From rprf526-int@intccop1.intevep.pdv.com Tue Nov 12 08:12:56 1996 Received: from firewall.intevep.pdv.com for rprf526-int@intccop1.intevep.pdv.com by www.ccl.net (8.8.2/950822.1) id HAA22990; Tue, 12 Nov 1996 07:32:53 -0500 (EST) Received: by firewall.intevep.pdv.com (4.1/SMI-4.1) id AA20518; Tue, 12 Nov 96 08:25:05-040 Received: from intevep.intevep.pdv.com(129.90.18.4) by firewall.intevep.pdv.com via smap (V1.3) id sma020516; Tue Nov 12 08:25:01 1996 Received: from intccop1.intevep.pdv.com by intevep (5.x/SMI-SVR4) id AA13560; Tue, 12 Nov 1996 08:18:37 -0400 Received: from cc:Mail by intccop1.intevep.pdv.com id AA847800745 Tue, 12 Nov 96 08:12:25 EST Date: Tue, 12 Nov 96 08:12:25 EST From: rprf526-int@intccop1.intevep.pdv.com (rprf526-int) Encoding: 262 Text Message-Id: <9610128478.AA847800745@intccop1.intevep.pdv.com> To: chemistry@www.ccl.net, rprf526-int@intccop1.intevep.pdv.com Return-Receipt-To: rprf526-int@intccop1.intevep.pdv.com (rprf526-int) Subject: MOPAC: parameters for transition metals Collegues: I am looking for parameters of metals, mainly transition ones, for MOPAC (MNDO or PM3) I really appreciate any information! Regards, Manuel J. Goncalves Proccess Department Intevep From pwalters@portal.vpharm.com Tue Nov 12 09:12:56 1996 Received: from portal.vpharm.com for pwalters@portal.vpharm.com by www.ccl.net (8.8.2/950822.1) id IAA23165; Tue, 12 Nov 1996 08:22:58 -0500 (EST) Received: from neoprene.vpharm.com by portal.vpharm.com (AIX 3.2/UCB 5.64/4.03) id AA26328; Tue, 12 Nov 1996 08:22:40 -0500 Sender: pwalters@portal.vpharm.com Message-Id: <3288924A.446B@portal.vpharm.com> Date: Tue, 12 Nov 1996 10:05:46 -0500 From: Pat Walters Organization: Vertex Pharmaceuticals X-Mailer: Mozilla 3.0 (X11; I; IRIX 5.3 IP22) Mime-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Re: Simulated Annealing References: <9611070633.AA28137@parcom.cdac.ernet.in> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit gadre@cdac.ernet.in wrote: > > Dear Sirs : > We are looking for optimization routines incorporating > Simulated Annealing. Are there any web sites or references? > Thank You, > Take a look at these sites : http://ntuix.ntu.ac.sg/~szli/book_1/Chapter_9/node149.html http://www.taygeta.com/annealing/simanneal.html http://www.sdsc.edu/~frost/Ebsa/WebTour/ Also see Press, Teukolsky, Vetterling, Flannery, Numerical Recipes in C, 2nd ed p444 Have fun, Pat ------------------------------------------------------------------ W. Patrick Walters, Ph.D. Scientist, Computational Chemistry and Molecular Modeling Vertex Pharmaceuticals, Inc., 130 Waverley St., Cambridge, MA 02139 Voice: (617)577-6000 FAX: (617)577-6400 From cgonzale@psc.edu Tue Nov 12 12:13:05 1996 Received: from evo.psc.edu for cgonzale@psc.edu by www.ccl.net (8.8.2/950822.1) id LAA25120; Tue, 12 Nov 1996 11:52:34 -0500 (EST) Received: from localhost (localhost [127.0.0.1]) by evo.psc.edu (8.7.4/8.7.3 PSC 1996/02/27 lambert) with SMTP id LAA02593; Tue, 12 Nov 1996 11:52:01 -0500 From: "Carlos A. Gonzalez" Message-Id: <199611121652.LAA02593@evo.psc.edu> X-Authentication-Warning: evo.psc.edu: Host localhost [127.0.0.1] didn't use HELO protocol To: Pat Walters cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:Simulated Annealing In-reply-to: Your message of "Tue, 12 Nov 96 10:05:46 EST." <3288924A.446B@portal.vpharm.com> Date: Tue, 12 Nov 96 11:52:00 -0500 X-Mts: smtp adre@cdac.ernet.in wrote: > > Dear Sirs : > We are looking for optimization routines incorporating > Simulated Annealing. Are there any web sites or references? > Thank You, > I have implemented a parallel version that scales very well on the CRAY T3D and T3E. The current version is being used at the Pittsburgh Supercomputing Center to optimize large atomic clusters. In addition, I implemented a library that can be used to optimize any mathematical function. If you need more information you can contact me at: cgonzale@psc.edu Regards; Carlos Gonzalez. From KIRBYR@biochem-pharma.com Tue Nov 12 12:34:25 1996 Received: from internet.biochem-pharma.com for KIRBYR@biochem-pharma.com by www.ccl.net (8.8.2/950822.1) id MAA25189; Tue, 12 Nov 1996 12:07:27 -0500 (EST) Received: from post.biochem-pharma.com (post.biochem-pharma.com [192.168.169.250]) by internet with SMTP (DuhMail/2.0) id QAA05991; Fri, 8 Nov 1996 16:53:55 -0500 Received: by post.biochem-pharma.com with Microsoft Mail id <3283D95B@post.biochem-pharma.com>; Fri, 08 Nov 96 17:07:39 PST From: "Kirby, Robert" To: "'CHEMISTRY@www.ccl.net'" Subject: Release of RPAC 11.0 Date: Fri, 08 Nov 96 14:08:00 PST Message-ID: <3283D95B@post.biochem-pharma.com> Return-Receipt-To: Encoding: 49 TEXT X-Mailer: Microsoft Mail V3.0 Announcement For The Computational Chemistry Community Release of RPAC 11.0 RPAC Molecular Properties Package, Version 11.0 (1996) University of Copenhagen, Denmark, 1996. Thomas D. Bouman, Aage E. Hansen, Keld L. Bak Thomas B. Pedersen and Robert A. Kirby Copyright 1996 by Aage E. Hansen, Department of Chemistry, H.C. Orsted Institute University of Copenhagen, DK-2100 Copenhagen, Denmark Abstract Program RPAC is a post-SCF package that computes electronic excitation and response properties in first-order (RPA/CHF) and second-order (SOPPA/SOLO) linear response theory. Electronic excitation properties include transition energies, oscillator and rotatory strengths, rotatory strength tensors, transition densities and excitation charge rearrangements. Electronic ground state response properties include nuclear magnetic shielding tensors, atomic polar and axial tensors for vibrational circular dichroism (CHF level only), and static and dynamic dipole polarizabilities. It provides analyses in molecular structural terms (not implemented for rotatory strength tensors) and output for graphic displays. Routines for graphical displays are included as stand alone programs in the distribution package. As a post-SCF package, RPAC 11.0 must be interfaced to an appropriate SCF program and it is assumed that such SCF packages are operated under proper license. Distribution Policy RPAC 11.0 is distributed free of charge and is ported onto a number platforms. The user is provided with source code, test files, and manual. To obtain a copy of RPAC 11.0, e-mail to Dr. Aa. E. Hansen at aaeh@rpac.ki.ku.dk and request the appropriate release form. When this form has been signed by the user and a responsible officer then ftp site information will be provided which will permit one to obtain RPAC 11.0. From ahocquet@tamarugo.cec.uchile.cl Tue Nov 12 12:50:40 1996 Received: from tamarugo.cec.uchile.cl for ahocquet@tamarugo.cec.uchile.cl by www.ccl.net (8.8.2/950822.1) id LAA25082; Tue, 12 Nov 1996 11:42:14 -0500 (EST) Received: from ([146.83.10.50]) by tamarugo.cec.uchile.cl (5.0/SMI-SVR4(Thom)) id AA16762; Tue, 12 Nov 1996 13:42:08 +0400 Message-Id: <3288EEF1.6E9A@tamarugo.cec.uchile.cl> Date: Tue, 12 Nov 1996 13:41:05 -0800 From: Alexandre Hocquet X-Mailer: Mozilla 2.02 (Win16; I) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: summary of eff comparisons Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable dear CCLers, Here is a list of references i have been sent regarding the original messag= e i posted a week ago about = empirical force field comparisons. Thank you very much to all who took the = time to answer. The original question : Dear Cclers, In a recent article in the Journal of Computational Chemistry (Cornell et a= l., 17, 1996, p1541), authors complain about too few comparative studies of force fields published. Thoug= h i dont have the article at the moment, i think i remember they only quote one reference : Hall et al., J: Comput. Chem., 5, 1984, p441. As for me, i noticed these other two : Gundertofte et al., J: Comput. Chem., 12, 1991, p200. Gundertofte et al., J: Comput. Chem., 17, 1996, p429. (And aparently, in Re= views in Computational Chemistry, volume 9) If you know about an article involved in force field comparisons, (later th= an, say, 1985 in order to avoid first generation force fields that are no more used), i would be very= interested in the reference and, if possible, a short description. I will summarise to the list. I am also interested in any kind of cooperation with other teams involved i= n this field. I am myself specialising in =93general audience software=94 force fields such as MM+, M= MX... Thanks in advance for your answers. -- Alexandre HOCQUET ____________________________________ Subject: = Re: CCL:Force fields comparisons in the litterature (francais-castellano-english) = Date: = Mon, 4 Nov 1996 13:47:04 -0800 = From: = "Volkhard Helms" To: = ahocquet@tamarugo.cec.uchile.cl, vhelms@chemcca10.ucsd.edu References: = 1 Hi Alexandre, we have performed a comparison of the CHARMM22, OPLS, CVFF, and GROMOS force fields with respect to their ability to reproduce free energies of hydrations of a series of small compounds (acetone, di-methylether, propane, cyclo-propane, camphor) calculated from molecular dynamics simulations. Sets of atomic charges of various magnitude were compared (ESP-derived charges scaled by 1.0, 0.8, and 0.6). The study has been accepted for publication in the Journal of Computational Chemistry and should appear soon. I would be happy to send you a preprint of this article. Best regards, Volkhard Helms Dept. of Chemistry UCSD ____________________________________ Subject: = force field comparison papers = Date: = Mon, 4 Nov 1996 18:13:01 -0500 (EST) = From: = Mike Beachy To: = ahocquet@tamarugo.cec.uchile.cl Hi- I'm no longer a reader of the CCL (too many messages were distracting me from work), but I recently got email from someone who follows it. She forwarded your request for comparative force field studies. We have just submitted such a study to JACS titled "Accurate Ab Initio Quantum Chemical Determination of the Relative Energetics of Peptide Conformations and Assessment of Empirical Force Fields", by Michael D. Beachy, David Chasman, Robert B. Murphy, Thomas A. Halgren, and Richard A. Friesner. In it, we calculate relative energies of 10 alanine tetrapeptide conformations at the LMP2/cc-pVTZ(-f)//HF/6-31G** level and use our results as a benchmark for the evaluation of different variations of MM2, MM3, OPLS, CFF95(DISCOVER), GROMOS, AMBER, CHARMM, and MMFF. Mike Beachy ____________________________________ ubject: = Re: CCL:Force fields comparisons in the litterature (francais-castellano-english) = Date: = Tue, 5 Nov 1996 10:41:08 GMT = From: = javier@fcu.um.es (Jose Javier Lopez Cascales) To: = Alexandre Hocquet Dear Alexandre, Hereby I send a reference to you, which could be of your interest concerened Force-field comparations in MD simiulations: authors: Aldert R. van Buuren, Siewert-Jan Marrink and H.J.C. Berendsen. J. Phys. Chem. (97), 9206-9212, 1993. With my best regards, Un abrazo, = Javier ***************************************************************************= **** Dr. Jose Javier Lopez Cascales | Office phone:Int-34-68-307100,ext:2190= * Departamento de Quimica-Fisica | Fax: Int-34-68-364148 = * Fac. de Quimica, Uni. de Murcia, | e-mail: javier@fcu.um.es = * Campus de Espinardo, 30071 Murcia, | www -> http://leonardo.fcu.um.es/~javi= er/* Spain | = * ***************************************************************************= **** ___________________________________ Subject: = Re: CCL:Force fields comparisons in the litterature (francais-castellano-english) = Date: = Tue, 5 Nov 1996 10:20:19 -0500 (EST) = From: = Richard Gillilan To: = ahocquet@tamarugo.cec.uchile.cl (Alexandre Hocquet) Richard Friesner at Columbia has a paper comparing a number of well-known force fields with large quantum calculations. I think it is going to appear in either JPC or JACS this month. Sorry I don't have the exact reference yet. Will let you know when I find out. This web page contains a brief overview of some differences: http://chemcca10.ucsd.edu/~chem215/lectures/special/special/node1.html Also William Jorgensen also has a paper that will come out (Nov issue of JACS?) comparing MMFF, AMBER and OPLS for liquid properties. Richard ------------------------------------------------------------------- stereo pair stereo pair Richard E. Gillilan H H H H Visualization Specialist \ | | \ Cornell Theory Center H--C---C--H H---C---C---H richard@tc.cornell.edu / | | / (607) 254-8757 H H H H ------------------------------------------------------------------- ____________________________________ Subject: = Re: CCL:Force fields comparisons in the litterature = Date: = Tue, 5 Nov 1996 11:34:44 -0500 (EST) = From: = "M. Nicklaus" To: = ahocquet@tamarugo.cec.uchile.cl CC: = mn1@helix.nih.gov Dear Dr. Hocquet, I have performed an 'addendum' study to the paper by Gundertofte et al., J. Comp. Chem., 17, 1996, p429, in which I am comparing the (MSI) CHARMm force field to the same experimental data Gundertofte et al. used. The bottom line was that CHARMm performed about as well as the force fields based on the MM2 or MM3 functional form, which had been found to perform best among the tested force fields. This paper has been accepted for publication by J. Comp. Chem., and is scheduled to appear in the March 1997 issue. I can send you a preprint if you wish. Please let me know. Hope that helps. Sincerely, Marc Nicklaus ------------------------------------------------------------------------ Marc C. Nicklaus Lab. of Medicinal Chemistry e-mail: mn1@helix.nih.gov National Cancer Institute, NIH Phone: (301) 402-3111 Bldg 37, Rm 5B29 Fax: (301) 496-5839 BETHESDA, MD 20892-4255 USA WWW: http://www.nci.nih.gov/intra/lmch/MCNBIO.HTM ------------------------------------------------------------------------ ____________________________________ Subject: = Re: CCL:Force fields comparisons in the litterature (francais-castellano-english) = Date: = Tue, 5 Nov 1996 10:48:55 -0600 (CST) = From: = Marcus G Martin To: = Alexandre Hocquet This is in regards to your search for force field comparisions. B. Smit, S. Karaborni, and J.I. Siepmann J. Chem Phys vol 102,no. 5 pp 2126-2140 1995 This paper compares the models of Jorgensen (OPLS), de Pablo,Toxvaerd, and proposes a new model. Gibbs ensemble monte carlo is used to determine the phase diagrams of linear alkanes as the test of the forcefields. Marcus Martin Siepmann group University of MN - twin cities ____________________________________ -- = Alexandre HOCQUET Laboratorio de Cristalograf=EDa Facultad de Ciencias F=EDsicas Universidad de Chile Blanco Encalada, 2008 Santiago Chile fax : 56 2 696 73 59 email : ahocquet@tamarugo.cec.uchile.cl From tfe@rzlimes.gbf-braunschweig.de Tue Nov 12 13:13:02 1996 Received: from rzgate.gbf-braunschweig.de for tfe@rzlimes.gbf-braunschweig.de by www.ccl.net (8.8.2/950822.1) id MAA25397; Tue, 12 Nov 1996 12:24:07 -0500 (EST) Received: (from uucp@localhost) by rzgate.gbf-braunschweig.de (8.6.9/8.6.9) id SAA23884 for ; Tue, 12 Nov 1996 18:23:50 +0100 Received: from rzlimes.gbf-braunschweig.de(1.1.1.233) by rzgate.gbf-braunschweig.de via smap (V1.3) id sma023880; Tue Nov 12 18:23:27 1996 Received: from msftfe (MSFTFE.gbf-braunschweig.de [1.1.2.9]) by rzlimes.gbf-braunschweig.de (8.6.12/8.6.12/bs01) with SMTP id SAA15485 for ; Tue, 12 Nov 1996 18:23:27 +0100 Message-Id: <199611121723.SAA15485@rzlimes.gbf-braunschweig.de> Comments: Authenticated sender is From: "Till Fechteler" To: CHEMISTRY@www.ccl.net Date: Tue, 12 Nov 1996 18:23:33 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Conformational search code Reply-to: fechteler@GBF-Braunschweig.DE Priority: normal X-mailer: Pegasus Mail for Win32 (v2.42a) Hello, does anybody know if there exist conformational search procedures for protein structure prediction on the net. The code (FORTRAN, C or C++) should be in the public domain. Many thanks in advance, Till Fechteler ____________________________________________________________________ Till Fechteler Gesellschaft fuer Biotechnologische Forschung mbH Molekulare Strukturforschung Mascheroder Weg 1 D-38124 Braunschweig Telefon +49 (0531) 6181 374 Email fechteler@gbf-braunschweig.de _____________________________________________________________________ From serge@yorku.ca Tue Nov 12 14:12:56 1996 Received: from sunspot.ccs.yorku.ca for serge@yorku.ca by www.ccl.net (8.8.2/950822.1) id NAA25806; Tue, 12 Nov 1996 13:21:56 -0500 (EST) Received: from localhost (serge@localhost) by sunspot.ccs.yorku.ca (8.7.6/8.6.11) with SMTP id NAA07438; Tue, 12 Nov 1996 13:21:25 -0500 (EST) X-Authentication-Warning: sunspot.ccs.yorku.ca: serge owned process doing -bs Date: Tue, 12 Nov 1996 13:21:25 -0500 (EST) From: Serge Gorelsky X-Sender: serge@sunspot.ccs.yorku.ca To: rprf526-int cc: chemistry@www.ccl.net Subject: Re: CCL:M:MOPAC: parameters for transition metals In-Reply-To: <9610128478.AA847800745@intccop1.intevep.pdv.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII New version of Spartan has PM3(tm) with some transition metals. Atomic parameters for MOPAC can be obtained from corresponding Spartan's parameter files. ________________________________________________________________ Serge Gorelsky Inorganic Chemistry Laboratory Department of Chemistry, York University 4700 Keele St., North York, Toronto, Ontario M3J 1P3, Canada tel.(416) 736-2100 ext#77720 ________________________________________________________________ On Tue, 12 Nov 1996, rprf526-int wrote: > Collegues: > > I am looking for parameters of metals, mainly > transition ones, for MOPAC (MNDO or PM3) > I really appreciate any information! > > Regards, > > Manuel J. Goncalves > Proccess Department > Intevep > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: rprf526-int@intccop1.intevep.pdv.com > -- Original Sender From: Address: rprf526-int@intccop1.intevep.pdv.com > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html >