From chemistry-request@server.ccl.net Mon Jan 24 18:30:59 2000 Received: from lrz.uni-muenchen.de (lsanca1-ar99-078-106.biz.dsl.gtei.net [4.3.78.106]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA11315 for ; Mon, 24 Jan 2000 18:30:58 -0500 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id OAA30014 for ; Mon, 24 Jan 2000 14:25:59 -0800 Resent-From: Eugene Leitl Resent-Message-ID: <14476.53622.501178.474846@lrz.uni-muenchen.de> Resent-Date: Mon, 24 Jan 2000 14:25:58 -0800 (PST) Resent-To: Delivered-To: all-eugene.leitl@lrz.uni-muenchen.de Message-Id: <388C47B0.43286BFA@ifm.liu.se> X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: sv MIME-Version: 1.0 References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-SLUIDL: 1B297625-D24011D3-9E23004F-4908FE7D From: To: Multiple recipients of list orglist Subject: ORGLIST: Varian->Bruker Date: Mon, 24 Jan 2000 13:38:08 +0100 Please reply to the original author (see From: line below). From: Jonas Nilsson How do I convert NMR-fid files from one format to another? Is there any free software? /jN -- _____________________ _____________________ | Jonas Nilsson | | | |Linkoping University | | Telephone | | IFM | | --------- | | Dept. of Chemistry | | work: +46-13-285690 | | 581 83 Linkoping | | fax: +46-13-281399 | | Sweden | | home: +46-13-130294 | |_____________________| |_____________________| __________________ ORGLIST - Organic Chemistry Mailing List Website and Archive: http://www.dq.fct.unl.pt/orglist/ To post a message (TO EVERYBODY) send to orglist@dq.fct.unl.pt To unsubscribe, send to listserver@dq.fct.unl.pt the message: unsubscribe orglist List coordinator: Joao Aires de Sousa (jas@mail.fct.unl.pt) From chemistry-request@server.ccl.net Tue Jan 25 04:18:29 2000 Received: from york.ac.uk (pump3.york.ac.uk [144.32.128.131]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA13886 for ; Tue, 25 Jan 2000 04:18:28 -0500 Received: from york.ac.uk (joker.chem.york.ac.uk [144.32.180.45]) by york.ac.uk (8.9.3/8.9.3) with ESMTP id IAA04387 for ; Tue, 25 Jan 2000 08:10:35 GMT Sender: meike@york.ac.uk Message-ID: <388D5B7D.AFC85327@york.ac.uk> Date: Tue, 25 Jan 2000 08:14:53 +0000 From: Meike Reinhold X-Mailer: Mozilla 4.7 [en] (X11; I; AIX 4.2) X-Accept-Language: en MIME-Version: 1.0 To: chemistry Subject: summary: DFT programs Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Some people asked me to summarise my results about density functional programs with free source code. The answers I got are listed below ( thanks to David, Peter, Bruno, Frank, Fred, Hub). Meike http://www.dl.ac.uk:/CFS/ http://www.chem.uottawa.ca/DeFT.html http://antas.agraria.uniss.it/software.html NWChem: http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html Pretty much does everything, from HF to Car-Parinello MD. Massively parallel, and so the warning from the authors is that it may not perform optimally on single processor workstations. DeFT: http://www.chem.uottawa.ca/DeFT.html Gaussian Orbital DFT, relative of DeMon. No symmetry, but source is included, and it builds on most platforms without too much trouble. And two more speculative programs. MPQC: http://aros.ca.sandia.gov/~cljanss/mpqc Massively parallel quantum chemistry program. DFT is not quite ready for prime-time, but the code is GPL'd and in C++, so if you feel like fixing it.... Jeep: http://irrmawww.epfl.ch/fg/jeep/jeep.html May or May not be still in development. Quantum MD code. Supposedly GAMESS-US is readying a release that will include a gridless DFT code. It's not there yet, but hte stub routines have appeared. Check their webpage, http://www.msg.ameslab.gov/gamess periodically. Hope this helps. Personally, I've used the first two, and DeFT is probably easier to get to use, but NWChem is far more complete. Depends what you want; geometries and charges: DeFT, Geometries, properties, lots of functionals, hybrid QM/MM, etc: NWChem. -fred From chemistry-request@server.ccl.net Tue Jan 25 08:02:41 2000 Received: from biol2.bio.nagoya-u.ac.jp ([133.6.127.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA15526 for ; Tue, 25 Jan 2000 08:02:39 -0500 Received: from [133.6.127.65] by biol2.bio.nagoya-u.ac.jp (8.8.8/1.1.22.3/26Dec99-0255AM) id UAA0000017285; Tue, 25 Jan 2000 20:57:34 +0900 (JST) Date: Tue, 25 Jan 2000 20:57:34 +0900 (JST) Message-Id: <200001251157.UAA0000017285@biol2.bio.nagoya-u.ac.jp> To: chemistry@ccl.net From: shinoda@biol2.bio.nagoya-u.ac.jp (Kazuki Shinoda) Subject: Program to convert CHARMM force field file to AMBER format MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear CCLers, Does anyone have a program to convert CHARMM format force field file to AMBER format ? Best regard, Kazuki ================================================ Kazuki Shinoda, MC2 Division of Biological Science, Graduate school of Science Nagoya University, Chikusa, Nagoya 464-8602, Japan E-mail : shinoda@biol2.bio.nagoya-u.ac.jp URL: http://bio.nagoya-u.ac.jp:8001/~kazuki/kazuki.html ================================================ From chemistry-request@server.ccl.net Tue Jan 25 05:44:15 2000 Received: from butler-se.pnu.com (butler-se.pnu.com [193.235.229.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA14195 for ; Tue, 25 Jan 2000 05:44:15 -0500 Received: from igw-se.pnu.com (igw-se-dmz.pnu.com [193.235.229.10]) by butler-se.pnu.com (8.8.8+Sun/8.8.8) with SMTP id KAA18669; Tue, 25 Jan 2000 10:38:21 +0100 (MET) Received: from ccMail by eu.pnu.com (IMA Internet Exchange 3.13) id 00283383; Tue, 25 Jan 2000 10:38:17 +0100 Mime-Version: 1.0 Date: Tue, 25 Jan 2000 10:35:52 +0100 Message-ID: <00283383.C21441@eu.pnu.com> From: Pieter.Stouten@eu.pnu.com (Pieter Stouten) Subject: Re: CCL:Summary: flexible docking program To: Computational Chemistry List , Renxiao Wang Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: 7bit Content-Description: cc:Mail note part I am pleased to be credited with the attached mail on Affinity. However, it was not me. This is what I had written: > If you have access to MSI software, you can use Affinity, which will > keep part of your enzyme rigid, part of it flexible but constrained > to starting (e.g. crystallographic) coordinates and part of it > completely flexible. It is basically an MD program (so it is not so > useful for large numbers of ligands), but expressing the rigid part > of the enzyme on a grid leads to dramatic speed ups. Affinity also > has a continuum solvation model, but that is not fully reliable. > However, if one does not study fully unconstrained proteins, the > solvation term may help. > > The MSI implementation of Affinity was a joint collaboration between > Ciongxin Liang (then with Biosym, now with Sugen) and the DuPont > Merck CADD group (Brock Luty, now at Agouron; me, now at P&U; and > Zelda Wasserman). Please let me know if you are interested in the > papers describing that work. Ciao, Pieter ______________________________ Reply Separator _________________________________ Date: Mon, 24 Jan 2000 09:55:33 +0100 From: Pieter.Stouten@eu.pnu.com (Pieter Stouten) You might want to look at Affinity from MSI (URL http://www.msi.com/life/products/insight/modules/affinity.html). It is an automatic docking module for Insight II that incorporates Monte Carlo and simulated annealing methods to place a ligand within a receptor. The method is designed so that after the Monte Carlo phase the receptor within the defined binding site is flexible by default. In other words, all you have to do is define the extent of the binding site. Every receptor atom within that region is flexible and free to move. Recent publications using Affinity are: 1. Kurinov, I. V., Myers, D. E., Irvin, J. D., Uckun, F. M. 1999. X-ray crystallographic analysis of the structural basis for the interactions of pokeweed antiviral protein with its active site inhibitor and ribosomal RNA substrate analogs. Prot. Sci. 8:1765-72 2. Read, M. A., Wood, A. A., Harrison, J. R., Gowan, S. M., Kelland, L. R., et al. 1999. Molecular Modeling Studies on G-Quadruplex Complexes of Telomerase Inhibitors: Structure-Activity Relationships. J. Med. Chem. San Diego, CA 92121 From chemistry-request@server.ccl.net Tue Jan 25 06:03:24 2000 Received: from raven.dcu.ie (raven.dcu.ie [136.206.1.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA14283 for ; Tue, 25 Jan 2000 06:03:23 -0500 Received: from ccmail-gw.dcu.ie by raven.dcu.ie (PMDF V5.1-10 #24113) with ESMTP id <01JL2ZDPGIC200007N@raven.dcu.ie> for chemistry@ccl.net; Mon, 24 Jan 2000 12:20:59 GMT Received: from ccmail.dcu.ie (ccmail.dcu.ie [136.206.5.1] (may be forged)) by ccmail-gw.dcu.ie (8.9.1a/8.9.1/893-FD) with SMTP id KAA12646 for ; Mon, 24 Jan 2000 10:10:42 +0000 (GMT) Received: from ccMail by ccmail.dcu.ie (ccMail Link to SMTP R8.31.00.5) id AA948704643; Mon, 24 Jan 2000 09:04:05 +0000 (GMT) Date: Mon, 24 Jan 2000 09:00:36 +0000 (GMT) From: DERMOT BROUGHAM Subject: Summary: PC or UNIX, G98 or Titan To: chemistry@ccl.net Message-id: <0001249487.AA948704643@ccmail.dcu.ie> MIME-version: 1.0 X-Mailer: ccMail Link to SMTP R8.31.00.5 Content-type: text/plain; charset=US-ASCII Content-description: "cc:Mail Note Part" Content-transfer-encoding: 7BIT Dear CCLers, I posted the following question quite some time ago, apologies for my slowness in sending this summary. Dermot The question was: >I have secured some (moderate) funding to get some hardware and software >for QC calculations. I can now go one of several routes, though it is >difficult to work out which is better (note there is a site licence here >for G98 on UNIX). > >1. A UNIX box running G98 >2. A PC running G98 under LINUX >3. A PC running TITAN >4. A combnation of 2 & 3 > >My first question is which will run quicker given that I will be doing >fairly large MP2 & B3LYP calculations and have the same sum to spend >whatever route I go. > > >My second question(s) (if I may) is about Titan: >1. Does it have a big library of basis sets and can you include basis sets >from elsewhere in the input (eg for Ru)? >2. Is it recognised, i.e. would I have any trouble publishing results from >it? >3. I am told the interface is good for both input and visualisation, is >this generally accaepted? >4. I presume geometry optimization will work on cartesian coordinates and >that it can transform to redundant internal coordinates. Can I input in >z-matrix format too? I quickly realised I couldn't run TITAN on PC with LINUX, I should have said Jaguar (which is the same code but without the nice windows front end of TITAN). The replies included: ****************************************************************** Most flexible would be a PC under Linux, running G98 and, if you could afford the additional license, Jaguar from Schroedinger. That would give you the compute functionality, if not the pretty front-end, of the Titan solution. According to Wavefunc's docs, and both their and Schroedinger's web pages, Titan is Wavefunction's Spartan front-end on top of Schroedinger's Jaguar PS-GVB back-end. So, the results should be acceptable, since it's a known program (jaguar) doing the computations, and according to messages in the CCL archive, it's about a factor of 10 faster than its (nameless) competitors. Personally, I prefer the Unix solution, but that's because of being familiar with the environment, and for G98 at least, the source-code being available, meaning that as better processors, etc, come along, you can recompile, tune, and optimize. It also lowers your chances of an OS revision breaking a pre-compiled executable, and leaving you stranded until the company builds a new one. -fred ****************************************************************** According to published results Jaguar is found to be 5 to 10 times faster as G98 when doing large compuational tasks esp. MPx or DFT. As Jaguar is integrated fully into Titan. This product seems to be a quite good combination in terms of speed, accuracy and good visualisation techniques. But there are two things which G98 handles better: 1. There is no source code. You get a fully precompiled version of either Titan / or Jaguar. 2. Not everything g98 does can be done with Jaguar like NMR calculations. Gaussian is the clear recognised standard in this field and you wont have any problems publishing results obtained from g98 calculations. So my recommendations are the following: 1. A fast PC running NT with Titan and G98W or 2. A fast PC running Linux with g98 and Jaguar. Kind regards, Alex ****************************************************************** I can't speak for Titan but my understanding was that it was a Windows product rather than Linux. You could dual boot to get G98 under Linux and Titan under Windows. You can add a copy of GaussView for an interface to Gaussian. Gaussian can do all of 1) and 4). The GaussView interface would do both input and visualization. Can't speak to performance comparisons as I have seen none for Titan. Douglas J. Fox Director of Technical Support help@gaussian.com ****************************************************************** With a moderate budget, I would suggest a combination hardware-software solution from Parallel Quantum Solutions. It is a small company of quantum chemistry specialists. They sell 4-16 processor PCs running Linux with already-optimized parallelized quantum software installed. Their software will read and run G98 input files. They are very fast on MP2 and DFT. I have bought and used a system of theirs and I am happy with it. See their web page at http://www.pqs-chem.com/ Best wishes, and I have no commercial interest in the company, Brian Teppen ****************************************************************** I have spoken to Parallel Quantum systems and some of their satisfied customers, it does seem like a good option and may be what I do in the end. Dermot From chemistry-request@server.ccl.net Tue Jan 25 19:39:11 2000 Received: from sungod.ccs.yorku.ca (iXcPFafGzM+QFZ4hg4iaWV25lKuVvoQS@sungod.ccs.yorku.ca [130.63.236.104]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA18746 for ; Tue, 25 Jan 2000 19:39:10 -0500 Received: from curl.gkcl.yorku.ca (curl.gkcl.yorku.ca [130.63.232.224]) by sungod.ccs.yorku.ca (8.9.3/8.9.3) with SMTP id SAA02420 for <@mailrelay.yorku.ca:chemistry@ccl.net>; Tue, 25 Jan 2000 18:33:06 -0500 (EST) Received: by curl.gkcl.yorku.ca (940816.SGI.8.6.9/940406.SGI) for chemistry@ccl.net id SAA02631; Tue, 25 Jan 2000 18:38:56 -0500 From: chan@curl.gkcl.yorku.ca (Wai-To-Chan) Message-Id: <200001252338.SAA02631@curl.gkcl.yorku.ca> Subject: Re: Summary: PC or UNIX, G98 or Titan To: chemistry@ccl.net Date: Tue, 25 Jan 100 18:38:55 -0500 (EST) X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit <<<<<<<< According to published results Jaguar is found to be 5 to 10 times faster as G98 when doing large computational tasks esp. MPx or DFT.>>> Correct me if I am wrong here. Comparison of performances of Jaguar and Gaussian98 has never been published if there is any. Wai-To Chan From chemistry-request@server.ccl.net Tue Jan 25 16:55:15 2000 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA17678 for ; Tue, 25 Jan 2000 16:55:14 -0500 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id PAA22090; Tue, 25 Jan 2000 15:51:13 -0500 (EST) Date: Tue, 25 Jan 2000 15:51:13 -0500 (EST) From: Iraj Daizadeh To: chemistry@ccl.net cc: sangeeta@bioinfo.ernet.in Subject: IN SUM: md simulations/small chunks of proteins/alpha-helices etc. In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello: Here are responses to my query concerning references describing the results of molecular dynamics calculations showing the stability of alpha-helices in solution and its comparison with experiment. In short, it seems that this sort of calculation either has been performed sometime ago (David/Bob), or is still too computationally expensive to be performed in its entirety -- as compared to experiment (Rick). Thanks to David van der Spoel, Rick Venable, and Bob Latour; their responses follow. It would be interesting to see if there is any work performed on alpha-helix-turn or any other elementary secondary structures in a systematic way. iraj Iraj Daizadeh, Ph.D. Harvard University Department of Cellular and Molecular Biology The Biological Laboratories 16 Divinity Avenue Cambridge, MA 02138 Phone: (617) 495-0783 (617) 495-0560 Fax: (617) 496-4313 Email: daizadeh@nucleus.harvard.edu xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Question: On Sat, 22 Jan 2000, Iraj Daizadeh wrote: > > Dear Members of the CCL: > > Here are some questions that I have been interested in for some time; your > thoughts would be appreciated. > > Here's the general problem: Given a alpha helix cut out from a PDB > protein, run md simulations to determine the folling: > > 1. How can we ensure from md simulations that the alpha helix is stable in > solution? We solvate the alpha helix the run md simulations for how long? > how much water [10 angstrom solvation shell?]? how many time steps? how > long will the calculation take? and on what machine-- Cray? > etc....details--details--details! > > 2. References showing that results of the above calculation have been > verified by experiment? References describing results of the above > calculations on such small subsets of PDB data? > > I ( as usual ) will post a summary of your responses. > > Thanks, Iraj. > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Responses: 1outof4: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Quite a feq MD simulations have been done on alpha-helices. I will point you to my own older work that has all the references: @Article{Spoel96a, author = {David van der Spoel and Bert L. de Groot and Steven Hayward and Herman J. C. Berendsen and Hans J. Vogel}, title = {Bending of the Calmodulin Central Helix: A Theoretical Study}, journal = "Prot. Sci.", year = 1996, volume = 5, pages = {2044-2053} } @Article{Spoel96b, author = {David van der Spoel and Hans J. Vogel and Herman J. C. Berendsen}, title = {Molecular Dynamics Simulations of {N}-terminal Peptides from a Nucleotide Binding Protein}, journal = "Proteins", year = 1996, volume = 24, pages = {450-466} } Especially this latter has a systematic search of peptides to test for stability. If you want to do calculations yourself: just get a couple of Pentium IIs, you can certainly do 1 or 2 ns a week per processor. You should not use a plastic bag (sphere) with water, since your helices will unfold and occupy a large volume. Use normal PBC, with a cubic or truncated octahedron box. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 2outof4: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx On Sat, 22 Jan 2000, Iraj Daizadeh wrote: > Here's the general problem: Given a alpha helix cut out from a PDB > protein, run md simulations to determine the folling: > > 1. How can we ensure from md simulations that the alpha helix is stable in > solution? I'd say you can't, not with 100% certainty; but with a good deal of work you might be able to develop a protocol with some degree of reliability, enough to be useful. One of the dilemmas in this area is evaluating the free energy of the folded state vs. the unfolded state, in large part because there are so many possible unfolded states. > We solvate the alpha helix the run md simulations for how long? Many nanoseconds, at least. You may need to determine that yourself, by testing against cases with known results, e.g. a couple cases where the helix is stable in water in expt, and a couple cases where it isn't. You should probably also deliberately refold the peptide into random coil configs (molten globule?) and subject it to the same protocol. > how much water [10 angstrom solvation shell?]? I recommend constant P,T methods in a periodic cell, with at least 12 A (typical nonbond cutoff) from the solute (protein) to the closest cell face. I wouldn't recommend using a sphere of water in general, and certainly not without employing e.g. a reaction field method. > how many time steps? Probably at least 10 ns per sim, but you should run sims of helices which are unstable when excised to determine that. > how long will the calculation take? A good Ph.D. project, or a very talented postdoc > and on what machine-- Cray? Whatever you can get access to-- considerable CPU time will be needed. Cray if you have the dollars or grant writing skills needed, but CHARMM on a Linux cluster would work for this as well. > 2. References showing that results of the above calculation have been > verified by experiment? References describing results of the above > calculations on such small subsets of PDB data? I know this has been done for paired helices, esp. the leucine zipper motif; the peptide GCN4-p1, 33 AA from the GCN4 protein, has been studied extensively by expt (X-ray crystal, NMR) and MD/MC techniques. > how long will the calculation take? A good Ph.D. project, or a very talented postdoc > and on what machine-- Cray? Whatever you can get access to-- considerable CPU time will be needed. Cray if you have the dollars or grant writing skills needed, but CHARMM on a Linux cluster would work for this as well. > 2. References showing that results of the above calculation have been > verified by experiment? References describing results of the above > calculations on such small subsets of PDB data? I know this has been done for paired helices, esp. the leucine zipper motif; the peptide GCN4-p1, 33 AA from the GCN4 protein, has been studied extensively by expt (X-ray crystal, NMR) and MD/MC techniques. Another area studied extensively by both expt and simulation techniques is helix bundles, including some with designed helices. I'm not as aware of the work on single, isolated helices; however, some of the dimer or bundle literature may have refs to single helix work. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or Rick_Venable@nih.gov | \ / |=| position of the FDA; for that, http://www.erols.com/rvenable \/ |=| see http://www.fda.gov ) xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 3outof4 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Dear Iraj, I cannot answer all your questions, but can give input on a couple. >1. How can we ensure from md simulations that the alpha helix is stable in >solution? > First of all, in general, I expect a free alpha helix NOT to be stable in aqueous solution - my argument is that the main-chain H-bonds should be able to form lower energy hydrogen bonds with water instead of its own chain elements if totally unconstrained. I suppose you could do a quick assessment by doing mechanics calc in water at various degrees of helix opening to assess energy changes to specifically address this. >how much water [10 angstrom solvation shell?]? Unfortunately, I think a stand alone solvation shell will only simulate a shell of water in a vacuum, which will be very different than in bulk water. I believe you need to use repeat boundary conditions with full hydration if you wish to simuate behavior in an aqueous environment. Best wishes, Bob Latour =========================================== Robert A. Latour Jr., Ph.D. Associate Professor of Bioengineering and Materials Science & Engineering 501 Rhodes Research Center Clemson University, Clemson, SC 29634 robert.latour@ces.clemson.edu tel: (864) 656 -5552 / fax: (864) 656-4466 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 4 outof4: xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx Dear Iraj, Yesterday I emailed you my opinion about your questions on alpha helix modeling and stability. The best reference that I have found on this is cited below - this paper does directly address alpha-helix stability and dynamics modeling in aqueous solution. M.J. Bodkin and J.M. Goodfellow, Competing interactions contributing to a-helical stability in aqueous solution, Protein Science, 4: 603-612 (1995). Regards, Bob Latour =========================================== Robert A. Latour Jr., Ph.D. Associate Professor of Bioengineering and Materials Science & Engineering 501 Rhodes Research Center Clemson University, Clemson, SC 29634 robert.latour@ces.clemson.edu tel: (864) 656 -5552 / fax: (864) 656-4466 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx