From chemistry-request@server.ccl.net Tue Aug 3 05:46:01 1999 Received: from relay0.unizar.es (tozal.unizar.es [155.210.3.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA23467 for ; Tue, 3 Aug 1999 05:45:57 -0400 Received: from posta.unizar.es (posta.unizar.es [155.210.11.16]) by relay0.unizar.es (8.9.3/8.9.1) with ESMTP id LAA17524 for ; Tue, 3 Aug 1999 11:39:45 +0200 (MET DST) Received: from posta.unizar.es ([155.210.88.191]) by posta.unizar.es (8.9.1/8.8.5) with ESMTP id LAA28057 for ; Tue, 3 Aug 1999 11:39:46 +0200 (MET DST) Message-ID: <37A6B7E7.D2914B42@posta.unizar.es> Date: Tue, 03 Aug 1999 11:35:36 +0200 From: Luis Salvatella =?iso-8859-1?Q?Ib=E1=F1ez?= X-Mailer: Mozilla 4.5 [en] (Win95; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Origin of (my) wrong B3LYP frequencies Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I have submitted a message some days ago describing some problems found with B3LYP frequencies. I thank everyone that replied my e-mail. The anomalous result corresponds to calculations carried out with Gaussian 98 (version A.6), compiled on a HP C160 workstation having a PA8000 processor. Instead, a frequency computation achieved on this workstation with the same G98 version, though compiled on a different computer, led to right result. Therefore, the origin of the wrong B3LYP frequencies lies on a compilation error. LUIS SALVATELLA From chemistry-request@server.ccl.net Tue Aug 3 06:00:00 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA23607 for ; Tue, 3 Aug 1999 05:59:59 -0400 Received: from Raven.und.ac.za (Raven.und.ac.za [146.230.128.50]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id FAA08818 for ; Tue, 3 Aug 1999 05:53:41 -0400 (EDT) Received: from gwmail (GWise-SMTP.und.ac.za [146.230.128.63]) by Raven.und.ac.za (8.9.3/8.9.3) with SMTP id LAA13771 for ; Tue, 3 Aug 1999 11:53:24 +0200 (SAT) Received: from Routing-Domain-Message_Server by gwmail with Novell_GroupWise; Tue, 03 Aug 1999 11:41:28 +0200 Message-Id: X-Mailer: Novell GroupWise 5.5 Date: Tue, 03 Aug 1999 09:08:10 +0200 From: "Gert Kruger" To: Subject: Re: G98 and %nproc=2 on Linux Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id GAA23608 Dear CCLrs, We are testing G98 on a dual CPU intel PC (2 x 450 MHz Xenon processors) with Redhat Linux 6.0 as OS. The program works fine with normal input files, but as soon as we include: %nproc=2, we get the following error: "shmget failed. Invalid argument" The message appears as a linux error and not in the output file of Gaussian. Any hints to overcome the problem? Gert Kruger ________________________________________ Dr HG Kruger, School of Pure & Applied Chemistry Univerity of Natal, King George 5th Ave Durban, 4001, South Africa Tel. +27-31-2602181 Fax. +27-31-2603091 Tel +27-31-2603090 (School secretary) email Kruger@scifs1.und.ac.za P.O. Box 18091, Dalbridge, 4014, South Africa ________________________________________ From chemistry-request@server.ccl.net Tue Aug 3 06:12:47 1999 Received: from Mercury.unix.acs.cc.unt.edu (mercury.acs.unt.edu [129.120.220.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA23723 for ; Tue, 3 Aug 1999 06:12:47 -0400 Received: from jove.acs.unt.edu (6930@jove.acs.unt.edu [129.120.220.41]) by Mercury.unix.acs.cc.unt.edu (8.8.8/8.8.8) with ESMTP id FAA28849; Tue, 3 Aug 1999 05:06:36 -0500 (CDT) Received: from localhost (aiz0001@localhost) by jove.acs.unt.edu (8.8.8/8.8.8) with ESMTP id FAA22218; Tue, 3 Aug 1999 05:06:29 -0500 (CDT) Date: Tue, 3 Aug 1999 05:06:28 -0500 (CDT) From: Anita Ilze Zvaigzne To: Peter Shenkin cc: chemistry@ccl.net Subject: Re: CCL:Levinthal's paradox In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII RE: Levinthal's Paradox and the Speed of Protein Folding: Does this theory take into account that protein folding is not necessarily an isolated event? That is, there may be chaperonins assisting the protein to achieve its final state rapidly -- as opposed to many years? Sincerely, Anita Zvaigzne ============================================================= On Fri, 30 Jul 1999, Peter Shenkin wrote: > On Fri, 30 Jul 1999, JATI KASTANJA wrote: > > does anyone know something about the Levinthal paradox? > >... > Therefore, protein folding must be a kinetically controlled process. > I.e., proteins fold to the most accessible minimum, rather than the > most stable minimum. In this, protein folding must resemble the > kinetically controlled reactions of organic (and bio-) chemistry. From chemistry-request@server.ccl.net Tue Aug 3 08:37:45 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA25462 for ; Tue, 3 Aug 1999 08:37:45 -0400 Received: from relay.ppco.com (relay.ppco.com [207.27.254.3]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id IAA10637 for ; Tue, 3 Aug 1999 08:31:03 -0400 (EDT) Received: by relay.ppco.com id HAA18601 (InterLock SMTP Gateway 4.2 for chemistry@www.ccl.net); Tue, 3 Aug 1999 07:29:40 -0500 Message-Id: <199908031229.HAA18601@relay.ppco.com> Received: by relay.ppco.com (Internal Mail Agent-1); Tue, 3 Aug 1999 07:29:40 -0500 Date: Tue, 03 Aug 1999 07:29:42 -0500 From: "George D. Parks" X-Mailer: Mozilla 4.61 [en] (WinNT; U) X-Accept-Language: en Mime-Version: 1.0 To: Gert Kruger Cc: chemistry@www.ccl.net Subject: Re: CCL:G98 and %nproc=2 on Linux References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit We had a similar problem. Here's a note we got from Doug Fox of Gaussian on how to correct the problem. George Parks Phillips Petroleum ============== Parallel operation uses shared memory, which is a kernel resource, instead of process memory. I have a note below on adjusting this. Also we find that the 2.2 kernel is far superior for parallel execution, also easier to adjust shared memory. Increasing the size of the Linux shared memory segment The size of the shared memory segment is set by the parameter SHMMAX, in /usr/src/linux/include/asm/shmparam.h. The default value in 2.0 and 2.2 kernels is 0x2000000, or 32MB. To increase the value of SHMMAX, edit shmparam.h, rebuild the kernel, and reboot. If you are comfortable with the process of building the Linux kernel, we suggest you try the recently released 2.2.1 kernel (get it from ftp.kernel.org or a mirror site). The 2.2 kernels have improved SMP performance and the ability to change the shared memory size on the fly, by changing the value in /proc/sys/kernel/shmmax. For example, # echo "67108864" >/proc/sys/kernel/shmmax would set the maximum shared memory segment size to 64MB. If you are not familiar with the procedure for building the kernel, and you are using the kernel distributed with Red Hat Linux 5.2, here is a step-by-step guide to rebuilding the Red Hat kernel: 1) Make sure the kernel source and headers are installed, by doing % rpm -qa | grep kern kernel-2.0.36-0.7 kernel-pcmcia-cs-2.0.36-0.7 kernelcfg-0.5-3 kernel-headers-2.0.36-0.7 kernel-source-2.0.36-0.7 If you do not see kernel-headers-2.0.36-0.7 kernel-source-2.0.36-0.7 you must install them from the Red Hat CD, by doing, as root # rpm -i kernel-headers-2.0.36-0.7.i386.rpm # rpm -i kernel-source-2.0.36-0.7.i386.rpm 2) Now, as root, edit /usr/src/linux/include/asm/shmparam.h and change the value of SHMMAX to an appropriate value (3/4 of the amount of physical memory would be reasonable). 3) Now do, as root # cd /usr/src/linux # make mproper # make config make config will ask a series of configuration questions, it will look like: # make config rm -f include/asm ( cd include ; ln -sf asm-i386 asm) /bin/sh scripts/Configure arch/i386/config.in # # Using defaults found in arch/i386/defconfig # * * Code maturity level options * Prompt for development and/or incomplete code/drivers (CONFIG_EXPERIMENTAL) [Y/n/?] and so on. To every question, TAKE THE DEFAULT VALUE BY HITTING ENTER. When you are done, do: # make dep; make boot A great deal of output will scroll by as a new kernel is compiled. When the build is complete, the new kernel will be in the file /usr/src/linux/arch/i386/boot/zImage. 4) Now you may test the new kernel by booting it from a floppy. Put a blank diskette in you floppy drive and do, as root: # dd if=/usr/src/linux/arch/i386/boot/zImage of=/dev/fd0 5) Now reboot from this floppy. If all seems well you may configure LILO to boot the new kernel, or continue to boot from floppy. The Red Hat Linux 5.2 manual discusses building a custom kernel, and using LILO to boot it in Section 11.6, pp 197-200, to which we refer you for further details. From chemistry-request@server.ccl.net Tue Aug 3 08:40:28 1999 Received: from mordor.ai.private (fw.apollo-imaging.com [195.26.208.226]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA25500 for ; Tue, 3 Aug 1999 08:40:13 -0400 Received: from vienna.at (gl@bombadil.ai.private [10.33.246.70]) by mordor.ai.private (8.9.2/8.9.2/Debian/GNU) with ESMTP id PAA16002 for ; Tue, 3 Aug 1999 15:43:10 +0200 (CEST) Sender: gl@apollo-imaging.com Message-ID: <37A6E1B6.533F1747@vienna.at> Date: Tue, 03 Aug 1999 14:33:58 +0200 From: Gerald Loeffler Reply-To: Gerald.Loeffler@vienna.at Organization: Apollo Imaging X-Mailer: Mozilla 4.5 [en] (X11; I; Linux 2.0.36 i686) X-Accept-Language: en MIME-Version: 1.0 CC: chemistry@ccl.net Subject: Re: CCL:Levinthal's paradox References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! Anita Ilze Zvaigzne wrote: > > RE: Levinthal's Paradox and the Speed of Protein Folding: > > Does this theory take into account that protein folding is not > necessarily an isolated event? That is, there may be chaperonins > assisting the protein to achieve its final state rapidly -- as opposed to > many years? No, the effect of chaperonins is not considered in Levinthals paradox - and it need not be, because small proteins _do_ reversibly fold in the absence of chaperonins (another classic: Anfinsen). First things first - before worrying about the influence of chaperonins one should try to understand (from a theoretical perspective) the "pure" protein folding problem. Apart from that, I think it's fair to say that the significance of the Levinthal paradox is now mostly historic. Although science is far from having solved the protein folding problem, the understanding has advanced to the extent that we find the idea ridiculous that a protein needs to exhaustively search phase space in order to find its native conformation. Rather, proteins move from "unfolded" conformations to "folded" conformations (however one exaclty makes this distinction) via accessible conformations. These accessible conformations vary between different folding events, which is why one speaks of "folding funnels" rather than "folding pathways". Whichever exact path a particular folding event takes, it is generally assumed that all folding events eventually lead to an ensemble of conformations close to the global minimum of free energy of the protein. Any opposition on this last point? cheers, gerald > > Sincerely, > Anita Zvaigzne > ============================================================= > On Fri, 30 Jul 1999, Peter Shenkin wrote: > > > On Fri, 30 Jul 1999, JATI KASTANJA wrote: > > > does anyone know something about the Levinthal paradox? > > >... > > Therefore, protein folding must be a kinetically controlled process. > > I.e., proteins fold to the most accessible minimum, rather than the > > most stable minimum. In this, protein folding must resemble the > > kinetically controlled reactions of organic (and bio-) chemistry. > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Gerald Loeffler Email: Gerald.Loeffler@vienna.at Smail: Apollo Imaging, Marchettigasse 7, A-1060 Vienna, Austria Phone: +43 676 3289588 (+43 1 5952333 27) Fax: +43 1 5952333 20 Keywords: Java, CORBA, OOA&D, Databases, Bioinformatics, Computational Biology, Computational Biophysics From chemistry-request@server.ccl.net Tue Aug 3 04:24:05 1999 Received: from nenuphar.saclay.cea.fr (nenuphar.saclay.cea.fr [132.166.192.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA23049 for ; Tue, 3 Aug 1999 04:24:04 -0400 Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.D20) with ESMTP id KAA15498 for ; Tue, 3 Aug 1999 10:17:58 +0200 (MET DST) Received: from styx.bruyeres.cea.fr (styx-e76.bruyeres.cea.fr [132.165.76.3]) by muguet.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.1.D20) with SMTP id KAA23865 for ; Tue, 3 Aug 1999 10:17:57 +0200 (MET DST) Received: by styx.bruyeres.cea.fr (CEANET-1.1+) id AA02511; Tue, 3 Aug 1999 10:17:58 +0200 Received: from indre.ripault.cea.fr(132.165.32.1) by styx via smap id sma002450; Tue Aug 3 10:17:11 1999 Received: from ripault.cea.fr (mathieu@claise.ripault.cea.fr [132.165.32.11]) by ripault.cea.fr. (8.8.7/8.7.3) with ESMTP id KAA12399 for ; Tue, 3 Aug 1999 10:16:08 +0200 Sender: mathieu@ripault.cea.fr Message-Id: <37A6A545.75EAC5F2@ripault.cea.fr> Date: Tue, 03 Aug 1999 10:16:05 +0200 From: Didier MATHIEU X-Mailer: Mozilla 4.08 [en] (X11; I; Linux 2.0.36 i686) Mime-Version: 1.0 To: chemistry@ccl.net Subject: Free Encyclopedia of Comput. Chem. ? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Hello everybody, addicted to internet and more specially to the CCL for a couple of years I enjoy getting free information and software this way. I noted that many subscribers use Linux, are looking for or annoucing free software... However, a kind of stuff that does not appear to be widely available for free are encyclopedias. I realize that it may be almost impossible to set up a general-purpose encyclopedia this way because of the need to avoid patented material, but in a specialized field such as computational chemistry, it might be possible unless there are some legal barriers I am unaware of. Therefore I wouldn't be surprised to heard about such an encyclopedia. Does anybody knows about such a project ? Otherwise, I wonder what CCLers think of the idea of developping an Encyclopedia of Computational Chemistry on the basis of volunteer contributions as for Linux ? To me it seems a priori that a high quality might require a "cathedral-style" development with the content well-planified in advance, however the wealth of good free softwave available suggests the opposite. In addition the rate of advancement of the field probably make it hard to design an encyclopedia in the standard way (I am considering buying the Encyclopedia of Computational Chemistry published by Wiley). The main question may be whether many people are ready to write contributions or trust such information which didn't go through a standard refereing process. According to me it would be conceivable to design "trust indexes" calculated from readers's responses and collect their comments as done for books on the site of the Amazon.com online bookshop. In the long-run, such an online encyclopedia should be useful to those working in industrial plants only anecdotically involved in the field, who are the only computational chemist in their lab and have to get an overview of many subfields according to the needs of their colleagues and customers, ...like me. Hence it would be a gift of academics to industry...-) Best regards. -- Didier MATHIEU CEA - Le Ripault, BP 16 37260 Monts (France) Tel. 33(0)2.47.34.41.85 From chemistry-request@server.ccl.net Tue Aug 3 10:28:19 1999 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA26231 for ; Tue, 3 Aug 1999 10:28:15 -0400 Received: from dwi01.dwi.rwth-aachen.de by mail.rwth-aachen.de (PMDF V5.1-12 #D3869) with ESMTP id <01JEC56A671Y0001GL@mail.rwth-aachen.de> for chemistry@ccl.net; Tue, 3 Aug 1999 16:21:54 +0200 Received: from DWI01/SpoolDir by dwi01.dwi.rwth-aachen.de (Mercury 1.44); Tue, 03 Aug 1999 16:22:02 +0000 Received: from SpoolDir by DWI01 (Mercury 1.44); Tue, 03 Aug 1999 16:21:56 +0000 Date: Tue, 03 Aug 1999 16:21:53 +0000 From: JATI KASTANJA Subject: CCL: SUMMARY - Levinthal Paradox To: chemistry@ccl.net Message-id: Organization: German Wool Research Institute Dear all, I've obtained a lot of helpful responses. I'd like to thank everybody who spent his time in giving me some suggestions with regard to the "Levinthal Paradox". Many thanks to Raman, Rick, Carlos, John, Jim, Peter, Tom and any other person I might have forgotten. Regards, Jati Subsequent a list of suggestions and papers which deal with the Levinthal Paradox ----------------------------------------------- >Peter S. Shenkin wrote If you do find the Journal, you will find that it contains only a passing reference to what has become known as the Levinthal paradox. The idea really derives from a comment Cyrus once made at a meeting. The idea is this. Take a 100-residue protein. Let's suppose each residue can have only, say, 3 conformational states. Then there are 3^100, or about 10^48, possible states. Now suppose the protein can explore a new state with every moleculear vibration. Suppose each vibration takes about a femtosecond. Then exploring all the states would take about 10^48 fs, or 10^33 s. There are about 10^8 s in a year, so exploring all the states would take about 10^25 years. But this is longer than the age of the universe. Now, in order for a protein to fold into its global thermodynamic energy minimum, the folding process has to be ergodic. That is, it has to explore all its states within the time-span of the process. But protein folding takes typically seconds to minutes. So a protein can't be folding into its thermodynamic energetic minimum, since it can't possibly find it in so short a time. Therefore, protein folding must be a kinetically controlled process. I.e., proteins fold to the most accessible minimum, rather than the most stable minimum. In this, protein folding must resemble the kinetically controlled reactions of organic (and bio-) chemistry. The reason it's considered a "paradox" is that most people don't believe it (at least for globular proteins as small as 100 residues). Cyrus didn't believe it either, in fact. But it is fun to think about, and it's great for impressing people at cocktail parties. (You have to go to the right cocktail parties, though. :-) ) -P. ----------------------------------------------- >C.S.Raman wrote: Well, the list I have provided at the end of this mail should help you track down all the literature pertinent to this problem. {*} Until now I am unsuccessful in finding out the journal where Cyrus {*} Levinthal first published something about this paradox. Cy's article is one of the most MISQUOTED in the literature. His original work was presented in a symposium: Levinthal, C (1969) in Mossbauer Spectroscopy in Biological Systems, (ed) Debrunner, P., & Tsibris, J.C.M., P. 22-24, University of Illinois, Urbana Champaign. How to Fold Graciously. Levinthal also published an article in J. Chim. Phys. (1968) 65: 44-45 entitled "Are there pathways for protein folding?", which is usually quoted as being the source of the paradox. This is incorrect and this article makes no mention of it. 1. Dill KA. Polymer principles and protein folding. Protein Science, 1999 Jun, 8(6):1166-80. 2. Yon JM. Protein folding: concepts and perspectives. Cellular and Molecular Life Sciences, 1997 Jul, 53(7):557-67. 3. Finkelstein, AV; Badretdinov, AY. Physical reason for fast folding of the stable spatial structure of proteins: A solution of the Levinthal paradox. MOLECULAR BIOLOGY, 1997 MAY-JUN, V31 N3:391-398. 4. Shakhnovich EI. Theoretical studies of protein-folding thermodynamics and kinetics. Current Opinion in Structural Biology, 1997 Feb, 7(1):29-40. 5. Dill KA; Chan HS. >From Levinthal to pathways to funnels. Nature Structural Biology, 1997 Jan, 4(1):10-9. 8. Finkelstein AV; Badretdinov AYa. Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold [published erratum appears in Fold Des 1998;3(1):67]. Folding and Design, 1997, 2(2):115-21. 9. Lattman EE. Remembering Cy Levinthal [editorial]. Proteins, 1995 Oct, 23(2):i. 10. Karplus M; Sali A. Theoretical studies of protein folding and unfolding. Current Opinion in Structural Biology, 1995 Feb, 5(1):58-73. 11. Durup, J. On ''Levinthal paradox'' and the theory of protein folding. THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE, 1998 FEB 9, V424 N1- 2:157-169. 12. Karplus, M. The Levinthal paradox: yesterday and today. FOLDING & DESIGN, 1997, V2 N4:S69-S75. 13. HONIG B. LEVINTHAL,CYRUS - IN MEMORIAM. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1991, V11 N4:239-241. 14. LATTMAN E. LEVINTHAL,CYRUS MAY 2, 1922 NOVEMBER 4, 1990 - IN MEMORIAM. PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1990, V8 N4:R1-R1. I hope this helps. -raman --------------------------------------------------- >Tom Ngo and Joe Marks wrote: Also relevant to your inquiry are the references below. We argue in the > first paper that the astronomical number of conformational states does not, > by itself, give reason to conclude that folding should take exponential > time. We show how the theory of NP-completeness can be brought to bear on > questions related to folding times. > > * J. Thomas Ngo, Joe Marks and Martin Karplus, "Computational Complexity, > Protein Structure Prediction, and the Levinthal Paradox," in The Protein > Folding Problem and Tertiary Structure Prediction, Kenneth Merz, Jr. and > Scott LeGrand, eds., pp. 433-506, Birkhauser, Boston, 1994. > > * J. Thomas Ngo and Joe Marks, "Computational Complexity of a Problem in > Molecular Structure Prediction," Protein Engineering 5(4):313- 321, June > 1992. The second paper above is on my web site, http://www.merl.com/people/marks/index.html. -- Joe Marks > --Tom Ngo ------------------------------------------------------------------ > Rick Venable wrote: I've appended a quick search result for "levinthal paradox"-- some of these papers (e.g. those by Dill, Karplus, or Shakhnovich) may hopefully refer to the original statement of the paradox. Parker JMR The relationship between peptide plane rotation (PPR) and similar conformations J COMPUT CHEM 20: (9) 947-955 JUL 15 1999 Iguchi K Exactly solvable model of protein folding: Rubik's magic snake model INT J MOD PHYS B 13: (4) 325-361 FEB 10 1999 Hamacher K, Wenzel W Scaling behavior of stochastic minimization algorithms in a perfect funnel landscape PHYS REV E 59: (1) 938-941 Part B JAN 1999 Durup J On "Levinthal paradox" and the theory of protein folding THEOCHEM-J MOL STRUC 424: (1-2) 157-169 FEB 9 1998 Finkelstein AV, Badretdinov AY Physical reason for fast folding of the stable spatial structure of proteins: A solution of the Levinthal paradox MOL BIOL+ 31: (3) 391-398 MAY-JUN 1997 Karplus M The Levinthal paradox: yesterday and today FOLD DES 2: (4) S69-S75 1997 Finkelstein AV, Badretdinov AY Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold FOLD DES 2: (2) 115-121 1997 Shakhnovich EI Theoretical studies of protein-folding thermodynamics and kinetics CURR OPIN STRUC BIOL 7: (1) 29-40 FEB 1997 Mirny LA, Abkevich V, Shakhnovich EI Universality and diversity of the protein folding scenarios: A comprehensive analysis with the aid of a lattice model FOLD DES 1: (2) 103-116 1996 Nakamura H, Tanimura R, Kidera A Side-chain conformations cooperatively restricted in protein secondary structure .2. Side-chain configurational entropies of alpha-helices in the folding nuclei P JPN ACAD B-PHYS 72: (7) 149-152 SEP 1996 Su ZD, Arooz MT, Chen HM, et al. Least activation path for protein folding: Investigation of staphylococcal nuclease folding by stopped-flow circular dichroism P NATL ACAD SCI USA 93: (6) 2539-2544 MAR 19 1996 KARPLUS M, SALI A THEORETICAL-STUDIES OF PROTEIN-FOLDING AND UNFOLDING CURR OPIN STRUC BIOL 5: (1) 58-73 FEB 1995 PERKYNS JS, PETTITT BM PEPTIDE CONFORMATIONS ARE RESTRICTED BY SOLUTION STABILITY J PHYS CHEM-US 99: (1) 1-2 JAN 5 1995 GULUKOTA K, WOLYNES PG STATISTICAL-MECHANICS OF KINETIC PROOFREADING IN PROTEIN-FOLDING IN-VIVO P NATL ACAD SCI USA 91: (20) 9292-9296 SEP 27 1994 ABKEVICH VI, GUTIN AM, SHAKHNOVICH EI SPECIFIC NUCLEUS AS THE TRANSITION-STATE FOR PROTEIN-FOLDING - EVIDENCE FROM THE LATTICE MODEL BIOCHEMISTRY-US 33: (33) 10026-10036 AUG 23 1994 SALI A, SHAKHNOVICH E, KARPLUS M HOW DOES A PROTEIN FOLD NATURE 369: (6477) 248-251 MAY 19 1994 DILL KA, YUE K, FIEBIG K PROTEIN-FOLDING - DRIVING FORCES AND THE LEVINTHAL PARADOX BIOPHYS J 66: (2) A241-A241 Part 2 FEB 1994 DILL KA FOLDING PROTEINS - FINDING A NEEDLE IN A HAYSTACK CURR OPIN STRUC BIOL 3: (1) 99-103 FEB 1993 CHAN HS, DILL KA ENERGY LANDSCAPES AND THE COLLAPSE DYNAMICS OF HOMOPOLYMERS J CHEM PHYS 99: (3) 2116-2127 AUG 1 1993 FIEBIG KM, DILL KA PROTEIN CORE ASSEMBLY PROCESSES J CHEM PHYS 98: (4) 3475-3487 FEB 15 1993 From chemistry-request@server.ccl.net Mon Aug 2 14:43:18 1999 Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA17465 for ; Mon, 2 Aug 1999 14:43:16 -0400 Received: from ruppert.phys.chemie.tu-muenchen.de by mailrelay2.lrz-muenchen.de for @dfvgate.lrz-muenchen.de:chemistry@server.ccl.net; Mon, 2 Aug 1999 20:37:14 +0200 Received: from physik.tu-muenchen.de by ruppert.phys.chemie.tu-muenchen.de via ESMTP (940816.SGI.8.6.9/930416.SGI) for id UAA07638; Mon, 2 Aug 1999 20:37:13 +0200 Sender: tmehnert@physik.tu-muenchen.de Message-Id: <37A5E558.29A50377@physik.tu-muenchen.de> Date: Mon, 02 Aug 1999 20:37:12 +0200 From: Mehnert Thomas X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: MM3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Does anybody know the internet page to download the Molecular Mechanic-Program by Allinger (MM3 or MM4)? Thanks Thomas From chemistry-request@server.ccl.net Tue Aug 3 08:48:50 1999 Received: from triton.mail.ru (triton.mail.ru [194.226.198.87]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA25593 for ; Tue, 3 Aug 1999 08:48:48 -0400 Received: from [212.0.205.39] (helo=smtp.mail.ru) by triton.mail.ru with smtp (Exim 3.02 #16) id 11Bdto-00027a-00 for chemistry@ccl.net; Tue, 03 Aug 1999 12:42:33 +0000 Date: Tue, 3 Aug 1999 15:47:30 +0300 From: Mike Peleah X-Mailer: The Bat! (v1.15) S/N B6042885 Reply-To: Mike Peleah Message-ID: <16657.990803@mail.ru> To: chemistry@ccl.net Subject: natural internal coordinates | Dear friends, : I would like to write program, that convert cartesian coordinates into natural internal coordinates. But I have a couple of problems: 1. How could I find point group of symmetry for a set of atoms? I find alghorthm how to finding it if you have all symmetry generators, but I don't know how to find this generators. 2. How should I select coefficients for natural internal coordinates? Could any body help me? Online sources are preferable (our library is very poor). Answers (if any) will be summarized and program sources will be published. Best regards, Mike mailto:MikePeleah@mail.ru From chemistry-request@server.ccl.net Tue Aug 3 13:20:05 1999 Received: from alchemy.chem.utoronto.ca (alchemy.chem.utoronto.ca [142.150.224.224]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA27601 for ; Tue, 3 Aug 1999 13:20:05 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.9.3/8.9.3) id NAA15814 for chemistry@ccl.net; Tue, 3 Aug 1999 13:13:53 -0400 (EDT) Date: Tue, 3 Aug 1999 13:13:53 -0400 (EDT) From: "E. Lewars" Message-Id: <199908031713.NAA15814@alchemy.chem.utoronto.ca> To: chemistry@ccl.net Subject: IR INTENSITIES: SUMMARY 1999 August 3 SUMMARY OF REPLIES TO QUESTION ABOUT IR INTENSITIES Reply #6 gives a ref to Raman intensities Thanks very much to all who responded to my question E. Lewars ========================= The question: 1999 July 25 INTENSITIES OF IR BANDS--HOW GOOD? A lot has been published on correction factors for the *positions* (i.e. the wavenumber values) of calculated IR bands; the canonical paper is A. P. Scott and L. Radom, J. Phys. Chem., 1996, 100, 16502. Has there been any published work on the the *relative intensities* of calculated IR bands? I mean purely empirical comparison of calc and experimental IR spectra, to see which methods give the best match to the real spectra, and how, if possible, one can correct calc intensities to match the experimental. Thanks. E. Lewars ==================== REPLIES TO QUESTION ABOUT IR INTENSITIES Note that #6 below gives a ref to Raman intensities. #1 Date: Sun, 25 Jul 1999 14:14:26 -0400 (EDT) Subject: Re: CCL:CALC IR INTENSITIES__HOW GOOD? On Sun, 25 Jul 1999, E. Lewars wrote: > INTENSITIES OF IR BANDS--HOW GOOD? Could you please send me on any references you get with respect to this issue? I am interested also :) thanks, Ruth ----------------------------------------------------------------------------- Ruth Tanner rtanner@uoguelph.ca M.Sc. Candidate in Physical Chemistry University of Guelph ---------------------------------------------------------------------------- To steal ideas from one person is plagiarism, To steal ideas from many is research. ============================================================================ #2 Sender: Bertrand.Illien@chimie.univ-nantes.fr Subject: Re: CCL:CALC IR INTENSITIES__HOW GOOD? hello E. Lewars If you get some answers, may you send it to me. thanks in advance Bertrand ------------------------- Bertrand ILLIEN Tel :(+33)(0)2 51 12 54 28 Laboratoire de Spectrochimie Fax :(+33)(0)2 51 12 54 12 Facult\351 des Sciences et Techniques, illien@chimie.univ-nantes.fr Universit\351 de Nantes 2, rue de la Houssini\350re BP 92208 44322 Nantes Cedex 3 FRANCE ============== #3 Date: Mon, 26 Jul 1999 11:02:48 +0300 (EET DST) Subject: Re: CCL:CALC IR INTENSITIES__HOW GOOD? Dear Lewars: It would be very good if you can find an answer to this problem. In short the answer to your question is no (this is an informal answer). But it might actually depend on what you exactly mean and want. You may look at the work of P. J. Stephens and the group of theoretical chemistry at Cambridge. Sorry I do not have refs. right now but I may look for some if you want. Best regards, Adel El-Azhary =========== #4 Jul 26 Jens Spanget-Larse (48) CCL:CALC RAMAN ACTIVITIES__HOW GOODCommand: Read MessageMessage 5/7 from Jens Spanget-Larsen Jul 26 '99 at 1:38 pm Organization: Roskilde Universitetscenter To: chemistry@ccl.net, "E. Lewars" Date: Mon, 26 Jul 1999 13:38:48 +0100 Subject: CCL:CALC RAMAN ACTIVITIES__HOW GOOD? Dear CCL: E. Lewars asked the following question (1999 July 25): > INTENSITIES OF IR BANDS--HOW GOOD? > > A lot has been published on correction factors for the *positions* (i.e. the > wavenumber values) of calculated IR bands; the canonical paper is A. P. Scott > and L. Radom, J. Phys. Chem., 1996, 100, 16502. > Has there been any published work on the the *relative intensities* of > calculated IR bands? I mean purely empirical comparison of calc and experiment > IR spectra, to see which methods give the best match to the real spectra, and > how, if possible, one can correct calc intensities to match the experimental. I would like to add the corresponding question concerning *Raman scattering activities*! Thank you, Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= =========== #5 Jul 26 Karl Irikura (179) Re: CCL:CALC IR INTENSITIES__HOW GOOD? Date: Mon, 26 Jul 1999 16:58:16 -0400 Subject: Re: CCL:CALC IR INTENSITIES__HOW GOOD? Dear Dr. Lewars, Please summarize, especially if you find something as definitive as the Scott/Radom paper you mention. I find the following three papers. (1) Halls, M. D.; Schlegel, H. B. Journal of Chemical Physics 1998, 109, 10587-10593. (2) Lampert, H.; Mikenda, W.; Karpfen, A. J. Phys. Chem. A 1997, 101, 2254-2263. (3) Stanton, J. F.; Lipscomb, W. N.; Magers, D. H.; Bartlett, R. J. J. Chem. Phys. 1989, 90, 3241-3249. Best wishes, Karl I. ---------------------------------------------- Dr. Karl K. Irikura National Institute of Standards and Technology 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice: 301-975-2510 fax: 301-869-4020 e-mail: karl.irikura@nist.gov http://www.nist.gov/compchem/ ---------------------------------------------- #6 Sender: mathieu@ripault.cea.fr Date: Thu, 29 Jul 1999 11:24:41 +0200 To: "E. Lewars" , jsl@virgil.ruc.dk Subject: Re: CCL:CALC IR INTENSITIES__HOW GOOD? A recent paper: M.D. Halls & H.B. Schlegel, J. Chem. Phys. 109 (1998) p. 10587 a nd ref. 10-14 therein. In this paper, a steady improvement is noted on going from lower (HF) to higher (Adiabatic Connection DFT) levels of theory, through local and gradient correcte d functionals. The improvement in force constants accuracy on going to higher levels seems to p lay a non-negligible role. Indeed the difference between HF and B3LYP intensities is less dramatic when a common force field is used as I did in a study with normal modes obtained from CFF91 force field and quantum calculations reserved for dipole moment derivative s: cf. Int. J. Quant. Chem. 69, 705-711 (1998) > how, if possible, one can correct calc intensities to match the experimental. Such a correction is suggested by Halls & Schlegel for HF intensities. [RAMAN]: With regard to Raman data: Chem. Phys. Lett. 247, 120-125 (1995) but there are probably more recent papers. Regards -- Didier MATHIEU CEA - Le Ripault, BP 16 37260 Monts (France) Tel. 33(0)2.47.34.41.85 ========== #7 1999 July 30 George Vacek (55) Re: CCL:CALC IR INTENSITIES__HOW GOOD? ``A Systematic Theoretical Study of the Harmonic Vibrational Frequencies for Polyatomic Molecules: The Single, Double, and Perturbative Triple Excitation Coupled-Cluster [CCSD(T)] Method,'' J. R. Thomas, B. J. DeLeeuw, G. Vacek and H. F. Schaefer, J. Chem. Phys. 98, 1336 (1993). ``The Balance Between Theoretical Method and Basis Set Quality: A Systematic Study of Equilibrium Geometries, Dipole Moments, Harmonic Vibrational Frequencies, and Infrared Intensities,'' J. R. Thomas, B. J. DeLeeuw, G. Vacek, T. D. Crawford, Y. Yamaguchi and H. F. Schaefer, J. Chem. Phys. 99, 403 (1993). ``The Chemical Applicability of Standard Methods in Ab Initio Molecular Quantum Mechanics,'' in Modern Electronic Structure Theory, H. F. Schaefer, J. R. Thomas, Y. Yamaguchi, B. J. DeLeeuw and G. Vacek, Editor D. R. Yarkony (World Scientific Publishing, Singapore, 1995) pp. 3--54. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= George Vacek + Schrodinger, Inc. (503) 299-1150 + 1500 SW First, Suite 1180 vacek@schrodinger.com + Portland, OR 97201 http://www.schrodinger.com/~vacek/ ================== #8 Subject: Re: CCL:CALC IR INTENSITIES__HOW GOOD? Hi, I don't have any denifite answer to your question, but the following literatures may be of some interest to you. Lampert, Heike; Mikenda, Werner; Karpfen, Alfred. line 1 [h for help]Molecular Geometries and Vibrational Spectra of Phenol, Benzaldehyde, and Salicylaldehyde: Experimental versus Quantum Chemical Data. J. Phys. Chem. A (1997), 101(12), 2254-2263. Nowak, Maciej J.; Lapinski, Leszek; Fulara, Jan; Les, Andrzej; Adamowicz, Ludwik. Matrix isolation IR spectroscopy of tautomeric systems and its theoretical interpretation: 2-hydroxypyridine/2(1H)-pyridinone. J. Phys. Chem. (1992), 96(4), 1562-9. Mathieu, Didier; Simonetti, Philippe. Harmonic IR spectra from empirical force fields and Ab initio dipole-moment derivatives. Int. J. Quantum Chem. (1998), 69(6), 705-711. Mathieu, Didier; Defranceschi, Mireille; Lecayon, Gerard; Grand, Andre; Delhalle, Joseph. Dependence of the vibrational frequencies and intensities on the configuration of polyacrylonitrile: an ab initio study on model oligomers. Chem. Phys. (1993), 171(1-2), 133-43. This topic is quite interesting to me also, so I would appreciate it very much if you would summarize the responses you have got. With best regards, Takanori Kanazawa ==================== From chemistry-request@server.ccl.net Tue Aug 3 15:30:10 1999 Received: from fred.interval.com (fred.interval.com [192.203.7.36]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA29215 for ; Tue, 3 Aug 1999 15:30:09 -0400 Received: from interval.interval.com (interval.interval.com [199.170.107.10]) by fred.interval.com with ESMTP id MAA14141; Tue, 3 Aug 1999 12:23:56 -0700 (PDT) Received: by interval.interval.com id MAA25828; Tue, 3 Aug 1999 12:23:54 -0700 (PDT) Received: by harp.interval.com with Internet Mail Service (5.5.2448.0) id ; Tue, 3 Aug 1999 12:23:49 -0700 Message-ID: <4910A1687590D21190050008C7B1E9F42E1FEC@harp.interval.com> From: Tom Ngo To: "'JATI KASTANJA'" Cc: "'chemistry@ccl.net'" Subject: RE: SUMMARY - Levinthal Paradox Date: Tue, 3 Aug 1999 12:23:47 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: multipart/mixed; boundary="----_=_NextPart_000_01BEDDE5.B5CCFEB4" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_000_01BEDDE5.B5CCFEB4 Content-Type: text/plain; charset="iso-8859-1" Jati, the following paper is also online: J. Thomas Ngo, Joe Marks and Martin Karplus, "Computational Complexity, Protein Structure Prediction, and the Levinthal Paradox," in The Protein Folding Problem and Tertiary Structure Prediction, Kenneth Merz, Jr. and Scott LeGrand, eds., pp. 433-506, Birkhauser, Boston, 1994. ftp://ftp.interval.com/pub/papers/ngo/merz.ps.gz --Tom > -----Original Message----- > From: JATI KASTANJA [mailto:jkastanja@dwi.rwth-aachen.de] > Sent: Tuesday, August 03, 1999 9:22 AM > To: chemistry@ccl.net > Subject: CCL:SUMMARY - Levinthal Paradox > > > > Dear all, > I've obtained a lot of helpful responses. I'd like to thank everybody > who spent his time in giving me some suggestions with regard to > the "Levinthal Paradox". > Many thanks to Raman, Rick, Carlos, John, Jim, Peter, Tom and > any other person I might have forgotten. > > Regards, Jati > > Subsequent a list of suggestions and papers which deal with the > Levinthal Paradox > ----------------------------------------------- > >Peter S. Shenkin wrote > If you do find the Journal, you will find that it contains only > a passing reference to what has become known as the Levinthal > paradox. The idea really derives from a comment Cyrus once > made at a > meeting. > > The idea is this. Take a 100-residue protein. Let's suppose each > residue can have only, say, 3 conformational states. Then there > are 3^100, or about 10^48, possible states. Now suppose the > protein > can explore a new state with every moleculear vibration. > Suppose > each vibration takes about a femtosecond. Then exploring all > the states would take about 10^48 fs, or 10^33 s. There are about > 10^8 > s > in a year, so exploring all the states would take about 10^25 years. > But this is longer than the age of the universe. > > Now, in order for a protein to fold into its global > thermodynamic energy minimum, the folding process has to > be ergodic. That is, it has to explore all its states > within the time-span of the process. But protein folding takes > typically seconds to minutes. So a protein can't be folding > into its thermodynamic energetic minimum, since it can't > possibly find it in so short a time. > > Therefore, protein folding must be a kinetically controlled process. > I.e., proteins fold to the most accessible minimum, rather than the > most stable minimum. In this, protein folding must resemble the > kinetically controlled reactions of organic (and bio-) chemistry. > > The reason it's considered a "paradox" is that most people > don't believe it (at least for globular proteins as small > as 100 residues). Cyrus didn't believe it either, in fact. > But it is fun to think about, and it's great for impressing > people at cocktail parties. (You have to go to the right cocktail > parties, though. :-) ) > > -P. > > ----------------------------------------------- > >C.S.Raman wrote: > Well, the list I have provided at the end of this mail should > help you track down all the literature pertinent to this problem. > > {*} Until now I am unsuccessful in finding out the journal where > Cyrus > {*} Levinthal first published something about this paradox. > > Cy's article is one of the most MISQUOTED in the literature. > His original work was presented in a symposium: > Levinthal, C (1969) in Mossbauer Spectroscopy in Biological > Systems, (ed) Debrunner, P., & Tsibris, J.C.M., P. 22-24, > University of Illinois, Urbana Champaign. How to Fold > Graciously. > > Levinthal also published an article in J. Chim. Phys. (1968) > 65: 44-45 entitled "Are there pathways for protein folding?", > which is usually quoted as being the source of the paradox. > This is incorrect and this article makes no mention of it. > > 1. Dill KA. > Polymer principles and protein folding. > Protein Science, 1999 Jun, 8(6):1166-80. > > 2. Yon JM. > Protein folding: concepts and perspectives. > Cellular and Molecular Life Sciences, 1997 Jul, 53(7):557-67. > > 3. Finkelstein, AV; Badretdinov, AY. > Physical reason for fast folding of the stable spatial structure of > proteins: A solution of the Levinthal paradox. > MOLECULAR BIOLOGY, 1997 MAY-JUN, V31 N3:391-398. > > 4. Shakhnovich EI. > Theoretical studies of protein-folding thermodynamics and > kinetics. > Current Opinion in Structural Biology, 1997 Feb, 7(1):29-40. > > 5. Dill KA; Chan HS. > >From Levinthal to pathways to funnels. > Nature Structural Biology, 1997 Jan, 4(1):10-9. > > 8. Finkelstein AV; Badretdinov AYa. > Rate of protein folding near the point of thermodynamic > equilibrium > between the coil and the most stable chain fold [published erratum > appears > in Fold Des 1998;3(1):67]. > Folding and Design, 1997, 2(2):115-21. > > 9. Lattman EE. > Remembering Cy Levinthal [editorial]. > Proteins, 1995 Oct, 23(2):i. > > 10. Karplus M; Sali A. > Theoretical studies of protein folding and unfolding. > Current Opinion in Structural Biology, 1995 Feb, 5(1):58-73. > > 11. Durup, J. > On ''Levinthal paradox'' and the theory of protein folding. > THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE, > 1998 FEB 9, V424 N1- 2:157-169. > > 12. Karplus, M. > The Levinthal paradox: yesterday and today. > FOLDING & DESIGN, 1997, V2 N4:S69-S75. > > 13. HONIG B. > LEVINTHAL,CYRUS - IN MEMORIAM. > PROTEINS-STRUCTURE FUNCTION AND GENETICS, > 1991, V11 N4:239-241. > > 14. LATTMAN E. > LEVINTHAL,CYRUS MAY 2, 1922 NOVEMBER 4, 1990 - IN > MEMORIAM. > PROTEINS-STRUCTURE FUNCTION AND GENETICS, > 1990, V8 N4:R1-R1. > > I hope this helps. > -raman > --------------------------------------------------- > >Tom Ngo and Joe Marks wrote: > Also relevant to your inquiry are the references below. We argue > in the > > first paper that the astronomical number of conformational > states does not, > > by itself, give reason to conclude that folding should take > exponential > > time. We show how the theory of NP-completeness can be > brought to bear on > > questions related to folding times. > > > > * J. Thomas Ngo, Joe Marks and Martin Karplus, > "Computational Complexity, > > Protein Structure Prediction, and the Levinthal Paradox," in The > Protein > > Folding Problem and Tertiary Structure Prediction, Kenneth > Merz, Jr. and > > Scott LeGrand, eds., pp. 433-506, Birkhauser, Boston, 1994. > > > > * J. Thomas Ngo and Joe Marks, "Computational Complexity of > a Problem in > > Molecular Structure Prediction," Protein Engineering 5(4):313- > 321, June > > 1992. > The second paper above is on my web site, > http://www.merl.com/people/marks/index.html. > > -- Joe Marks > > --Tom Ngo > > ------------------------------------------------------------------ > > Rick Venable wrote: > I've appended a quick search result for "levinthal paradox"-- some > of > these papers (e.g. those by Dill, Karplus, or Shakhnovich) may > hopefully > refer to the original statement of the paradox. > > Parker JMR > The relationship between peptide plane rotation (PPR) and > similar > conformations > J COMPUT CHEM 20: (9) 947-955 JUL 15 1999 > > Iguchi K > Exactly solvable model of protein folding: Rubik's magic snake > model > INT J MOD PHYS B 13: (4) 325-361 FEB 10 1999 > > Hamacher K, Wenzel W > Scaling behavior of stochastic minimization algorithms in a > perfect > funnel landscape > PHYS REV E 59: (1) 938-941 Part B JAN 1999 > > Durup J > On "Levinthal paradox" and the theory of protein folding > THEOCHEM-J MOL STRUC 424: (1-2) 157-169 FEB 9 1998 > > > Finkelstein AV, Badretdinov AY > Physical reason for fast folding of the stable spatial > structure of > proteins: A solution of the > Levinthal paradox > MOL BIOL+ 31: (3) 391-398 MAY-JUN 1997 > > Karplus M > The Levinthal paradox: yesterday and today > FOLD DES 2: (4) S69-S75 1997 > > Finkelstein AV, Badretdinov AY > Rate of protein folding near the point of thermodynamic > equilibrium > between the coil and the > most stable chain fold > FOLD DES 2: (2) 115-121 1997 > > Shakhnovich EI > Theoretical studies of protein-folding thermodynamics and > kinetics > CURR OPIN STRUC BIOL 7: (1) 29-40 FEB 1997 > > Mirny LA, Abkevich V, Shakhnovich EI > Universality and diversity of the protein folding scenarios: A > comprehensive analysis with the > aid of a lattice model > FOLD DES 1: (2) 103-116 1996 > > Nakamura H, Tanimura R, Kidera A > Side-chain conformations cooperatively restricted in protein > secondary structure .2. Side-chain > configurational entropies of alpha-helices in the folding nuclei > P JPN ACAD B-PHYS 72: (7) 149-152 SEP 1996 > > Su ZD, Arooz MT, Chen HM, et al. > Least activation path for protein folding: Investigation of > staphylococcal nuclease folding by > stopped-flow circular dichroism > P NATL ACAD SCI USA 93: (6) 2539-2544 MAR 19 1996 > > KARPLUS M, SALI A > THEORETICAL-STUDIES OF PROTEIN-FOLDING AND > UNFOLDING > CURR OPIN STRUC BIOL 5: (1) 58-73 FEB 1995 > > PERKYNS JS, PETTITT BM > PEPTIDE CONFORMATIONS ARE RESTRICTED BY > SOLUTION STABILITY > J PHYS CHEM-US 99: (1) 1-2 JAN 5 1995 > > GULUKOTA K, WOLYNES PG > STATISTICAL-MECHANICS OF KINETIC > PROOFREADING IN PROTEIN-FOLDING > IN-VIVO > P NATL ACAD SCI USA 91: (20) 9292-9296 SEP 27 1994 > > ABKEVICH VI, GUTIN AM, SHAKHNOVICH EI > SPECIFIC NUCLEUS AS THE TRANSITION-STATE FOR > PROTEIN-FOLDING - > EVIDENCE FROM > THE LATTICE MODEL > BIOCHEMISTRY-US 33: (33) 10026-10036 AUG 23 1994 > > SALI A, SHAKHNOVICH E, KARPLUS M > HOW DOES A PROTEIN FOLD > NATURE 369: (6477) 248-251 MAY 19 1994 > > DILL KA, YUE K, FIEBIG K > PROTEIN-FOLDING - DRIVING FORCES AND THE > LEVINTHAL PARADOX > BIOPHYS J 66: (2) A241-A241 Part 2 FEB 1994 > > DILL KA > FOLDING PROTEINS - FINDING A NEEDLE IN A > HAYSTACK > CURR OPIN STRUC BIOL 3: (1) 99-103 FEB 1993 > > CHAN HS, DILL KA > ENERGY LANDSCAPES AND THE COLLAPSE > DYNAMICS OF HOMOPOLYMERS > J CHEM PHYS 99: (3) 2116-2127 AUG 1 1993 > > FIEBIG KM, DILL KA > PROTEIN CORE ASSEMBLY PROCESSES > J CHEM PHYS 98: (4) 3475-3487 FEB 15 1993 > ------_=_NextPart_000_01BEDDE5.B5CCFEB4 Content-Type: application/octet-stream; name="merz.ps.gz.url" Content-Disposition: attachment; filename="merz.ps.gz.url" [InternetShortcut] URL=ftp://ftp.interval.com/pub/papers/ngo/merz.ps.gz Modified=E0EBC562E5DDBE0173 ------_=_NextPart_000_01BEDDE5.B5CCFEB4-- From chemistry-request@server.ccl.net Tue Aug 3 20:03:20 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA31159 for ; Tue, 3 Aug 1999 20:03:19 -0400 Received: from fozzie.chem.wisc.edu (mail.chem.wisc.edu [128.104.68.11]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id TAA00893 for ; Tue, 3 Aug 1999 19:57:02 -0400 (EDT) Received: from skin6.chem.wisc.edu (skin6 [128.104.70.254]) by fozzie.chem.wisc.edu (8.8.7/8.8.5) with SMTP id SAA10066 for ; Tue, 3 Aug 1999 18:53:52 -0500 Received: by skin6.chem.wisc.edu (5.65v3.2/1.1.10.5/04May99-0931AM) id AA08407; Tue, 3 Aug 1999 18:54:06 -0500 Date: Tue, 3 Aug 1999 18:54:06 -0500 Message-Id: <9908032354.AA08407@skin6.chem.wisc.edu> From: Evelina Tsoncheva To: chemistry@www.ccl.net Subject: Anharmonicity Force Constant for Carbonmonoxy Vibration X-Face: *,.!Rb#sJv}/b9Ew-Bjg%e2x@IE0~D+nkJqnpJSy%3iEW({(p1,VV))Fv`4CIgP'hi%J]%> 3r4@-'|gN~Pb4vPTM6Q['20ys7;{#X9p4fj7Pgn'@:VRPvh@e8ky@,V4|l2n74.5uppgC$Opiv?u}& 7 Hi all, Does somebody know what the typically used anharmonicity force constants for CO (carbonmonoxy) vibration are? Preferably for its bound-to-heme-proteins state (or whatever bound states). Or else, could somebody refer me to some articles containing information about that? Thanks! From chemistry-request@server.ccl.net Tue Aug 3 20:40:49 1999 Received: from alchemy.yonsei.ac.kr (alchemy.yonsei.ac.kr [165.132.31.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA31365 for ; Tue, 3 Aug 1999 20:40:48 -0400 Received: (from lordmiss@localhost) by alchemy.yonsei.ac.kr (8.8.7H1/8.8.7) id JAA08946; Wed, 4 Aug 1999 09:32:54 +0900 (KST) Date: Wed, 4 Aug 1999 09:32:54 +0900 (KST) From: Kim Hanjo To: chemistry@ccl.net Subject: SUMMARY:CoMSIA Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, everyone. I posted the following answer about CoMSIA a few days ago. --------------------------------------------------- Dear CCLers Does anybody tell me about CoMSIA(Comparative Molecular Similarity Indexes Analysis)? Any details of this method or references will be great help to me. I will summerize later. Thank you in advance. --------------------------------------------------- Below is the greatly helpful reply from Dr. Wolfgang Utz. --------------------------------------------------- Hello Kim, for references look at: Klebe, G., et al., J. Med. Chem., 37, 4130-4146 (1994) Klebe , G. Comparative Molecular Similarity indices: CoMSIA, in "3D QSAR in Drug Design", H. Kubinyi et al. (eds.), Kluwer, Academic Publishers, Great Britain, 1998, Vol. 3, pages 87-104 ComSIAs strategy is comparable to standard CoMFA. There are at least 2 main differences: the interaction with a lattice surrounding the aligned molecules does not have cutoffs, a gaussian curve is used instead of the Lennard-Jones potential; second, the lattice is used to elucidate similarity between the molecules, not just giving descriptors for each one molecule. Please look at the references for more information. Hope this helps Wolfgang ---------------------------------------------------- I found that many references describing the CoMSIA methods and applications were available. CA or SCI search of CoMSIA will give many hits. I heard that the latest version of Sybyl program from Tripos is implemented with CoMSIA. (Indeed, I don't know any other program that uses CoMSIA.) Thank all repliers, especially Wolfgang. Hope this help Cheers, Kim Hanjo ___ __(___)__ (o o) +-------------------oOOO-(_)------------------------+ | **** Kim Hanjo **** | | Medicinal & Bioorganic Chemistry Laboratory | | Dept. of Chemistry, Yonsei Univ., Seoul, Korea | | email : lordmiss@alchemy.yonsei.ac.kr | | pager : 015-8411-6834 | +-----------------------------oOOO------------------+ |__|__| I can do everything || || in Him who gives me ooO Ooo strength !! From chemistry-request@server.ccl.net Tue Aug 3 21:17:15 1999 Received: from plmsc.psu.edu (kotelyan@raman.plmsc.psu.edu [128.118.156.124]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA31644 for ; Tue, 3 Aug 1999 21:17:15 -0400 Received: from localhost (kotelyan@localhost) by plmsc.psu.edu (8.8.7/8.8.7) with SMTP id VAA08254; Tue, 3 Aug 1999 21:07:26 GMT Date: Tue, 3 Aug 1999 21:07:26 +0000 (GMT) From: Mike To: Mike Peleah cc: chemistry@ccl.net Subject: Re: CCL:natural internal coordinates In-Reply-To: <16657.990803@mail.ru> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Mike, excuse my ignorance, what do you call "natural internal coordinates"? Are they - torsional angles, bond angles, and bond lengths Michael ------------------------------------------------------------------------------- Michael J. Kotelyanskii Phone (814) 863 43 81 Polymer Science Program FAX (814) 865 29 17 Department of Materials Science and Engineering kotelyan@plmsc.psu.edu Pennsylvania State University http://www.plmsc.psu.edu/~kotelyan University Park, PA 16802, USA -------------------------------------------------------------------------------- On Tue, 3 Aug 1999, Mike Peleah wrote: > | Dear friends, > : > > I would like to write program, that convert cartesian coordinates into > natural internal coordinates. But I have a couple of problems: > > 1. How could I find point group of symmetry for a set of atoms? I find > alghorthm how to finding it if you have all symmetry generators, but I > don't know how to find this generators. > > 2. How should I select coefficients for natural internal coordinates? > > Could any body help me? Online sources are preferable (our library is > very poor). Answers (if any) will be summarized and program sources > will be published. > > Best regards, > Mike mailto:MikePeleah@mail.ru > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > >