From CHMORA@LSUVAX.SNCC.LSU.EDU Wed May 24 00:39:24 1995 Received: from sn01.sncc.lsu.edu for CHMORA@LSUVAX.SNCC.LSU.EDU by www.ccl.net (8.6.10/930601.1506) id AAA26634; Wed, 24 May 1995 00:26:09 -0400 Received: from LSUVAX.SNCC.LSU.EDU by LSUVAX.SNCC.LSU.EDU (PMDF V4.2-14 #3426) id <01HQUZAB5SS0A2D72I@LSUVAX.SNCC.LSU.EDU>; Tue, 23 May 1995 23:28:07 CST Date: Tue, 23 May 1995 23:28:07 -0600 (CST) From: CHMORA@LSUVAX.SNCC.LSU.EDU Subject: Amber's new parameters for proteins and nucleic acids. To: chemistry@ccl.net Message-id: <01HQUZAB6LPUA2D72I@LSUVAX.SNCC.LSU.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters: I just read in the latest JACS issue (JACS 1995, 117, 5179-5197) a VERY interesting article about the developing of new parameters for the simulation of proteins and nucleic acids (such parameters include hydrogen-bonding interactions!). It is also mention here a WWW site where those parameters can be found and downloaded. These parameters ar for AMBER. Could anybody please tell me: 1) What does exactly AMBER do? (strong and weak points). 2) Is AMBER available for PCs? if so, under what Operating System? 3) Who distributes AMBER? Latest Version? Price? 4) Computer requirements to run AMBER? All comments about AMBER will be also welcome. A summary will be provided upon request. Thanks a lot in advance. Sincerely, Guillermo A. Morales =============================================================================== Guillermo A. Morales Phone:(504) 388-2706 Chemistry Department Fax: (504) 388-3458 Louisiana State University Baton Rouge, LA. 70803-1804 E-mail: chmora@sn01.sncc.lsu.edu U.S.A. =============================================================================== =============================================================================== ========= ============ ======== /// //////// /// /// ============= ======= /// /// /// /// ============== ====== /// //////// /// /// =============== ===== /// /// /// /// ================ ==== /////// //////// ///////// ================= === ================== =============================================================================== =============================================================================== From ross@cgl.ucsf.EDU Wed May 24 02:09:25 1995 Received: from socrates.ucsf.EDU for ross@cgl.ucsf.EDU by www.ccl.net (8.6.10/930601.1506) id BAA27418; Wed, 24 May 1995 01:59:19 -0400 From: Received: (from ross@localhost) by socrates.ucsf.EDU (8.6.12/GSC4.24) id WAA11547 for chemistry@ccl.net; Tue, 23 May 1995 22:59:18 -0700 Date: Tue, 23 May 1995 22:59:18 -0700 Message-Id: <199505240559.WAA11547@socrates.ucsf.EDU> To: chemistry@ccl.net Subject: Re: Amber's new parameters I just read in the latest JACS issue (JACS 1995, 117, 5179-5197) a VERY interesting article about the developing of new parameters for the simulation of proteins and nucleic acids ... It is also mention here a WWW site where those parameters can be found and downloaded. These parameters ar for AMBER. The parameters will soon be on http://www.amber.ucsf.edu/amber/amber.html (sometime on Wednesday, I expect). There are already some writeups there on practical considerations in developing compatible parameters. 1) What does exactly AMBER do? (strong and weak points). Aside from the force field, there is a program package called AMBER. Both are described on the web pages. 2) Is AMBER available for PCs? if so, under what Operating System? It has been compiled using f2c-based f77 under linux and bsd on PCs. Using Unix, one can generate source for e.g. DOS for use with a DOS fortran compiler. My guess is that using a fortran compiler rather than f2c/f77 (which uses C-translated source) gives a speedup of about 2x. AMBER has most commonly been run on workstations & supercomputers, but now that PCs have gotten faster, this contingent is growing. 3) Who distributes AMBER? Latest Version? Price? University of California, San Francisco and Oxford Molecular. Latest version is 4.1, academic price is $200. Contact info is on the web pages; briefly for those w/out web access: UCSF amber-request@cgl.ucsf.edu (also for joining the amber mail reflector) Oxford Molecular USA support@presto.ig.com UK support@oxmol.co.uk France support@madison.polytechnique.fr Germany onciul@oml.ccc.uni-erlangen.de Bill Ross From ivarm@boc.ic.ee Wed May 24 04:24:27 1995 Received: from argus.chemnet.ee for ivarm@boc.ic.ee by www.ccl.net (8.6.10/930601.1506) id EAA28765; Wed, 24 May 1995 04:21:37 -0400 Received: from boc.ic.ee (boc.ic.ee [193.40.63.200]) by argus.chemnet.ee (8.6.9/8.6.9) with SMTP id LAA02989 for ; Wed, 24 May 1995 11:03:05 +0300 Received: from argus.chemnet.ee by boc.ic.ee id aa08806; Wed, 24 May 95 12:14:38 estonia From: "Ivar Martin" Date: Wed, 24 May 95 11:12:30 EST Message-Id: <3666.ivarm@boc.ic.ee_POPMail/PC_3.2.2> Reply-To: X-POPmail-Charset: English To: chemistry@ccl.net Subject: Imaginary frequency and rate constant Dear CCL people, Last week I posted the question about imaginary frequency at TS and rate constant calculation. The original question was: As it is expected, MOPAC calculates one and only one negative vibrational frequency at TS. The value lies (-300 - -150 cm-1). Is it correct to use this frequency as pre-exponent factor (frequency factor) in Arrhenius rate constant equation? The reaction I study is C-C single bond forming (or splitting) reaction. I got several responses from people who asked me kindly to share the answers I might get: J. Pat Cannady Rene Fournier Jerzy M Rudzinski Robert W. Zoellner Emiel Rorije Henk Verhaar Sanja Sekusak Unfortunately, I didn't get any explanation to this question from CCL. What I only have is my own understanding that the exponential part of the Arrhenius rate constant equation gives the number of molecules in TS. (N_TS/N_GS)=exp[-deltaG#/(R*T)] where N_TS - number of molecules in transition state N_GS - number of molecules in ground state If the imaginary frequency is the measure of translational movement of atoms bearing this imaginary vibrational mode in TS, why not to use this frequency as pre-exponent frequency factor in Arrhenius equation! Also, I have the opinion of Prof. Arvi Rauk from the University of Calgary who said: ... the imaginary frequency only measures the curvature of the reaction coordinate at the transition state. It may be used in the Bell formula for a quantum mechanical tunnelling correction to the classical rate which would only be a funcion of the barrier height ... I'm pretty sure there should be people in CCL who could give exhaustive explanation. _______________________________ Dr. Ivar Martin Department of Bioorganic Chemistry tel: +372 2 526510 Institute of Chemistry fax: +372 2 536371 Akadeemia tee 15 EE0026 e-mail: ivarm@boc.ic.ee Tallinn, ESTONIA From ccl@cric.chemres.hu Wed May 24 10:24:32 1995 Received: from cric.chemres.hu for ccl@cric.chemres.hu by www.ccl.net (8.6.10/930601.1506) id KAA03287; Wed, 24 May 1995 10:24:09 -0400 From: Received: by cric.chemres.hu (AIX 3.2/UCB 5.64/4.03) id AA07941; Wed, 24 May 1995 16:22:11 +0200 Date: Wed, 24 May 1995 16:22:11 +0200 (DFT) To: Ivar Martin Cc: chemistry@ccl.net Subject: Re: CCL:Imaginary frequency and rate constant In-Reply-To: <3666.ivarm@boc.ic.ee_POPMail/PC_3.2.2> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 24 May 1995, Ivar Martin wrote: > Dear CCL people, > > Last week I posted the question about imaginary frequency at TS > and rate constant calculation. The original question was: > > As it is expected, MOPAC calculates one and only one negative > vibrational frequency at TS. The value lies (-300 - -150 cm-1). Is it > correct to use this frequency as pre-exponent factor (frequency factor) in > Arrhenius rate constant equation? The reaction I study is C-C single bond > forming (or splitting) reaction. > > ..... > > Unfortunately, I didn't get any explanation to this question > from CCL. What I only have is my own understanding that the > exponential part of the Arrhenius rate constant equation gives the > number of molecules in TS. > > (N_TS/N_GS)=exp[-deltaG#/(R*T)] > > ..... > > Also, I have the opinion of Prof. Arvi Rauk from the University of > If the imaginary frequency is the measure of translational > Calgary who said: ... the imaginary frequency only measures the curvature > of the reaction coordinate at the transition state. It may > be used in the Bell formula for a quantum mechanical > tunnelling correction to the classical rate which would only > be a funcion of the barrier height ... > > > I'm pretty sure there should be people in CCL who could give > exhaustive explanation. > BDear Colleague, The existence of an "immaginary frequency" at the TS is a reformulation of the fact, that the enrgy has a maximum (and not a minimum) along a given (normal) coordinate. Although it is expressed in frequency units, it is really a measure of the curvature of that point only, and has nothing to do directly with any reaction rate. The "quasi-termodinamic" formulation of Eyring's "absolute reaction rate" or "transitiuon state" theory was a great-scale misunderstanding, which caused very much harm to science. 20 years ago I wrote: "The activated complexes are not true chemical species, do not fulfil the conditions defining a canonic ensemble, and therefore cannot be considered as independent subjects of the canonic distribution." (J. Chem. Phys. 60, 2564, 1974). This also means that there is no meaning to attribute any termodynamic quantities to the TS. This does not mean that there can be no modern variants of transition state theory, which are free of the deffects of the old one. Best regards, Yours sincerely, Prof. Istvan Mayer e-mails: mayer@cric.chemres.hu IB13LVIB@HUEARN.sztaki.hu H1376May@ella.hu Central Research Institute for Chemistry of the Hungarian Academy of Sciences H-1525 Budapest, P.O.Box 17 Hungary From jkl@ccl.net Wed May 24 16:09:39 1995 Received: for jkl@ccl.net by www.ccl.net (8.6.10/930601.1506) id QAA11640; Wed, 24 May 1995 16:01:04 -0400 Date: Wed, 24 May 1995 16:01:04 -0400 From: Jan Labanowski Message-Id: <199505242001.QAA11640@www.ccl.net> To: chemistry@ccl.net Subject: Please do not post to CCL now. Cc: jkl@ccl.net Dear Netters, We will be changing our nameserver and diskserver today (May 24, 6pm, EDT). Please do not post anything to CCL for about 12 hours starting now, since God only knows what will happen... Jan Labanowski jkl@ccl.net