. somebody who has calculated, using any of the molecular mechanics programs, the energy of the molecule using the crystalographic coordinates found for example in the PDB. I would also appreciate very much information on MM2 parameters for amino acids. Thanks in advance: Tsuyoshi Sumiya From graham@sentex.net Wed Jan 25 08:39:33 1995 Received: from quartz.sentex.net for graham@sentex.net by www.ccl.net (8.6.9/930601.1506) id IAA07240; Wed, 25 Jan 1995 08:24:47 -0500 Received: from kw-ttyD2.sentex.net (kw-ttyD2.sentex.net [204.50.3.20]) by quartz.sentex.net (8.6.5/8.6.9) with SMTP id IAA14061; Wed, 25 Jan 1995 08:25:12 -0500 Date: Wed, 25 Jan 1995 08:25:12 -0500 Message-Id: <199501251325.IAA14061@quartz.sentex.net> X-Sender: graham@quartz.sentex.net X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: lrbu00@xd88.kodak.com, chemistry@ccl.net From: graham@sentex.net (Graham Hurst) Subject: Re: CCL:VI editor for DOS/PC At 01:17 PM 1/24/95 -0500, John McKelvey wrote: >Netters: > >Is anyone aware of a unix-like VI editor for DOS/PC's ? > > >Thanks in advance! > >Regards, > >John McKelvey MKS (Mortice Kern Systems) in Waterloo, Ontario, Canada inlcudes a faithful implementation of vi in their toolkit of Unix utilities for DOS. The toolkit can make DOS very UNIX-like if one desires. I think they are on the net, but don't know the address... Watcom includes a vi-like editor with it's C compiler, including a Windows version, but it's purposely not identical to vi (eg. it includes mouse support and gives more visual feedback). Watcom is on the Web at www.watcom.on.ca. Sorry for posting to the group, but I thought many CCLers might be wishing that their PCs were more like Unix! Cheers, Graham ------- Graham Hurst, PhD or Cambridge, Ontario, Canada From mmh1203@ggr.co.uk Wed Jan 25 08:50:30 1995 Received: from gate.ggr.co.uk for mmh1203@ggr.co.uk by www.ccl.net (8.6.9/930601.1506) id IAA07323; Wed, 25 Jan 1995 08:30:27 -0500 Received: from mailhub.ggr.co.uk by gate.ggr.co.uk; Wed, 25 Jan 1995 13:28:13 GMT Message-Id: <26481.199501251320@mailhub.ggr.co.uk> Received: from UKSYSA.ggr.co.uk by mailhub.ggr.co.uk; Wed, 25 Jan 1995 13:20:35 GMT From: Dr M M Hann Date: 25 Jan 95 13:17:00 GMT Subject: MGMS bursaries for students at meeting in Australia To: chemistry@ccl.net Bursaries for Australia - Student members of the MGMS Students are invited to apply for bursaries to attend the 14th Annual International Conference of the Molecular Graphics and Modelling Society sponsored by the Molecular Graphics and Modelling Society (UK). To qualify, students must be prepared to present a poster at the meeting and must submit an abstract in advance to the MGMS Committee. In their application they must also specify other meetings attended, what benefit they hope to obtain from this meeting and a letter of support from their supervisor confirming that they are a bona fide student. Applicants must also be a member of the Molecular Graphics and Modelling Society; student membership costs 15.00 pounds sterling and is available by contacting Caroline Myers at the University of York, England (myers@yorvic.york.ac.uk). Bursary applications should be addressed to Dr Mike Hann, Glaxo Research and Development, Greenford Rd, Greenford, Middlesex, UB6 0HE, England by March 30th. The successful applicants will be notified by the middle of April. From FS300627@Sol.YorkU.CA Wed Jan 25 09:39:45 1995 Received: from Sol.YorkU.CA for FS300627@Sol.YorkU.CA by www.ccl.net (8.6.9/930601.1506) id IAA07694; Wed, 25 Jan 1995 08:50:23 -0500 From: Received: from Sol.YorkU.CA by Sol.YorkU.CA (PMDF V4.3-7 #6007) id <01HM9A9KRJO08WW8T8@Sol.YorkU.CA>; Wed, 25 Jan 1995 08:50:11 EST Date: Wed, 25 Jan 1995 08:50:11 -0500 (EST) Subject: Structure searches though the Internet To: chemistry@ccl.net Message-id: <01HM9A9KU8428WW8T8@Sol.YorkU.CA> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Greetings, I would like to know which 3D databases can be searched for possible structurally similair compounds. I am not interested in buying a whole database but I am willing to pay for a 'search fee' and possibly an 'entry fee' to do the search via the internet. If anyone has knowledge of this could they please mail me the information as well as where I could apply, and what software I need (using a PC) I will, if there is interest, summarize for the net. Regards, Patrick ************************************************************************** ** Patrick van der Valk | It is a capital mistake to theorize * ** BioMimic | before one has data. Insensibly one * ** | begins to twist facts to suit theories * ** e-mail:FS300627@Sol.YorkU.Ca | instead of theories to suit facts. * ** Phone: (416) 736-5747 | * ** Fax: (416) 650-3558 | -Sherlock Holmes- * ************************************************************************** From dave@terminus.chem.yale.edu Wed Jan 25 09:51:49 1995 Received: from terminus.chem.yale.edu for dave@terminus.chem.yale.edu by www.ccl.net (8.6.9/930601.1506) id JAA08259; Wed, 25 Jan 1995 09:11:18 -0500 Received: by terminus.chem.yale.edu; Wed, 25 Jan 95 09:12:35 -0500 From: David Maxwell Message-Id: <9501251412.AA15734@terminus.chem.yale.edu> Subject: RE: Crystal structures To: CHEMISTRY@ccl.net (Computational Chemistry List) Date: Wed, 25 Jan 95 9:12:35 EST X-Mailer: ELM [version 2.3 PL11] In response to Charles Letner's message: I am involved with force field parameterization, so I feel competent in dealing with this issue. The following question was proposed: > So the question that comes to mind is: Are the simulation methods that are > being developed really moving towards reproducing cystal conformations? > If so, can the current force fields be used to get solution conformations? I guess it really depends on what you using as the basis for your parameterization. If you are primarily using single molecule ab initio calculations to guide fitting, then your structures will likely match well with the gas phase structures. If you parameterize with liquid properties in mind, then you will, hopefully, match the liquid properties and structure. If you want to match X-ray ...., etc. With any force field, it is difficult to match everything perfectly. Some do well with matching heats of formation and other gas phase properties, while others do better in liquids, and still others are good for NMR or X-ray structures. Yes, a more advanced force field could, in principle, solve this problem, but it brings up other problems, one of which is a decrease in computational efficiency. You said: > Many times when reading papers on "optimizing" simulations or > verifying force fields (I'm speaking to molecular mechanics calculations > here) the authors compare the simulation results to the crystal structure. > In many cases the authors chose the best simulation by the simulation that > deviates the least from the crystal structure. I see nothing wrong with comparing to crystal structures, especially if it is the only structural data you have to make comparisions with. I would hope that all force fields would give structures in reasonable agreement to the X-ray structure. In the case of proteins, the X-ray structure gives us important tertiary information that still plays a key role in understanding how proteins "work their wonders" in a biological setting. Although their is no reason why the X-ray structure and the real structure in its natural setting have to be the same, I think most people would agree that they are similiar . As has been stated above and by others; the crystal packing effects and intermolecular forces between any liquid and the structure would cause the major deviation between the natural and X-ray structures. -Dave Maxwell Yale University dave@terminus.chem.yale.edu From monique@ibs.ibs.fr Wed Jan 25 10:39:37 1995 Received: from ibs.ibs.fr for monique@ibs.ibs.fr by www.ccl.net (8.6.9/930601.1506) id KAA09314; Wed, 25 Jan 1995 10:08:08 -0500 From: Received: from [192.134.36.156] (rmnmacmonique.ibs.fr [192.134.36.156]) by ibs.ibs.fr (8.6.9/8.6.9) with SMTP id PAA18656 for ; Wed, 25 Jan 1995 15:50:28 +0100 Date: Wed, 25 Jan 1995 15:50:28 +0100 Message-Id: <199501251450.PAA18656@ibs.ibs.fr> To: chemistry@ccl.net Subject: Conference : QM Simulations in Biology ================================================================================ * CONFERENCE ANNOUNCEMENT - LAST CIRCULAR * ================================================================================ * QUANTUM MECHANICAL SIMULATION METHODS FOR STUDYING BIOLOGICAL SYSTEMS * ================================================================================ Place and date: Centre de Physique des Houches FRANCE 2-7 May 1995 Abstract: An important area of current theoretical research is the examination of the structure and the function of biological macromolecules such as proteins and nucleic acids. For many phenomena, such as the investigation of the equilibrium structures of a biological polymer, simulations based upon classical mechanics are sufficiently accurate. However, in other cases, such as the simulation of electron transfer or of enzymatic reactions, it is necessary to use quantum mechanical methods. The aim of the workshop is to assess the state-of-the-art in the field and to highlight areas for future research by bringing together reseachers who develop quantum mechanical simulation methods and apply them to biological systems. Topics: Ab Initio Molecular Dynamics; Quantum Dynamical Simulations; Electronic Structure Calculations; Density Matrix Methods; Electron and Proton Transfer Reactions. Invited Speakers: H.J.C. Berendsen (Groningen), P.L. Dutton (Pennsylvania), N.C. Handy (Cambridge), J.T. Hynes (Boulder), B. Lesyng (Warszawa), J.N. Onuchic (UCSD), M. Parrinello (Stuttgart), A. St.Amant (Ontario), K. Schulten (Urbana-Champaign), A. Warshel (UCLA), M.C. Zerner (Gainesville). Organizing Committee: D.J. Bicout (IBS, Grenoble), M.J. Field (IBS, Grenoble), A. Szabo (NIH, Bethesda). Information for Participants: Les Houches is a resort village in the Chamonix valley of the French Alps. Established in 1951, the school is situated in a mountain village surrounded by meadows and woods at an elevation of 1000m. It is ideally located for mountaineering, skiing or touring as well as for intellectual pursuits. The fee of 3000 FF includes board, lodging at the centre during the workshop and a copy of the proceedings. Attendance is limited to 60 participants. A limited number of grants to help with the registration and subsistence expenses of selected young researchers will be available. Applications, including a brief C.V. and recent publications, should be sent before March 1st, 1995 to: Mme Monique Marchand Institut de Biologie Structurale - Jean-Pierre Ebel 41, Avenue des Martyrs F-38027 Grenoble Cedex 1 FRANCE Fax: (33)-76-88-54-94 Email: monique@ibs.fr Note: As space is limited all applicants will be informed as soon as possible after March 1st if a place has been reserved for them. ================================================================================ * APPLICATION FORM * ================================================================================ Surname: First Name: Nationality: Sex: Address to which any correspondence should be sent: Telephone: E-mail: Telefax: Telex: Research Activity: Relevant Publications (if any): Employer: Present Position: Do you intend to bring your spouse and/or other persons? Seminar and/or Poster Sessions: ------------------------------- If you want to contribute to the Seminar and/or Poster Sessions, please enclose an abstract and give a title here: Date: Signature: Monique Marchand I.B.S. 41, avenue des Martyrs 38027 GRENOBLE Cedex 1 (France) From chanser@oci.unizh.ch Wed Jan 25 12:42:11 1995 Received: from rzusuntk.unizh.ch for chanser@oci.unizh.ch by www.ccl.net (8.6.9/930601.1506) id LAA12091; Wed, 25 Jan 1995 11:52:09 -0500 From: Received: from rzurs10.unizh.ch by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA29119; Wed, 25 Jan 95 17:51:20 +0100 Received: by rzurs10.unizh.ch (AIX 3.2/UCB 5.64/4.03) id AA18981; Wed, 25 Jan 1995 17:51:19 +0100 Date: Wed, 25 Jan 1995 17:51:19 +0100 Message-Id: <9501251651.AA18981@rzurs10.unizh.ch> To: chemistry@ccl.net Subject: reaction dynamics -- Message removed on author's request -- From olson@bioorganic.ucsb.edu Wed Jan 25 21:39:40 1995 Received: from hub.ucsb.edu for olson@bioorganic.ucsb.edu by www.ccl.net (8.6.9/930601.1506) id UAA22999; Wed, 25 Jan 1995 20:45:17 -0500 Received: from bioorganic (bioorganic.ucsb.edu) by hub.ucsb.edu; id AA23929 sendmail 4.1/UCSB-2.1-sun Wed, 25 Jan 95 17:45:13 PST for chemistry@ccl.net Received: by bioorganic (931110.SGI/930416.SGI) for @hub.ucsb.edu:chemistry@ccl.net id AA08166; Wed, 25 Jan 95 17:50:33 -0800 Date: Wed, 25 Jan 95 17:50:33 -0800 From: olson@bioorganic.mechanisms.ucsb.edu (Leif Olson) Message-Id: <9501260150.AA08166@bioorganic> To: chemistry@ccl.net Subject: dynamics analysis software needed Our group needs software for analysis of molecular dynamics results of oligonucleotides. We know of a program (newhel) which is good for single structures, but we want a program which will allow analysis of many sequential structures (propeller twist, base distances, etc). There is supposedly a program called Curves, Dials, and Windows or something like that which might fill our needs, but it is our understanding that this program is considered to be out of date and is thus no longer available. Meanwhile, the newest version is not yet ready for release. Are there any reasonably up-to-date versions of this software (or something which will do the same job) out there? Thank you, Leif Olson, Ph.D. UC Santa Barbara Chemistry Department olson@bioorganic.ucsb.edu From stuart@wucmd.wustl.edu Wed Jan 25 21:52:29 1995 Received: from wugate.wustl.edu for stuart@wucmd.wustl.edu by www.ccl.net (8.6.9/930601.1506) id VAA23340; Wed, 25 Jan 1995 21:52:29 -0500 Received: by wugate.wustl.edu (5.67b/WUSTL-0.3) with SMTP id AA01978; Wed, 25 Jan 1995 20:52:27 -0600 Received: by wucmd (931110.SGI/911001.SGI) for @wugate.wustl.edu:CHEMISTRY@ccl.net id AA25487; Wed, 25 Jan 95 18:48:11 -0600 Date: Wed, 25 Jan 1995 18:43:25 -0600 (CST) From: Stuart Green Sender: Stuart Green Reply-To: Stuart Green Subject: Availability of CADPAC To: CHEMISTRY@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Could someone please mail me with information regarding the Cambridge Analytical Derivatives Packages (CADPAC). Does it still exist? who do I contact? which version? how much? what platforms? etc. Many thanks, Stuart --- Stuart M. Green stuart@wucmd.wustl.edu Center for Molecular Design Campus Box 1099 Washington University Tel 314-935-4671 St. Louis, MO 63130-4899 Fax 314-935-4979 From hcj@mazda.wavefun.com Wed Jan 25 23:39:44 1995 Received: from wavefun.com for hcj@mazda.wavefun.com by www.ccl.net (8.6.9/930601.1506) id WAA23787; Wed, 25 Jan 1995 22:42:57 -0500 Received: from mazda.wavefun.com by wavefun.com via SMTP (931110.SGI/930416.SGI) for chemistry@ccl.net id AA09354; Wed, 25 Jan 95 19:42:58 -0800 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA17768; Wed, 25 Jan 95 19:42:59 -0800 Date: Wed, 25 Jan 95 19:42:59 -0800 From: hcj@mazda.wavefun.com (Harry C. Johnson) Message-Id: <9501260342.AA17768@mazda.wavefun.com> To: chemistry@ccl.net Subject: receptor-ligand structure Reply-To: hcj@wavefun.com Dear chem netters, I am looking for some simple examples of receptor-ligand structures. I would prefer PDB, macromodel, sybyl mol and mol2, or, of course, Spartan input files. Thanks in advance for your assistance! -Harry +-----------------------+--------------------------------------------+ |Harry C. Johnson | /--- ----\ /---/ ---\ ----- /---/ /| / | |Computational Chemist | \ / / / / / / / / / / | / | |Wavefunction Inc. | \ /---/ /---/ /---/ / /---/ / | / | |E-mail: hcj@wavefun.com|---/ / / / / \ / / / / |/ | +-----------------------+--------------------------------------------+