From rino@gpc.ibc.wustl.edu Fri Apr 10 18:23:45 1998 Received: from wugate.wustl.edu for rino@gpc.ibc.wustl.edu by www.ccl.net (8.8.3/950822.1) id SAA04507; Fri, 10 Apr 1998 18:07:09 -0400 (EDT) Received: from [128.252.137.150] ([128.252.137.150]) by wugate.wustl.edu (8.8.8/8.8.5) with ESMTP id RAA32556 for ; Fri, 10 Apr 1998 17:07:08 -0500 (CDT) Date: Fri, 10 Apr 1998 17:07:08 -0500 (CDT) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Rino Ragno Subject: trajectory: summary Hi, few days ago I posted the following: >Given the initial(A) and final(B) geometry of two conformation of a protein >how can I generate the trajectory of the interconversion A <-> B and store >the intermediate files, say for istance 20 conformation? >Is any of you out there aware of a program that solve the above problem. Next are the answers I got. 1 =================================================== The simplest is to run an MD trajectory with distance (and maybe other) constraints starting with your initial conformation while constraints are extracted from your final conformation any MD program such as CHARMM or Discover or other Philippe 2 =================================================== From: Michael Hodgson Well I've never tried anything like this, but I believe it might be possible using travel, under CHARMM. I've never read the documentation but it is available on the web at: http://yuri.harvard.edu/charmm/travel.html -Michael 3 =================================================== From: Richard Gillilan Obtaining actual trajectories connecting initial and final conformations is a problem in variational calculus (of great interest in Semiclassical calculations and other areas). I have a paper in JCP some years ago that describes what I call the "Variational Verlet" method, which is quite simple in concept but leads to equations that are difficult to solve globally. The problem is that trajectories of any significant length are generally saddle points in the multidimensional space of of possible solutions rather than minima or maxima. This is a fundamental problem that you will encounter with any such calculation that gives a true trajectory. Back when I did my calculations in 1992, I worked with only about 100 atoms and finding convergent solutions was difficult but not impossible. The theory does have some very interesting properties: there is formally NO accumulation of integration error with time (sounds impossible doesn't it? One pays for it in other ways I suspect). Bill Hoover at Livermore has introduced Lagrange multipliers into the equations to obtain true nonequilibrium const Temp trajectories. Here are the papers: "Shadowing, rare events and rubber bands. A variational Verlet algorithm for molecular dynamics", Richard E. Gillilan and Kent R. Wilson J. Chem Phys. 97 (3) 1 Aug 1992 William Hoover Phys Lett A vol 204 p133 (1995) Sorry, the code was rather specialized and not designed for biomolecules, perhaps someday I'll integrate it with my simulation suite that uses MMFF94. If you don't need true trajectories, I suggest you look at Ron Elber's work on reaction path calculations. His code is publically available and works with proteins: R. Czerminski and R. Elber, Int. J. Quant. Chem. 24, 167 (1990) 4 =================================================== From: Rick Venable I know CHARMM can be used to do such things, and I suspect AMBER, DISCOVER, and GROMOS can as well. None are free, but all but DISCOVER are available to academic sites for a few hundred dollars from research groups at the originating university. However, depending on the number of degrees of freedom involved in going from state A to state B, there may be more than one pathway. 5 =================================================== From: Ferenc Molnar Dear Rino: take a look at: J. Schlitter, M. Engels, P. Kr\"uger, E. Jacoby, A. Wollmer, "Targeted Molecular Dynamics Simulation of Conformational Change - Application to the T <-> R Transition in Insulin", Molecular Simulation, _10_, 291-308 (1993). J. Ma, M. Karplus, "Molecular switch in signal transduction: Reaction path of the conformational changes in ras p21", Proc.Natl.Acad.Sci. USA, _94_, 11905-11910 (1997). Cheers, Ferenc 6 =================================================== From: ponder@dasher.wustl.edu Rino, You need one of the reaction path methods of Ron Elber, et al. The simplest of his methods is implemented in TINKER as the "path" tool. It works well on small molecules through medium-sized peptides, and might be pushed to do some small protein problems. Some of Elber's more sophisticated versions can certainly do big protein problems. All of these Elber methods do exactly what you asked for -- they take two endpoint structures as input and generate a series of structures on the conformational path connecting them. Jay 7 =================================================== From: "Adrian Roitberg" Unfortunately, not what you ask for is not trivial. You should look at Ron Elber's work over the last 8-9 years for a reaction path between those conformations, and to his recent work ('97" for actual trajectories. 8 =================================================== From: Ryszard Czerminski Hi Rino, Check (1) http://www.fh.huji.ac.il/members/Elber/index.html and program Moil (2) http://dasher.wustl.edu/tinker Moil and Tinker have implementation of some of the aproaches published in @ARTICLE{Elber87, author = "Ron Elber and Martin Karplus", title = {}, journal = CPL, year = 1987, volume = 139, pages = "375" } \item {11.}{R. Czermi\'nski, R. Elber "Reaction Path Study of Conformational Transitions and Helix Formation in a Tetrapeptide" Proc. Nat. Acad. Sci. 86, 6963 (1989) \item {12.}{R. Czermi\'nski, R. Elber "Reaction Path Study of Conformational Transitions in Flexible Systems: Applications to Peptides" J. Chem. Phys. 92, 5580 (1990) \item {17.}{R. Czermi\'nski, R. Elber "Self Avoiding Walk Between Two Fixed Points as a Tool to Calculate Reaction Paths in Large Molecular Systems" Int. J. Quant. Chem. 24, 167 (1990) R. Olender and Ron Elber, "Caclulation of classical trajectories with a very large time step: Formalism and numerical examples", J. Chem. Phys. 105,9299-9315(1996) (3) http://yuri.harvard.edu (CHARMM HomePage) It has implementation of PATH and TRAVEL (developed by Stefan Fisher) @ARTICLE{FisherKarplus92, author = "S. Fisher and M.Karplus", title = {}, journal = CPL, year = 1992, volume = "194", pages = "252" } @PHDTHESIS{Fisher92, author = "S. Fisher", title = {Curvilinear reaction-coordinates of conformational change in macromolecules. Application to rotamase catalysis}, school = {Harvard University}, year = 1992, address = {Cambridge, MA} } 9 =================================================== From: Devapriya Choudhury Hello, I guess one should do energy minimisation where the RMS diff. between A and B is added to the potential energy (after suitable weighting). However, I don't know whether there are any programs to do this, or even if there is any better way to do this. Please post me any replies you get on this issue. cheers Deva 10 =================================================== From: Lutz.Ehrlich@EMBL-Heidelberg.de Juergen Schlitter devised an algorithm called targeted molecular dynamics (TMD), which you'll find described in Schlitter J, Engels M, Kruger P: J Mol Graph 1994 Jun;12(2):84-89 "Targeted molecular dynamics: a new approach for searching pathways of conformational transitions." J. Schlitters web page can be found at http://www.bph.ruhr-uni-bochum.de/~juergen/ Hope this helps, Lutz 11 =================================================== From: Andrew Dalke Hello, I wrote a simple linear interpolation script for the program VMD. The example and tutorial is at http://www.ks.uiuc.edu/Research/vmd/mailing_list/ Once it is generated you can animate it, save it, etc. VMD is available for several version of unix. For every program there will be a problem of how to define the transformation that takes you from one set of coordinates to the other in a physically realistic manner. I don't think there is any program that can do that -- or we would have the protein folding problem solved :) 12 =================================================== From: "Jeffrey L. Nauss" This exactly what CHARMm will do using the TRAVEL routine. Look at either the MSI or Harvard WWW site for documentation. If you have difficulty finding anything about TRAVEL, please let me know. I'll go through my sources when I return to my office on Thursday or Friday. =================================================== =================================================== Thanks a lot to all Rino ++-----------------------------------------------------------------------++ ++-----------------------------------------------------------------------++ || || || Dr. Rino Ragno E-mail: ragno@axrma.uniroma1.it || || Institute for Biomedical Computing or: rino@gpc.wustl.edu || || Center for Molecular Design Phone : 314-362-22721 || || Box8036, Washington University FAX : 314-362-0234 || || 700 South Euclid Avenue || || St. Louis, Missouri 63110 || || U. S. A. || || || || WEB PAGE : www.ibc.wustl.edu/cmd/people/rino/rino.html || || || ++-----------------------------------------------------------------------++ ++-----------------------------------------------------------------------++ From jerzy@tiger.jsums.edu Mon Apr 13 02:24:14 1998 Received: from tiger.jsums.edu for jerzy@tiger.jsums.edu by www.ccl.net (8.8.3/950822.1) id CAA12462; Mon, 13 Apr 1998 02:10:55 -0400 (EDT) Received: by tiger.jsums.edu (951211.SGI.8.6.12.PATCH1502/930416.SGI.AUTO) for CHEMISTRY@www.ccl.net id BAA09090; Mon, 13 Apr 1998 01:11:45 -0500 Date: Mon, 13 Apr 1998 01:11:45 -0500 From: jerzy@tiger.jsums.edu (Jerzy Leszczynski) Message-Id: <199804130611.BAA09090@tiger.jsums.edu> To: CHEMISTRY@www.ccl.net Subject: 7th Conference CCTCC First Announcement April 9, 1998 Dear Colleague: We are pleased to announce the seventh conference on Current Trends in Computational Chemistry. This symposium, organized by Jackson State University, will cover all areas of computational chemistry as well as quantum chemistry. The local host of the conference is the US Army Corps of Engineers Waterways Experiment Station (WES) in Vicksburg, Mississippi. The meeting will be held at the Holiday Inn of Vicksburg, Mississippi (40 miles west of Jackson) on November 6 and 7, 1998. The format consists of a series of plenary lectures and poster presentations on Friday and Saturday, covering applications as well as theory. In addition, a banquet is scheduled for Friday evening and a dinner and reception for Saturday evening. The 7th conference will also feature another talk given in the ancillary "Noble Lecture Series." This series was initiated during the 7 CCTCC by a remarkable presentation by Istvan Hargittai entitled "The Molecules Among Us: Conversation with Famous Chemists." The lectures in this series are presented in a relaxed, after-dinner atmosphere by the noble speakers and are devoted to noble scientific events and people. As such, it is an exceptional lecture to the conference and contrary to the regular talks, might not necessarily report any Current findings. This year the talk will be delivered by Eiji Osawa who will speak on "Past and Future of the Fullerene Story." We are planning to publish extended abstracts (up to four pages each) of all invited talks and poster presentations. Original scientific contributions will be published in a special issue of the Journal of Molecular Structure (THEOCHEM). Manuscripts for inclusion in the special issue should be submitted in triplicate upon arrival at the registration desk. Submitted papers will be subject to the journal's standard referee procedures. Sincerely, Jerzy Leszczynski Chairman of the Organizing Committee INVITED SPEAKERS David Buckingham University of Cambridge Piet van Duijnen University of Groningen William A. Goddard III California Institute of Technology Magdolna Hargittai Hungarian Academy of Sciences Ivan Hubac Comenius University, Bratislava Kimihiko Hirao University of Tokyo William L. Jorgensen Yale University Richard Lavery Institut de Biologie Physico-Chimique, Paris Modesto Orozco Universitat de Barselona Eiji Osawa* Toyohashi University of Technology Pekka Pyykko University of Helsinki Krishnan Raghavachari Bell Labs David Singh Naval Research Lab Harel Weinstein Mount Sinai School of Medicine * After-dinner "Noble Lecture Series" 7TH CONFERENCE ON Current Trends In Computational Chemistry NOVEMBER 6 & 7, 1998, Vicksburg, Mississippi. 1. NAME:___________________________________________________________________ MAILING ADDRESS:________________________________________________________ ________________________________________________________________________ TELEPHONE: _____________ FAX: ______________ E-MAIL:__________________ 2. If you wish to present a poster, please indicate the title below. All abstracts are due by September 1, 1998 (up to 4 pages in length, presenting author underlined, photo ready quality, in duplicate) to ensure publication in the Conference Materials. TITLE:__________________________________________________________________ ________________________________________________________________________ AUTHORS:________________________________________________________________ 3. Conference materials, banquet and reception fee, all meals from breakfast Friday through dinner Saturday, coffee, and refreshments are included per paid participant. MAKE CHECKS PAYABLE TO: Current Trends in Computational Chemistry. Registration fee before September 1, 1998 US $150.00 $_________ Registration fee thereafter 200.00 $_________ Registration fee at student discount 75.00 $_________ 4. HOUSING: The organizers will not make housing reservations. To reserve a room at the special conference rate of $50.00-$60.00 per room, contact the Holiday Inn of Vicksburg, 3330 Clay Street, Vicksburg, MS 39180, Tel:(601)636-4551, Fax:(601)636-4552. Reservations should be arranged with the Holiday Inn prior to October 10, 1998. I do _____ do not _____ plan to stay at the conference hotel. I do _____ do not _____ plan to submit a paper to the special issue of THEOCHEM. ____________________ Signature http://tiger.jsums.edu/~cctcc Department of Chemistry, Jackson State University, Jackson, MS 39217, USA Conference Chairman: Dr. Jerzy Leszczynski, Tel: 601-973-3482, Email: jerzy2.iris5.jsums.edu. Conference Secretary: Ms. Shonda Allen, Tel: 601-973-3723, Email: srallen@stallion.jsums.edu. From ccl@www.ccl.net Mon Apr 13 15:24:22 1998 Received: from ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id PAA16505; Mon, 13 Apr 1998 15:20:45 -0400 (EDT) Received: from gatekeeper.eastman.com (gatekeeper.eastman.com [164.89.253.3]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id PAA01548 for ; Mon, 13 Apr 1998 15:20:45 -0400 (EDT) Received: by gatekeeper.eastman.com; id QAA21844; Mon, 13 Apr 1998 16:10:27 -0400 (EDT) Received: from emngw1.eastman.com(164.89.254.2) by gatekeeper.eastman.com via smap (3.2) id xma021614; Mon, 13 Apr 98 16:10:05 -0400 Received: by eastman.com id AA51278 (5.67b/IDA-1.5 for chemistry@ccl.net); Mon, 13 Apr 1998 15:19:45 -0400 Received: from ntd150.kpt.emn.com by eastman.com with SMTP id AA34123 (5.67b/SMI-4.1 for ); Mon, 13 Apr 1998 15:18:44 -0400 Received: by ntd150.kpt.emn.com with Internet Mail Service (5.5.1960.3) id <2Q0KL4WJ>; Mon, 13 Apr 1998 15:18:53 -0400 Message-Id: From: "Wilson, Bruce E " To: "'chemistry@ccl.net'" Subject: who said we could compute everything? Date: Mon, 13 Apr 1998 15:18:52 -0400 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.1960.3) Content-Type: text/plain I know I've seen this on CCL, and I tried four different approaches to searching the archives, with no luck. Perhaps I'm mis-remembering things. Basically, I'm after the relatively famous quote to the effect that we shall soon reach the time when all chemical phenomena will be subject to computation. Who said it, and what was the exact quote. Thanks. ====================================================== Bruce E. Wilson (bewilson@eastman.com) Eastman Chemical Company, Chemicals Research Division Lincoln St, B-150B, Box 1972 Kingsport, TN 37662-5150, USA Office: (423) 229-8886; FAX: (423) 229-4558 From jayres@ycpo.yavapai.cc.az.us Tue Apr 14 16:24:37 1998 Received: from smtp04.primenet.com for jayres@ycpo.yavapai.cc.az.us by www.ccl.net (8.8.3/950822.1) id PAA24554; Tue, 14 Apr 1998 15:26:04 -0400 (EDT) Received: (from daemon@localhost) by smtp04.primenet.com (8.8.8/8.8.8) id MAA26947 for ; Tue, 14 Apr 1998 12:25:58 -0700 (MST) Received: from ip-17-086.prc.primenet.com(207.218.17.86), claiming to be "ycpo.yavapai.cc.az.us" via SMTP by smtp04.primenet.com, id smtpd026889; Tue Apr 14 12:25:48 1998 Message-ID: <3533B8EF.8C086722@ycpo.yavapai.cc.az.us> Date: Tue, 14 Apr 1998 12:28:48 -0700 From: Jeff Ayres Organization: Mesa/Yavapai Comm. College X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: DNA Chime Web page Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello CCLers, Mesa Community College has allowed placing online a web page developed to present data collected about DNA dinucleotide annealling Gibbs Free Energy. The web page requires using the molecular modelling plugin CHIME to view. If you enjoy it or have questions or comments contact me at jayres@ycpo.yavapai.cc.az.us http://www.mc.maricopa.edu/users/ayres/org_molecules/chime1.htm Jeff Ayres