From bruno@copssg.univ-lyon1.fr Wed Mar 20 07:17:36 1996 Received: from copssg.univ-lyon1.fr for bruno@copssg.univ-lyon1.fr by www.ccl.net (8.7.1/950822.1) id HAA14968; Wed, 20 Mar 1996 07:17:14 -0500 (EST) Received: by copssg.univ-lyon1.fr (950911.SGI.8.6.12.PATCH825/930416.SGI) for CHEMISTRY@www.ccl.net id NAA19407; Wed, 20 Mar 1996 13:17:08 +0100 From: "Bruno Fong-Ponne" Message-Id: <9603201317.ZM19405@copssg.univ-lyon1.fr> Date: Wed, 20 Mar 1996 13:17:07 +0100 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Retrieved eigenvalues from gaussian94 output files Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="PART-BOUNDARY=.19603201317.ZM19405.univ-lyon1.fr" -- --PART-BOUNDARY=.19603201317.ZM19405.univ-lyon1.fr Content-Type: text/plain; charset=us-ascii Dear CClers, I perform some g94 abinitio calculation trough the Sybyl6.2 software to evaluate the charges of a "gamma dodecalactone". The dat file from sybyl is : %chk=g12r_g94_1903.chk # HF/6-31G OPT POP=CHELPG SCFCYC=120 0 1 8 6 1 R2 6 2 R3 1 A3 6 3 R4 2 A4 1 T4 6 1 R5 2 A5 3 T5 1 2 R6 1 A6 3 T6 6 2 R7 1 A7 3 T7 1 3 R8 2 A8 1 T8 1 3 R9 2 A9 1 T9 1 4 R10 3 A10 2 T10 1 4 R11 3 A11 2 T11 8 5 R12 1 A12 2 T12 1 7 R13 2 A13 1 T13 6 7 R14 2 A14 1 T14 1 7 R15 2 A15 1 T15 6 14 R16 7 A16 2 T16 1 14 R17 7 A17 2 T17 1 14 R18 7 A18 2 T18 6 16 R19 14 A19 7 T19 1 16 R20 14 A20 7 T20 1 16 R21 14 A21 7 T21 6 19 R22 16 A22 14 T22 1 19 R23 16 A23 14 T23 1 19 R24 16 A24 14 T24 6 22 R25 19 A25 16 T25 1 22 R26 19 A26 16 T26 1 22 R27 19 A27 16 T27 6 25 R28 22 A28 19 T28 1 25 R29 22 A29 19 T29 1 25 R30 22 A30 19 T30 6 28 R31 25 A31 22 T31 1 28 R32 25 A32 22 T32 1 28 R33 25 A33 22 T33 1 31 R34 28 A34 25 T34 1 31 R35 28 A35 25 T35 1 31 R36 28 A36 25 T36 variables are R2 R5 R7 R12 A7 T4 T5 T7 T12 T19 The problem occurs when I'M trying to retrieve the total energy with sybyl : i've got : The total energy could not be retrieved from the output file. Examine the output file for errors or problems. The eigenvalues could not be retrieved from the output file. Examine the output file for errors or problems. the last set of eigenvalues is : Berny optimization. Search for a local minimum. Step number 10 out of a maximum of 216 All quantities printed in internal units (Hartrees-Bohrs-Radians) Update second derivatives using information from points 5 6 7 8 9 10 Trust test= 1.02D+00 RLast= 3.14D-03 DXMaxT set to 7.07D-01 Eigenvalues --- 0.00191 0.00411 0.00474 0.00493 0.00494 Eigenvalues --- 0.00495 0.00497 0.00499 0.00603 0.00957 Eigenvalues --- 0.02578 0.03510 0.03574 0.03577 0.03582 Eigenvalues --- 0.03583 0.03609 0.03644 0.03650 0.04119 Eigenvalues --- 0.04792 0.04901 0.04913 0.04915 0.04917 Eigenvalues --- 0.04918 0.04948 0.04959 0.05372 0.05550 Eigenvalues --- 0.05644 0.05676 0.06258 0.07069 0.08157 Eigenvalues --- 0.08388 0.08415 0.08463 0.08481 0.08494 Eigenvalues --- 0.08496 0.08506 0.08565 0.08881 0.11342 Eigenvalues --- 0.12209 0.12272 0.12290 0.12304 0.12306 Eigenvalues --- 0.12314 0.12409 0.15546 0.15927 0.16000 Eigenvalues --- 0.16027 0.20315 0.21825 0.21907 0.21909 Eigenvalues --- 0.21914 0.21917 0.22233 0.23079 0.23312 Eigenvalues --- 0.26196 0.28022 0.29279 0.29643 0.30152 Eigenvalues --- 0.30312 0.30318 0.30348 0.30398 0.30529 Eigenvalues --- 0.31008 0.32312 0.32605 0.32696 0.32722 Eigenvalues --- 0.32733 0.32734 0.32735 0.32738 0.32741 Eigenvalues --- 0.32747 0.32754 0.32784 0.32793 0.32843 Eigenvalues --- 0.32978 0.33082 0.33182 0.33514 0.33807 Eigenvalues --- 0.33874 0.33895 0.34265 0.36248 0.40330 Eigenvalues --- 0.47765 1.003721000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.000001000.000001000.000001000.00000 Eigenvalues --- 1000.000001000.00000 They seems to be very strange for me but I 'm not very familiar with ab initio. So I would very pleased to know what's wrong with my datas. Thanks in advance -- Bruno Fong-Ponne LCOPS Universite Claude Bernard tel (+33) 72 43 11 39 43 BD du 11 novembre 1918 fax (+33) 72 43 81 36 F-69622 Villeurbanne e-mail bruno@copssg.univ-lyon1.fr FRANCE --PART-BOUNDARY=.19603201317.ZM19405.univ-lyon1.fr X-Zm-Content-Name: g12r_g94_1903.dat Content-Description: Text Content-Type: text/plain ; name="g12r_g94_1903.dat" ; charset=us-ascii %chk=g12r_g94_1903.chk # HF/6-31G OPT POP=CHELPG SCFCYC=120 geometrie de depart obtenue par mopac PM3 chrg 0 1 8 6 1 R2 6 2 R3 1 A3 6 3 R4 2 A4 1 T4 6 1 R5 2 A5 3 T5 1 2 R6 1 A6 3 T6 6 2 R7 1 A7 3 T7 1 3 R8 2 A8 1 T8 1 3 R9 2 A9 1 T9 1 4 R10 3 A10 2 T10 1 4 R11 3 A11 2 T11 8 5 R12 1 A12 2 T12 1 7 R13 2 A13 1 T13 6 7 R14 2 A14 1 T14 1 7 R15 2 A15 1 T15 6 14 R16 7 A16 2 T16 1 14 R17 7 A17 2 T17 1 14 R18 7 A18 2 T18 6 16 R19 14 A19 7 T19 1 16 R20 14 A20 7 T20 1 16 R21 14 A21 7 T21 6 19 R22 16 A22 14 T22 1 19 R23 16 A23 14 T23 1 19 R24 16 A24 14 T24 6 22 R25 19 A25 16 T25 1 22 R26 19 A26 16 T26 1 22 R27 19 A27 16 T27 6 25 R28 22 A28 19 T28 1 25 R29 22 A29 19 T29 1 25 R30 22 A30 19 T30 6 28 R31 25 A31 22 T31 1 28 R32 25 A32 22 T32 1 28 R33 25 A33 22 T33 1 31 R34 28 A34 25 T34 1 31 R35 28 A35 25 T35 1 31 R36 28 A36 25 T36 R2 = 1.44020 R5 = 1.36993 R7 = 1.52956 R12 = 1.20736 A7 = 109.3301 T4 = -12.7504 T5 = 9.4068 T7 = 122.0163 T12 = 177.7497 T19 = 179.6816 R3 = 1.54891 R4 = 1.52664 R6 = 1.11423 R8 = 1.10625 R9 = 1.10364 R10 = 1.10502 R11 = 1.10547 R13 = 1.10876 R14 = 1.52045 R15 = 1.10875 R16 = 1.52062 R17 = 1.10856 R18 = 1.10912 R19 = 1.52028 R20 = 1.10873 R21 = 1.10872 R22 = 1.52036 R23 = 1.10886 R24 = 1.10866 R25 = 1.52013 R26 = 1.10875 R27 = 1.10873 R28 = 1.52061 R29 = 1.10869 R30 = 1.10860 R31 = 1.51218 R32 = 1.10822 R33 = 1.10816 R34 = 1.09736 R35 = 1.09816 R36 = 1.09805 A3 = 107.5517 A4 = 104.9041 A5 = 109.7757 A6 = 105.1659 A8 = 111.4557 A9 = 111.2951 A10 = 112.7308 A11 = 112.6036 A12 = 114.4165 A13 = 110.4049 A14 = 111.4122 A15 = 108.9040 A16 = 111.1253 A17 = 109.9486 A18 = 110.1637 A19 = 111.1743 A20 = 110.0676 A21 = 109.9662 A22 = 111.3297 A23 = 109.9243 A24 = 109.9806 A25 = 111.2852 A26 = 109.9406 A27 = 109.9643 A28 = 111.3890 A29 = 109.9735 A30 = 109.9723 A31 = 111.4362 A32 = 109.8488 A33 = 109.8852 A34 = 111.2955 A35 = 111.5947 A36 = 111.6534 T6 = -119.0318 T8 = 107.8176 T9 = -134.4223 T10 = 131.4979 T11 = -108.4989 T13 = -44.5967 T14 = 77.9023 T15 = -161.0369 T16 = 177.8882 T17 = -60.0575 T18 = 55.8900 T20 = -58.1899 T21 = 57.6716 T22 = 179.5675 T23 = -58.3582 T24 = 57.4207 T25 = 179.5919 T26 = -58.2938 T27 = 57.4843 T28 = 179.6577 T29 = -58.2355 T30 = 57.5282 T31 = 179.5958 T32 = -58.2448 T33 = 57.4147 T34 = 179.6741 T35 = 59.6787 T36 = -60.3754 --PART-BOUNDARY=.19603201317.ZM19405.univ-lyon1.fr-- From pachterr@ml.wpafb.af.mil Wed Mar 20 10:17:36 1996 Received: from riker.ml.wpafb.af.mil for pachterr@ml.wpafb.af.mil by www.ccl.net (8.7.1/950822.1) id JAA17265; Wed, 20 Mar 1996 09:19:09 -0500 (EST) Received: from cliff.ml.wpafb.af.mil by riker.ml.wpafb.af.mil (5.65/Ultrix3.0-C) id AA12593; Wed, 20 Mar 1996 09:19:05 -0500 Received: by ml.wpafb.af.mil; id AA12650; Wed, 20 Mar 1996 09:19:01 -0500 Alternate-Recipient: allowed Auto-Forwarded: prohibited Content-Return: allowed Disclose-Recipients: prohibited Conversion: prohibited Importance: normal Priority: normal Sensitivity: Company-Confidential Subject: Final Call for Papers From: Ruth Pachter To: chemistry@www.ccl.net (Reply requested) Message-Id: <960320091859.628@cliff.ml.wpafb.af.mil.0> Date: Wed, 20 Mar 96 09:19:00 -0500 X-Mailer: MAILworks 1.7-A-1 Final Call for Papers 212th National American Chemical Society Meeting COMP Division August 25-30, 1996, Orlando, Florida GLOBAL ENERGY MINIMIZATION AND PROTEIN FOLDING Abstracts Due April 15, 1996 A symposium entitled "Global Energy Minimization and Protein Folding" will be held at the ACS Meeting in Orlando, Florida, during August 25-30, 1996. Topics will comprise, among others, of algorithms for global optimization, aspects of parallel computing, new methods for the prediction of secondary and tertiary structure, and large scale molecular dynamics and molecular mechanics simulations. A partial list of invited speakers includes: B. Eskow (University of Colorado); C. A. Floudas (Princeton University); R. Judson (Sandia National Laboratories); J. Onuchic (University of California, San Diego); H. A. Scheraga (Cornell University); J. Straub (Boston University); D. Thirumalai (University of Maryland); A. Tropsha (University of North Carolina). Submit Abstracts by April 15 to: Dr. Ruth Pachter Materials Directorate, Wright Laboratory WL/MLPJ, 3005 P St. Suite 1 Wright-Patterson AFB, Ohio 45433-7702 Tel: (513) 255-6671x3158 Fax: (513) 255-1128 E-mail: pachterr@ml.wpafb.af.mil Obtain Abstract Forms from ACS: 7by calling 1-800-227-5558 (press 9-4-0) by writing to: 7American Chemical Society 1155 Sixteenth Street, N.W. Washington, D.C. 20036 7via the World-Wide Web: htpp:3/18/96/www.acs.org/memgen/meetings/abrqst.htm From Eugene.Leitl@lrz.uni-muenchen.de Wed Mar 20 11:17:37 1996 Received: from cd1.lrz-muenchen.de for Eugene.Leitl@lrz.uni-muenchen.de by www.ccl.net (8.7.1/950822.1) id KAA20275; Wed, 20 Mar 1996 10:45:13 -0500 (EST) Received: from sun2.lrz-muenchen.de by cd1.lrz-muenchen.de; Wed, 20 Mar 96 15:49:20 +0100 Received: by sun2.lrz-muenchen.de (5.x/SMI-SVR4) id AA29974; Wed, 20 Mar 1996 15:49:08 +0100 Date: Wed, 20 Mar 1996 15:49:08 +0100 (MET) From: Eugene Leitl X-Sender: ui22204@sun2 Cc: chemistry@www.ccl.net Subject: CCL: any mechanosynthesis specialists in here? In-Reply-To: <9603191528.ZM20454@dax.sci.port.ac.uk> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone mechanosynthesis computations, meaning AFM/STM tip chemistry in here? Thanks, -- Eugene From Steven.Creve@chem.kuleuven.ac.be Wed Mar 20 11:26:01 1996 Received: from hartree.quantchem.kuleuven.ac.b for Steven.Creve@chem.kuleuven.ac.be by www.ccl.net (8.7.1/950822.1) id KAA20276; Wed, 20 Mar 1996 10:45:21 -0500 (EST) Received: by hartree.quantchem.kuleuven.ac.be id AA36156 (5.67b/IDA-1.5 for Computational Chemistry List ); Wed, 20 Mar 1996 16:44:46 +0100 Date: Wed, 20 Mar 1996 16:44:44 +0100 (NFT) From: Steven Creve X-Sender: steven@hartree To: Computational Chemistry List Subject: CCL:problems with DFT Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, From my own work and that of others, is has emerged that DFT has problems in investigating transition structures for H-radical reactions (additions and eliminations) with a low energy barrier. Often, the lack of exact Hartree-Fock exchange in some functionals is blamed for this. I ask you all, if you have any references on this matter, let me know. I'll summarize to the net. Steven, -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie steven@hartree.quantchem.kuleuven.ac.be Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From groeger@hp9000.hrz.uni-oldenburg.de Wed Mar 20 12:17:39 1996 Received: from hp9000.hrz.uni-oldenburg.de for groeger@hp9000.hrz.uni-oldenburg.de by www.ccl.net (8.7.1/950822.1) id MAA21416; Wed, 20 Mar 1996 12:01:33 -0500 (EST) Received: from [134.106.36.108] by hp9000.hrz.uni-oldenburg.de (8.6.12/1.1.3) with SMTP id QAA10230 for ; Wed, 20 Mar 1996 16:47:02 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Date: Wed, 20 Mar 1996 16:57:08 +0000 To: chemistry@www.ccl.net From: groeger@uni-oldenburg.de (Harald Groeger) Subject: TS of phosphite anions addition reactions Hi all, does anyone have informations about calculations of TS of phosphite anion addition to C=3DX bonds (X =3D O,N) using semiempirical methods ? Any information would be greatly appreciated. =46urthermore any references to semiempirical calculations on phosphite anions and derivatives would be most welcome. I will summarize the responses to the net. Thanks in advance to all responders, Harald ---------------------------------------------------------------------------- ---------- Harald Groeger =46achbereich Chemie Universit=E4t Oldenburg Postfach 2503 26111 Oldenburg Germany E-Mail: groeger@hp9000.hrz.uni-oldenburg.de ---------------------------------------------------------------------------- ---------- From WILLSD@conrad.appstate.edu Wed Mar 20 13:17:43 1996 Received: from listserv.appstate.edu for WILLSD@conrad.appstate.edu by www.ccl.net (8.7.1/950822.1) id MAA21519; Wed, 20 Mar 1996 12:20:25 -0500 (EST) Received: from spd.appstate.edu ([152.10.1.23]) by listserv.appstate.edu with ESMTP id <13720-151>; Wed, 20 Mar 1996 12:20:09 -0500 Received: from conrad.appstate.edu by conrad.appstate.edu (PMDF V5.0-6 #8642) id <01I2K7YY2SVKAFU5BQ@conrad.appstate.edu>; Wed, 20 Mar 1996 12:19:49 -0400 (EDT) Date: Wed, 20 Mar 1996 12:19:46 -0400 (EDT) From: willsd@conrad.appstate.edu Subject: Transition States & Unichem (Summary) To: CHEMISTRY@www.ccl.net Cc: mw8519 Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT Many thanks to all who responded to my question about using unichem in the search for transition states. The responses fell into two categories: 1) don't use unichem for this (at least not without help from some other program), and 2) look at url xxx for information on general features of ts searching. The urls were quite helpful.... The original post was: I would like to learn about using unichem (initially just the semi-empirical methods, but later dgauss and/or gaussian) to model transition states. I thought a simple case to start with would be the keto-enol transition state for 2-butanone. In MOPAC and gaussian there are methods to help get close to the transition state (saddle and lst or qst) that start with initial state and final state geometries. Unichem does have an option to optimize to a transistion state, but seems to lack the tools needed to find an approximate structure that is close enough for the optimizer to take over. I have made several unsucessful attempts at "guessing" what this ts might look like, but so far have not found a good enough guess. I am using unichem's implementation of am1, and so far have only found structures whose gradients are too large for computation of frequencies, and so I have no confidence that I have found the ts. Any suggestions? ******************************************************************** Just a simple suggestion based on my own limited experience: if the reaction coordinate can be expressed in a realatively simple way in terms of the length of a single interatomic distance (eg, H---O), then a reaction coordinate driving process, which constrains and optimizes the structure at successively smaller (or larger) distances can often be a quick and easy way to find the approximate TS. Why not give it a try. Eilert Ofstead ************************************************************************** I am also using programs such as MOPAC and Gaussian to calculate transition states (hetero Diels-Alder) and have found very quickly that manuals and other peoples experience in the area is very limited. I would be greatful if you could share and answers that are passed to you directly, avoiding CCL. If you have any problems in the future with Gaussian, try doug.fox@gaussian.com as he has been very helpful to me. Yours Carl Windsor ********************************************************************* Please do not use my name or my affiliation if you happen to summarize the answers to your question. The straightforward answer to your question about doing transition state optimizations in the Unichem package is ... don't do it! Use Mopac if you wish for semiempirical methods or use Gaussian for molecular orbital and DFT methods. Experience has shown me that the transition state optimizer is NOT robust at all in the Unichem package for either the semiempirical or DFT methods. Someday this will change, I'm sure. ******************************************************************** Re the query about finding the 2-butanone keto/enol TS: one possibility is to find the keto/enol TS for the _simplest_ keto/enol tautomerization, ethanal/ ethenol (acetaldehyde/ vinyl alcohol), then replace the appropriate H's by CH3 groups, and subject this new structure to a TS optimization. Errol Lewars ******************************************************************* Yes, it's true UniChem lacks multi-structure input routines. Given that semiempirical methods that have them require a half-guess at the structure to not thrash [or at least they have in my cases!] You might be best off doing a reaction coordinate. If you absolutely insist on having Unichem do your z-matrix, instead of doing it by hand, get Babel to let you convert to a z-matrix you can manipulate to vary the reaction coordinate. Using the structure closest to the TS in UniChem [use Babel to convert it to PDB so UniChem can read it] may work. Another approach is to use a known TS as a guess for yours. I believe that Warren Hehre & co-workers give such a structure in some of the books they've written for use with the Spartan code - you can do most of the exercises they give with UniChem, & they give LOTS of examples of TS's for organic reactions. If you don't have access to the books, I recommend a lit. search for an analogous TS to use as an initial guess. Good luck! Irene Newhouse ********************************************************************* I don't know exactly about Unichem, but why use it if MOPAC itself has provisions to locate a TS? You can do grid search by varying two variables, which could be C--H and O--H distances in this case. Gnuplot will even make a plot of the output, if the grid of numbers isn't enough. This procedure will allow you to get very close to the TS, from you can apply the TS keyword. Exactly this procedure is the subject of a www course I composed: http://www.caos.kun.nl/~borkent/compcourse/comp.html Best regards, ***** J.H. (Hens) Borkent, CAOS/CAMM Center, ***************************************************************** Why not have a look at the WWW pages I have setup that include a number of TSs (fully optimized and characterized) from PM3 and AM1 calculations. These should give you a good starting point for experimentation on a number of derivatives or alternative parameter sets. If you (or anyone else for that matter) has TSs that there willing to share with others I would welcome them being deposited at this location. The URL is: http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm Addtionally, if you (or anyone else) generates TSs via semi-empirical methods I would be prepared to help generate an animation sequence and multi-structure file of the reaction being simulated. Please contact me if your interested. Dr. Jeff Gosper *********************************************************************** Hi I'm using Dgauss for TS, but my way to obtain TS structure is via MOPAC . First of all I prepare the approximation of TS by AM1 or PM3 method than I do calculation using DGauss or Gamess. I send you the TS state for this reactinon obtained by MOPAC. Stanislaw Oldziej am1 results snipped out..... ************************END of SUMMARY************************* So, I tried some of the listed ts structures in the web pages and found that unichem's semi-empirical methods would verify that these were in fact ts structures, when I asked unichem to optimize to a transition state (starting from a structure that was very, very close..) the semi-empirical code converged to a quite different, energy minimum structure. The ts optimizer for DGAUSS was more robust and would optimize to a ts, given a good initial guess and a semi-empirical hessian... The web pages of Borkent and Gosper referred to above were particularly helpful. I will stick to MOPAC and Gaussian (and perhaps DGAUSS) for this sort of work. Steve Williams Chemistry ASU Boone, NC 28608 From klein@cgl.ucsf.EDU Wed Mar 20 14:17:39 1996 Received: from socrates.ucsf.EDU for klein@cgl.ucsf.EDU by www.ccl.net (8.7.1/950822.1) id NAA23164; Wed, 20 Mar 1996 13:27:36 -0500 (EST) From: Received: (from klein@localhost) by socrates.ucsf.EDU (8.7.3/GSC4.25) id KAA17467; Wed, 20 Mar 1996 10:27:16 -0800 (PST) Date: Wed, 20 Mar 1996 10:27:16 -0800 (PST) Message-Id: <199603201827.KAA17467@socrates.ucsf.EDU> To: announce@santafe.edu, chemistry@www.ccl.net Subject: Modern Concepts in Macromolecular Modeling (Call for Papers) Call for Papers Modern Concepts in Macromolecular Modeling Pacific Symposium on Biocomputing (http://cgl.ucsf.edu/psb) Ritz-Carlton Kapalua, Maui, Hawaii January 6-9, 1997 Co-chairs Chairs: Jurgen Bajorath, Bristol-Myers Squibb Research Institute Teri E. Klein, University of California, San Francisco The Pacific Symposium on Biocomputing (PSB-97) is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. We are currently soliciting manuscripts for a highly interactive workshop-like session "Modern Concepts in Macromolecular Modeling" and/or abstracts for an accompanying poster session. The session will assess state-of-the-art approaches in the area of macromolecular modeling, in particular protein modeling, to highlight their opportunities, caveats, and limitations. Contributions which introduce or illustrate novel computational methods and which present contemporary applications are equally encouraged. Scientific focal points include: * the development and application of various energy functions for - analysis of the energetics and dynamics of macromolecular structures and their interactions - protein fold recognition - ab initio folding of proteins on the computer - evaluation and assessment of molecular models * techniques to construct protein models in the presence of "twilight zone" sequence similarities such as - analysis of multiple sequences and/or structures - generation of sequence-structure alignments - interactive or automated computer modeling programs Scientific context: While the use of predictive methods to generate and analyze three-dimensional models is increasing, the objectives of such modeling and the problems involved are changing. Classical homology modeling on the basis of significant sequence similarity has more or less introduced macromolecular modeling at times when only a rather limited number of experimentally determined protein structures were available. The scenario has changed dramatically. Many more structures have been determined, and it is a significant task in itself to compare, analyze, and classify these structures. It has become possible to study many intra- and intermolecular interactions in detail, and much effort is currently being spent to understand such interactions in more quantitative energetic terms; be it on the basis of various (free) energy calculations or automated docking procedures. Implications of these studies for drug or protein design are evident. Sequence databases grow at even much faster pace than structural databases, and this is considered a major reason for the increasing interest in modeling. However, popular targets of protein modeling attempts often display, if at all, low or barely detectable sequence similarities to known structures. In these cases, it is difficult to establish structural relationships, even if they exist, and to identify structural templates for modeling. The advent of inverse folding and fold recognition methods has changed the approach to some of these problems. Nevertheless, to apply the results of a fold recognition study, to generate a precise and global sequence-structure alignment, and to actually build a model remains difficult and still requires many subjective decisions. In parallel to novel structure-based or comparative approaches, computational ab initio folding of (small) proteins is, for the first time, successfully performed, albeit at still limited resolution. INSTRUCTIONS FOR AUTHORS PSB '97 will publish peer-reviewed full papers in an archival proceedings. Each accepted paper will be allocated 12 pages in the proceedings volume. Manuscripts adhering to the guidelines set forth on the the PSB web pages will be accepted. Full papers must not have been previously presented or published, nor currently submitted for journal publication. Once accepted to the conference, a paper may be submitted for journal publication. Each manuscript will be refereed by at least four reviewers. Due dates -------------- May 15, 1996 300 word abstract to bajorath@protos.bms.com June 15, 1996 Five copies of the manuscript August 15, 1996 Notification of accepted papers September 15, 1996 Accepted camera ready manuscripts Five copies of all full papers must be submitted to: PSB-97 c/o Section on Medical Informatics Stanford University Medical School, MSOB X215 Stanford, CA 94305-5479 USA Authors who do not wish to submit a full paper are welcome to submit 1-2 page abstract adhering to the guidelines set forth on the PSB web pages, which will be distributed at the meeting separately from the archival proceedings. Due dates -------------- May 15, 1996 300 word abstract to bajorath@protos.bms.com August 15, 1996 Notification of accepted abstract/poster September 15, 1996 Accepted camera ready abstract Please send abstracts and questions regarding this session to: Jurgen Bajorath Bristol-Myers Squibb Res. Inst. 3005 First Avenue Seattle, WA 98121 bajorath@protos.bms.com klein@cgl.ucsf.edu Tel (206) 727-3612 Fax (206) 727-3602 For more information on the Pacific Symposium on Biocomputing, please see our web site at http://cgl.ucsf.edu/psb or contact: Ms. Sharon Surles PSB Coordinator Interactive Simulations, Inc. 5330 Carroll Canyon Road, Suite 203 San Diego, CA 92121 psb@intsim.com Phone: +1 (619) 658-9782 FAX: +1 (619) 658-9463 From JOHNSONB@B.PSC.EDU Wed Mar 20 16:17:50 1996 Received: from B.PSC.EDU for JOHNSONB@B.PSC.EDU by www.ccl.net (8.7.1/950822.1) id QAA25657; Wed, 20 Mar 1996 16:09:30 -0500 (EST) Date: Wed, 20 Mar 1996 16:08:57 -0500 (EST) From: JOHNSONB@CPWSCA.PSC.EDU To: Steven.Creve@chem.kuleuven.ac.be CC: JOHNSONB@CPWSCA.PSC.EDU, chemistry@www.ccl.net Message-Id: <960320160857.2020597e@CPWSCA.PSC.EDU> Subject: Re: Problems with DFT for reaction barriers Dear Dr. Creve, >From my own work and that of others, is has emerged that DFT has problems >in investigating transition structures for H-radical reactions (additions >and eliminations) with a low energy barrier. Often, the lack of exact >Hartree-Fock exchange in some functionals is blamed for this. We published a study on this type of problem after finding that regular Kohn-Sham DFT is generally a complete failure for radical H abstractions. We took a step back and examined the simplest such reaction, H + H2 -> H2 + H, and found that much of the problem can be traced to the spurious self-interaction of the electrons in approximate density functionals. The effect can be dramatic: for the LSDA, regular KS theory predicts H3 to be *stable* with respect to H + H2 (!) but after a simple approximate self-interaction correction (SIC) to the potential surface the transition structure was restored. The reference is B.G. Johnson, C.A. Gonzalez, P.M.W. Gill and J.A. Pople, Chem. Phys. Lett. 221, 100 (1994). I don't really agree with the lack of HF exchange as the explanation for the poor performance of DFT in the case of reaction barriers. "Hybrid" functionals like B3LYP have been shown to give good results on some reaction barriers in practice, but it is worrisome that the methods being mixed in these hybrids, i.e. Hartree-Fock and pure DFT, give reaction barriers which are significantly higher than experiment in one case (HF) and significantly lower than experiment in the other (DFT). This leads one to wonder whether the good hybrid results simply come from fortuitous cancellation of errors -- the effect of the spurious residual self-energy in DFT roughly cancelling that of the neglect of electron correlation in Hartree-Fock. Having said this, SIC is certainly more difficult and expensive to do rigorously in practice than to use a hybrid HF-DFT functional; I do think, though, that one should be cautious of the results when using hybrid methods for this type of problem, for the reasons mentioned above. Regards, Benny Johnson ------------------------------------------------------------------------------- Benny G. Johnson, Ph.D. Phone: (412) 828-7106 President Fax: (412) 828-0483 Q-Chem, Inc. E-mail: johnsonb@psc.edu 317 Whipple St. Pittsburgh, PA 15218 USA ------------------------------------------------------------------------------- From insenk@sbu.ac.uk Wed Mar 20 17:24:24 1996 Received: from psb.sbu.ac.uk for insenk@sbu.ac.uk by www.ccl.net (8.7.1/950822.1) id QAA26435; Wed, 20 Mar 1996 16:39:54 -0500 (EST) From: Received: from HYDRA (BIG::SYSTEM) by PSB (MX V4.2 VAX) with SMTP (DECnet); Wed, 20 Mar 1996 21:40:11 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Wed, 20 Mar 1996 21:39:17 GMT Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Wed, 20 Mar 1996 21:38:23 GMT Received: from PSB (PSB::SYSTEM) by BIG (MX V4.1 VAX) with SMTP (DECnet); Sat, 16 Mar 1996 05:03:07 GMT Received: from www.ccl.net by psb.sbu.ac.uk (MX V4.1 VAX) with SMTP; Fri, 15 Mar 1996 23:47:21 GMT Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.1/950822.1) id SAA00051; Fri, 15 Mar 1996 18:17:19 -0500 (EST) Received: from harfang.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.7.1/950822.1) id SAA29965; Fri, 15 Mar 1996 18:00:57 -0500 (EST) Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by harfang.CC.UMontreal.CA with ESMTP id RAA28647 (8.6.11/IDA-1.6 for ); Fri, 15 Mar 1996 17:59:56 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id RAA06688; Fri, 15 Mar 1996 17:59:56 -0500 Received: by cyclone.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id RAA13452; Fri, 15 Mar 1996 17:59:55 -0500 Date: Fri, 15 Mar 1996 17:59:55 -0500 Message-ID: <199603152259.RAA13452@cyclone.ERE.UMontreal.CA> To: CHEMISTRY@www.ccl.net Subject: CCL:File format question Originally-From: hinsenk@ere.umontreal.ca I am trying to prepare a somewhat special picture with XMol. To do so I must be able to feed connectivity information into the program. But the only two file formats understood by XMol for which I have documentation are PDB and XYZ. XYZ does not allow connectivity data, and the PDB connectivity records seem to be ignored by XMol. Therefore I am looking for a file format that satisfies the following requirements: 1) It is understood by XMol, including connectivity information. 2) Its description is publicly available. Any help would be greatly appreciated. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. Centre-Ville | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: hinsenk@ERE.UMontreal.CA -- Original Sender From: Address: hinsenk@ERE.UMontreal.CA 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 From aholder@cctr.umkc.edu Wed Mar 20 17:29:19 1996 Received: from axp2.umkc.edu for aholder@cctr.umkc.edu by www.ccl.net (8.7.1/950822.1) id QAA26402; Wed, 20 Mar 1996 16:36:50 -0500 (EST) Received: from andy.chem.umkc.edu (holder.chem.umkc.edu) by axp2.umkc.edu (MX V4.1 AXP) with SMTP; Wed, 20 Mar 1996 15:36:33 CST X-Mailer: InterCon TCP/Connect II 2.3.1 MIME-Version: 1.0 Message-ID: <9603201536.AA27234@andy.chem.umkc.edu> Date: Wed, 20 Mar 1996 15:36:27 -0500 From: "Andy Holder" To: chemistry@www.ccl.net Subject: ** Visit Semichem at ACS ** Content-Type: Multipart/Mixed;boundary=part_AD75D67B000223BD00000001 --part_AD75D67B000223BD00000001 Content-Type: Text/Plain; charset=US-ASCII Content-Disposition: Inline ********************************************************* * Come and Visit Semichem in Booth 1328 in New Orleans! * ********************************************************* Semichem will be showing AMPAC 5.1 with Graphical User Interface and our new QSAR offering, CODESSA. CODESSA is a state-of-the-art QSAR/QSPR program that will allow you to extract descriptor data directly from your AMPAC files. CODESSA also computes many of the popular topological and reactivity indices directly. CODESSA's statistical package automates correlation anal- ysis and allows speedy and meanigful interpretation and development of models to fit your specific needs. Spend your time thinking rather than doing time-consuming and tedious clerical tasks! Make the right choices the first time, integrating all of the knowledge available to you. AMPAC 5.1 with GUI has several new features including enhanced support for GAUSSIAN file formats and increased speed and robustness in the configuration interation (CI), geometry optimization and SCF convergence sections. Also, AMPAC includes the SAM1 semiempirical method, which explicitly treats d-orbitals. Current parameter sets for SAM1 include the transition metals Cu and Fe. Ni, Ti, and Zn are slated for release in the near future. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER President Semichem, Inc. || Internet Addr: aholder@cctr.umkc.edu 7128 Summit || Phone Number: (913) 268-3271 Shawnee, KS, 66216 || FAX Number: (913) 268-3445 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= --part_AD75D67B000223BD00000001-- From sunger@A.crl.com Wed Mar 20 19:17:40 1996 Received: from A.crl.com for sunger@A.crl.com by www.ccl.net (8.7.1/950822.1) id SAA27503; Wed, 20 Mar 1996 18:35:13 -0500 (EST) Received: from [168.75.101.10] (A105012.sfo5.as.crl.com) by A.crl.com with SMTP id AA04859 (5.65c/IDA-1.5 for ); Wed, 20 Mar 1996 15:34:02 -0800 Date: Wed, 20 Mar 1996 15:34:02 -0800 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: sunger@a.crl.com (Stefan Unger) Subject: Online Resource for Commercial Life Sciences Software 3/20/96 BIO ONLINE OFFERS COMMERCIAL LIFE SCIENCE SOFTWARE THROUGH WORLD WIDE WEB Bio Online, a very popular web site dedicated to the biopharmaceutical industry (http://www.bio.com), has added an extensive, growing and convenient collection of life sciences-related software for sale in the Bio Online Marketplace Store. 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There are up-to-date news and events sections, corporate biotech directories, press releases, and product information, as well as hot-links to other Internet research, education and government sites. The site is sponsored by KPMG Peat Marwick, Heller Ehrman White & McAuliffe and Corning Pharmaceutical Services. Technical software is made available through a collaborative effort with BioSoftware Marketing. @@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@@#@@#@@#@@#@@#@@#@@#@@# Stefan Unger, Ph.D. President BioSoftware Marketing 4151 Middlefield Rd., Ste 109 Palo Alto, CA 94303-4743 sunger@a.crl.com BioSoftware Marketing specializes in a full range of marketing services (market studies to collateral design and production) for start-up and small technical software companies, especially biopharm related. E-mail your full mailing address to receive a full-color brochure describing these services. We also offer consulting on computer aided drug design and biological/chemical databases. Product Manager, Scientific Software, Bio Online Store (www.bio.com) @@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@#@@@#@@#@@#@@#@@#@@#@@# From smori@utsc.s.u-tokyo.ac.jp Wed Mar 20 20:17:41 1996 Received: from utsc.s.u-tokyo.ac.jp for smori@utsc.s.u-tokyo.ac.jp by www.ccl.net (8.7.1/950822.1) id TAA28282; Wed, 20 Mar 1996 19:56:24 -0500 (EST) Received: by utsc.s.u-tokyo.ac.jp (5.67+1.6W/TISN-1.3/R2) id AA07724; Thu, 21 Mar 96 09:55:17 JST Date: Thu, 21 Mar 96 09:55:17 JST From: Seiji Mori Message-Id: <9603210055.AA07724@utsc.s.u-tokyo.ac.jp> To: chemistry@www.ccl.net Subject: MacGridzo program Dear netters, I am looking for MacGridzo program when I am reading Gronert, et al. JOC, 1995, 60, 6731. It is contour generation program for Macintosh (?), Rockware Inc. Wheat Ridge, CO. In this program, which are QM calculation packages avalable other than PROAIM program? Where can I get this information from? (WWW, email) Seiji Mori ############################################################## Seiji Mori Graduate student in Nakamura Laboratory (Lab. of Physical Organic Chemistry) Department of Chemistry The University of Tokyo Hongo 7-3-1, Bunkyou-ku, Tokyo 113, JAPAN. email:smori@utsc.s.u-tokyo.ac.jp --- Now my homepage is under construction. http://www.chem.s.u-tokyo.ac.jp/personal/nakamuralab/smori.html ############################################################## From Bernd.Hartke@RUS.Uni-Stuttgart.DE Tue Mar 19 04:30 EST 1996 Received: from artemis.rus.uni-stuttgart.de for Bernd.Hartke@RUS.Uni-Stuttgart.DE by www.ccl.net (8.7.1/950822.1) id EAA24566; Tue, 19 Mar 1996 04:30:44 -0500 (EST) Received: from servus02.rus.uni-stuttgart.de (servus02-fd.rus.uni-stuttgart.de [129.69.18.202]) by artemis.rus.uni-stuttgart.de with SMTP id KAA09219 (8.6.12/IDA-1.6 for ); Tue, 19 Mar 1996 10:30:14 +0100 Received: from servus07.rus.uni-stuttgart.de by servus02.rus.uni-stuttgart.de (AIX 3.2/UCB 5.64/SERVus-1.2) id AA43804; Tue, 19 Mar 1996 10:30:14 +0100 Received: by servus07.rus.uni-stuttgart.de (AIX 3.2/UCB 5.64/4.03) id AA23465; Tue, 19 Mar 1996 10:30:13 +0100 From: Message-Id: <9603190930.AA23465@servus07.rus.uni-stuttgart.de> Subject: Re: pronunciation of conformer To: chemistry@www.ccl.net Date: Tue, 19 Mar 1996 10:30:12 +0100 (MEZ) Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Content-Length: 2852 Status: R Hello Fellow-CCL-ers, I feel the urge to add my $0.02 to the discussion on the pronunciation of "conformer". Let me emphasize from the outset that I am German; English was my second foreign language in school (after starting out with Latin and before continuing with ancient Greek - unfortunately, I do not remember much of my Latin and Greek, but it still helps me sometimes...). So far, it seems to me that all of you have missed one vital point: It is obviously correct that "conFORmer" (with or without capital "m") is the everyday ( = non-chemical) pronunciation of "conformer" as someone who conforms. In this sense, "conformer" is formed from its root "conform" (from con-formare in Latin, as correctly pointed out already -- note that the "m" belongs to the root!) in one of several possible ways to form nouns in English, namely by adding the suffix "-er" (as in "think" -> "thinker" or "wait" -> "waiter" etc.; we have almost the same mechanism in German). BUT: For the chemical meaning of "conformer" this analysis is not valid! As the analogy to "isomer" (and to all the other "-mer"'s in chemistry, like "monomer", "polymer", etc.) shows, the suffix "-mer" clearly is an entity with its own meaning since "iso-" (like "mono-", "poly-", etc.) merely is a simple prefix. The meaning of "-mer" can be found in English dictionaries that give some etymological background; for example, my "Collins Concise Dictionary" (English-English, not English-German) tells me this: "-mer": suffix forming nouns. denoting a substance of a particular class: monomer, polymer (from Greek: "meros" = part) Obviously, in forming the _chemical_ "conformer" from "con-form-" and "-mer" it is convenient (and commonplace) to drop one of the "m"'s, although this obscures the true origin and leads to confusion with the above analysis of "con-form-er" (someone who conforms). So much for the etymology. Since I am neither a native English speaker nor an expert in English but merely a German theoretical chemist who happens to know some English, you native English speakers have to settle the question of where to put the stress in "conformer" for yourself. Incidentally, in German we would say "konFORmer" for someone who conforms -- if we had such a word. But all German chemists say "/con/-for-MER" (secondary stress on first syllable, primary stress on the last; or "MOnoMER" with about equal stress on the first and last syllables). I guess this clever way out is not open for English chemists... Bernd -- Dr. Bernd Hartke e-mail: bernd.hartke@rus.uni-stuttgart.de Dep. of Theoretical Chemistry http://www.theochem.uni-stuttgart.de/~hartke University of Stuttgart Pfaffenwaldring 55 Phone: +49-711-685-4409 70569 Stuttgart FAX: +49-711-685-4442 GERMANY From polowin@hyper.hyper.com Tue Mar 19 11:50 EST 1996 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.7.1/950822.1) id LAA01669; Tue, 19 Mar 1996 11:50:49 -0500 (EST) Received: from hyper.hyper.com (hyper.hyper.com [204.50.97.9]) by www.hyper.com (8.6.12/8.6.12) with SMTP id MAA15631 for <@www.hyper.com:CHEMISTRY@www.ccl.net>; Tue, 19 Mar 1996 12:07:29 -0500 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:CHEMISTRY@www.ccl.net id AA22153; Tue, 19 Mar 96 12:07:18 -0500 Date: Tue, 19 Mar 96 12:07:18 -0500 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9603191707.AA22153@hyper.hyper.com> To: CHEMISTRY@www.ccl.net Subject: HyperChem Lite demo at ACS Content-Type: text Content-Length: 880 Status: R I'd like to jump on the promotional bandwagon and extend a brief invitation to those of you who will be attending the ACS conference in New Orleans to stop by the Hypercube booth, #929, in the exhibitors' area. We'll be showing off our new "HyperChem Lite" software package (and our new display booth). People who place orders at the show will receive their choice of a free HyperChem T-shirt or golf shirt. We'll have information and demo disks for HyperChem Lite at the show, and of course we can mail them on request. Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com WWW: http://www.hyper.com/ From topper@cooper.edu Wed Mar 20 16:09 EST 1996 Received: from magnum.cooper.edu for topper@cooper.edu by www.ccl.net (8.7.1/950822.1) id QAA25660; Wed, 20 Mar 1996 16:09:43 -0500 (EST) Received: from zeus.cooper.edu by magnum.cooper.edu with SMTP id AA09598 (5.65c/IDA-1.4.4 for ); Wed, 20 Mar 1996 16:09:32 -0500 Received: by zeus.cooper.edu id AA29564 (5.67b/IDA-1.5); Wed, 20 Mar 1996 16:05:06 -0500 From: TOPPER ROBERT Message-Id: <199603202105.AA29564@zeus.cooper.edu> Subject: WWW Molecular Monte Carlo Page To: CHEMISTRY@www.ccl.net Date: Wed, 20 Mar 1996 16:05:05 -0500 (EST) Cc: topper@cooper.edu, freeman@mozart.chm.uri.edu, truhlar@t1.chem.umn.edu X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Content-Length: 2157 Status: R Dear colleagues, On the eve of the ACS meeting, which will feature a special session on Monte Carlo methods in the COMP division, we wish to announce the opening of a new World-Wide-Web resource for information on Monte Carlo simulations, random walks, and their applications in molecular modeling. In the Molecular Monte Carlo home page, we plan to highlight the research efforts of those who have provided descriptions of their research programs on the web by providing links to their sites. This will help to improve communication between the various groups who are using these methods. We also provide pointers to sites containing useful numerical tools for practitioners of stochastic methods, like random number generators, etc.. Finally, in the near future we hope to establish a series of hypertext tutorials on various stochastic methods, such as the Metropolis algorithm, brownian dynamics, GLE dynamics and other, related methods. Submissions to the page (including tutorials and graphics!) and comments for additions and improvements may be directed to topper@cooper.edu. We hope that this will be a useful resource for beginners as well as for experts in the field. The address of the page is http://www.cooper.edu/engineering/chemechem/monte.html Best regards to all, Robert Topper ************************************************************************ Robert Q. Topper email: topper@cooper.edu Department of Chemistry phone: (212) 353-4378 The Cooper Union FAX: (212) 353-4341 51 Astor Place subway: take the 6 to Astor Place New York, NY 10003 USA or the N/R to 8th St/NYU http://www.cooper.edu/engineering/chemechem/depts_info/topper.html ************************************************************************ The Cooper Union for the Advancement of Science and Art, founded in 1859, is a private institution of higher learning where all students receive full-tuition scholarships to study engineering, architecture and art. ************************************************************************ From tropsha@gibbs.oit.unc.edu Wed Mar 20 22:17:43 1996 Received: from gibbs.oit.unc.edu for tropsha@gibbs.oit.unc.edu by www.ccl.net (8.7.1/950822.1) id VAA00268; Wed, 20 Mar 1996 21:58:17 -0500 (EST) Received: from localhost by gibbs.oit.unc.edu (8.6.4.3/10.1) id VAA25559; Wed, 20 Mar 1996 21:57:18 -0500 Date: Wed, 20 Mar 1996 21:57:17 -0500 From: Alex Tropsha To: chemistry@www.ccl.net Subject: Call for Papers Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Call for Papers 212th National American Chemical Society Meeting COMP Division August 25-30, 1996, Orlando, Florida MOLECULAR DYNAMICS AND FREE ENERGY PERTURBATION METHODS Abstracts Due April 15, 1996 A symposium entitled "Molecular Dynamics and Free Energy Pertubation Methods" will be held at the ACS Meeting in Orlando, Florida, during August 25-30, 1996. The Symposium will include three tracks: Forcefield Development for MD Simulations; Large-Scale Molecular Dynamics Simulations; Free Energy Simulations: Methods and Applications. A partial list of confirmed speakers includes: B. Brooks (NIH), C. Brooks (Scripps), V. Daggett (UW-Seattle), T. Darden (NIEHS-RTP), J. Hermans (UNC-Chapel Hill), P. Kollman (UCSF), K. Schulten (UI-Urbana), B. Tidor (MIT), D. York (Duke). We are inviting both oral and poster presentations. Please submit Abstracts by April 15 to: Alexander Tropsha, Ph.D. Assistant Professor, Director the Laboratory for Molecular Modeling CB # 7360, Beard Hall School of Pharmacy University of North Carolina Chapel Hill, NC 27599-7360 Tel. (919) 966-2955 Fax (919) 966-6919 e-mail: tropsha@gibbs.oit.unc.edu Obtain Abstract Forms from ACS: by calling 1-800-227-5558 (press 9-4-0) by writing to: American Chemical Society 1155 Sixteenth Street, N.W. Washington, D.C. 20036 via the World-Wide Web: http://www.acs.org/memgen/meetings/abinfo.htm