From DSMITH@uoft02.utoledo.edu Mon Sep 13 03:43:54 1993 Date: Mon, 13 Sep 1993 08:43:54 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: Re: SGI comp-chem /sci-vis software To: tjlee@austin.wes.army.mil Message-Id: <01H2W6L3L6GY001P4N@UOFT02.UTOLEDO.EDU> As I have posted before, the AVS Chemistry Viewer, currently available from MSI (although write directly to me for additional information not yet publicly available) is one of the best, because AVS runs on all these platforms, currently talks to several MO and MM/MD packages (with more in the works) and is user extensible. Doug Douglas A. Smith Assistant Professor of Chemistry and of Medicinal and Biological Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From berkley@wubs.wustl.edu Mon Sep 13 03:41:35 1993 Date: Mon, 13 Sep 1993 08:41:35 -0500 From: Mr. Berkley Shands Message-Id: <9309131341.AA01466@wubs> To: chemistry@ccl.net Subject: More benchmarks Here is another round of benchmark info - I've dropped the VAX line since my only accessable machine would now take >8 hours to run this program to completion :-) The AXP 3000/300 cost just under $10K new. The IBM RS6K/560 was over $80K, new. The IRIS R4K (Indy2) was over $12K with discounts new. Receptor (TM - Tripos Associates) Beta Release version V2.4 timings for the ACE series. Uniform distance space scanning at 0.05A maximum increment with Adaptive Scanning in modified mode applied. Side chains scanned at 20 degrees. Minimum scan factor 0.45 degrees, maximum scan factor 2.81 degrees. ******************************************************************************* Benchmarks of the complete ACE series of 71 molecules Dynamic scan factors ******************************************************************************* Top CPU Top Elps Top Sys Chg CPU Chg Elps CPU Type and notes ======= ======== ======= ======= ======== ================== 1168.15 1287 12.95 1114.95 1159 SUN 4/c SPARCstation 2 40mb -O4 1041.10 1231 82.35 1017.05 1184 IRIS Indigo (IP12) 48mb R3KA@35Mhz -O2 955.27 1101 66.83 931.43 1063 IRIS Indigo (IP12) 48mb R3KA@35Mhz -O3 753.31 801 3.55 738.58 760 E&S ESV (M120 R3K@40Mhz) Mips 2.3 -O2 659.77 792 9.25 638.55 706 DEC Alpha AXP (3K/300L) 32mb OSF1 V1.3 -O2 539.17 555 1.72 512.38 520 IBM RS-6K-560 128Mb (AIX 3.2.1) 422.97 694 8.37 412.98 665 IRIS Indigo (IP20) 32mb R4K@50Mhz -O3 -mips Load 2.0 431.90 464 4.08 409.83 422 DEC Alpha AXP (3K/300) 32mb OSF1 -O2 438.35 472 4.40 416.68 425 DEC Alpha AXP (3K/300) 32mb OSF1 -O3 331.85 xxx 3.65 320.88 xxx DEC Alpha AXP (4K/610 - axposf) 128Mb load 3.00 OSF V1.3 Thanks to DEC for the system time. ******************************************************************************* Notes: "Top CPU" is the recorded total CPU for all forked processes, including overhead and I/O. "Top Elps" is the recorded elapsed time from command line parsing to the exit of the last child processes. "Top Sys" is the recorded UNIX system overhead from the times() function "Chg CPU" is the algorithmic chargable time from initial rotations to termination (child process CPU) "Chg Elps" is the elapsed time spent rotating and computing. ***************************************************************************** Berkley Shands From albo@RUUCI9.chem.ruu.nl Mon Sep 13 07:19:37 1993 From: albo@RUUCI9.chem.ruu.nl (Alexandre Bonvin) Message-Id: <9309132219.AA18297@RUUCI9> Subject: Summary NMR chem. shift refinement To: CHEMISTRY@ccl.net Date: Mon, 13 Sep 1993 15:19:37 -0800 (PDT) Dear netters, I posted some time ago a request about references on the use of NMR chemical shift as structural constraints for protein structure refinement. Here is a short summary of the answers I obtained on this subject. Most of the publications in this area treat of the computation of NMR chemical shifts from a structure with prospective applications for secondary structure prediction, assignment of NMR spectra and determination of three-dimensional structure. The recent theoretical developments permit the prediction of 1H, 13C 15N and 19F NMR chemical shift. Here are a few references dealing mainly with the theoretical calculations of chemical shifts: * A. de Dios, J.G. Pearson and E. Oldfield (1993). Secondary and Tertiary Structural Effects on Protein NMR Chemical Shifts: An ab Initio Approach. Science 260, 1491-1496. * M.P. Williamson, T. Asakura, E. Nakamura and M. Demura (1992). A Method for the Calculation of Protein a-CH Chemical Shifts. J. Biomol. NMR 2, 83-98. * D.S. Wishart, B.D. Sykes and F.M. Richards (1991). Relationship Between NMR Chemical Shift and Protein Secondary Structure. J. Mol. Biol. 222, 311-333. * K. Osapay and D.A. Case (1991). A New Analysis of Proton Chemical Shifts in Proteins. J. Am. Chem. Soc. 113, 9436-9444. Additional references can be found in these articles. About the refinement of protein structure with NMR chemical shift as constraints... There are only two groups I know of that are presently working in this field. Osapay and Case at Scripps Clinic, San Diego, have used chemical shifts as structural constraints for the structure refinement of myoglobin. Results of this work have been presented at conferences this year and a paper is actually in preparation. The other group is the one of Prof. van Gunsteren at the ETHZ in Zurich and a paper on the use of NMR chemical shifts for the refinement of BPTI and EGF has been published. The reference is: * T.S. Harvey and W.F van Gunstern (1993). The Application of Chemical Shifts Calculation to Protein Structure Determination by NMR. In: "Techniques in Protein Chemistry IV". Academic Press Inc, 615-622. Thanks for your help. Alexandre _________________________________________________________________________ Alexandre Bonvin Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 Tel. : int+31.30.533959 CH 3584 Utrecht Fax. : int+31.30.537623 The Netherlands Email: albo@nmr.chem.ruu.nl _________________________________________________________________________ From smb@smb.chem.niu.edu Mon Sep 13 03:40:29 1993 Date: Mon, 13 Sep 93 08:40:29 -0500 From: smb@smb.chem.niu.edu (Steven Bachrach) Message-Id: <9309131340.AA23369@smb.chem.niu.edu> To: CHEMISTRY@ccl.net Subject: My previous note concerning G-92 I would just like to add a comment related to something D. Feller mentioned in passing. My comment concerning G-92 in no way should be taken as a knock against the program. I have been using Gaussian for more than ten years now and am truly appreciative of the fine work the Gaussian folks have done. Please take my comments as looking for clarification from a satisfied costumer! Steven Bachrach Department of Chemistry Northern Illinois University DeKalb, Il 60115 smb@smb.chem.niu.edu From Tom_Kavassalis.XRCC@xerox.com Mon Sep 13 00:45:51 1993 Date: Mon, 13 Sep 1993 07:45:51 PDT From: Tom_Kavassalis.XRCC@xerox.com Subject: ACS Workshop on Molecular Simulation of Structure and Properties of Polymer Systems To: chemistry@ccl.net Message-Id: <"13-Sep-93 10:45:51".*.Tom_Kavassalis.XRCC@Xerox.com> MOLECULAR SIMULATION OF STRUCTURES AND PROPERTIES IN POLYMER SYSTEMS REMINDER The early registration deadline is this Friday, September 17th, 1993. To avoid the $50 late registration fee contact: Diane Morrill Virginia Polytechnic Institute Tel: 703-231-3029 Fax: 703-231-8517 Final Program and Additional Information Follows: Workshop organizers: T. A. Kavassalis (Xerox Research Centre of Canada) S. L. Hsu (University of Massachusetts) The Polymer Chemistry Division of the American Chemical Society is offering an interdisciplinary workshop on Molecular Simulation of Structure and Properties in Polymer Systems. It will be held at the Asilomar Conference Center, Pacific Grove California on October 17-20, 1993. WHO SHOULD ATTEND This interdisciplinary workshop has been organized to facilitate the dissemination of new research in the development and use of molecular simulation methodologies in polymer science and will be of interest to graduate students, university researchers and industrial researchers. The workshop will offer invited lectures dealing with: 1. Prediction of Polymer Structure and Properties. 2. Simulation of Phase Behavior 3. The Link Between Experimentation and Molecular Simulation 4. New Developments in Molecular Simulation PRESENTATIONS A poster session is planned in order to give the conferees the opportunity to present their innovative efforts in molecular simulation. Anyone wishing to present a poster should send a title with authors and affiliations and a 200-word abstract to: Dr. T.A. Kavassalis Xerox Research Centre of Canada 2660 Speakman Drive Mississauga, Ontario Canada L5K 2L1 Tel. 416-823-7091 FAX 416-822-7022 OR Professor S. L. Hsu Polymer Science & Engineering Dept. University of Massachusetts Amherst, MA 01003 USA Tel. 413-545-0433 FAX 413-545-0082 SUNDAY, OCTOBER 17 5:00 Registration 6:00 Reception 7:30 PLENARY LECTURE Martin Karplus (Harvard University) MONDAY OCTOBER 18 Prediction of Polymer Structure and Properties CHAIR: M. Karplus 9:00 a.m. Transport and Solubility of Small Molecules in Solid Polymers U. Suter (ETH-Zurich) 9:45 Molecular Simulations of Amorphous Polymers J.H.R. Clarke (UMIST, Manchester) 10:30 Break 10:45 Simulation and Analysis of Chain-Molecule Transitions A.P. Hopfinger (University of Illinois, Chicago) 11:30 Molecular Dynamics Simulations of Tethered Chains G. Grest (Exxon Research and Engineering) The Link Between Experimentation and Molecular Simulation CHAIR: S. L. Hsu 7:30 p.m. Properties of Ensemble-Averaged Vibrational Spectra of Flexible Chain Molecules R.G. Snyder (University of California, Berkeley) 8:15 X-ray Studies of Transesterfication in Thermotropic Copolyesters J. Blackwell (Case Western Reserve University) TUESDAY OCTOBER 19 Molecular Simulation and Phase Behavior CHAIR: U. Suter 9:00 a.m. Pattern Selection in Complex Fluids M. Muthumukar (University of Massachusetts) 9:45 Isotropic/Nematic Phase Behaviors in Rigid Rod Systems I.C. Sanchez (University of Texas, Austin) 10:30 Break 10:45 Molecular Simulation of Chain Molecules and their Phase Behaviors J. de Pablo (University of Wisconsin) 11:30 Entropic Phase Transitions in Simple and Complex Fluids D. Frenkel (FOM, Amsterdam) 4:00 Poster Session The Link Between Experimentation and Molecular Simulation CHAIR: I.C. Sanchez 7:30 p.m. Simulations of Self-Assembled Block Copolymers W. Mattice (University of Akron) 8:15 Compositional Heterogeneity or Clustering in Hydrogen Bonded Polymer Blends P.C. Painter (Pennsylvania State University) WEDNESDAY OCTOBER 20 New Developments in Molecular Simulation CHAIR: T.A. Kavassalis 9:00 a.m. MD of Polymers in Solution Subject to Shear Flow J.-P. Rychaert (UniversitBe Libre de Bruxelles) 9:45 Mobility of Small Particles in Amorphous Polymers F. MHuller-Plathe (ETH-Zurich) 10:30 Break 10:45 New Developments for Million Atom Simulations W.A. Goddard, III(California Institute of Technology) From tristan@Kodak.COM Mon Sep 13 09:30:43 1993 Date: Mon, 13 Sep 93 09:32:50 EDT From: tristan@Kodak.COM (James Nonnemacher) Message-Id: <9309131332.AA27175@icts01.Kodak.COM> To: CHEMISTRY@ccl.net Subject: Gaussian 92 for Windows Does anyone have experience with Gaussian 92 for Windows? Is it worth getting? From balducci@serine.phr.utexas.edu Mon Sep 13 05:22:50 1993 Message-Id: <9309131523.AA05268@serine.phr.utexas.edu> To: CHEMISTRY@ccl.net Subject: Dreiding force field Date: Mon, 13 Sep 1993 10:22:50 -0500 From: Renzo Balducci Hi everybody --- I would like to find out some information regarding the Dreiding force field. In particular, I'm interested in pointers to the literature describing the force field definition and comparing its performance with that of other popular force fields. I would also appreciate any pointers to public domain implementations of this force field and to the "offical" sources of the Dreiding parameterization. Thanks a lot, ---Renzo Balducci ----------------------------------------------------------------------- Renzo Balducci balducci@phenyl.phr.utexas.edu Research Associate & System Manager balducci@vax.phr.utexas.edu College of Pharmacy balducci@ccwf.cc.utexas.edu Univ. of Texas --- Austin, TX 78712 (512) 471-8509; FAX: 471-8762 ----------------------------------------------------------------------- From pseida@cc.brynmawr.edu Mon Sep 13 07:39:18 1993 Message-Id: <9309131539.AA01888@cc.brynmawr.edu> Subject: X and modems To: chemistry@ccl.net Date: Mon, 13 Sep 93 11:39:18 EDT From: Seida Pamela R Does anyone know of a way to have an X-windows session over a 9600 baud modem from a Mac to a UNIX box of some variety? Any help would be greatly appreciated. I'll summarize to the net if there is sufficient interest (and I get any answers ;-)). Pamela Seida Chemistry Department Bryn Mawr College From dhr@kumoto.chem.iupui.edu Mon Sep 13 07:15:31 1993 Date: Mon, 13 Sep 93 11:15:31 -0400 From: dhr@kumoto.chem.iupui.edu (Daniel H. Robertson) Message-Id: <9309131515.AA07261@kumoto.chem.iupui.edu> To: chemistry@ccl.net Subject: Dipole Moments Chemistry Netters, I am interested in calculating dipole moments (and possibly higher moments) for small organic solvents using semi-empirical or ab initio methods. What method or level of calculations give consistent results and the best correlation to experimental values? Any citations on studies involving dipole moments would also be appreciated. You can reach me at the email address below. Thanks in advance, Dan ----------------------------------------------------------------------------- F | Dan Robertson, Manager | I C | Facility for Computational Molecular and Biomolecular Science | U M | Department of Chemistry | P B | Indiana University - Purdue University at Indianapolis | U S | robertson@chem.iupui.edu (317) 278-2202 | I From luca@aeolus.ethz.ch Mon Sep 13 17:10:31 1993 Date: Mon, 13 Sep 1993 17:10:31 +0000 From: Luca Toldo Message-Id: <30*/S=luca/OU=aeolus/O=ethz/PRMD=switch/ADMD=arcom/C=ch/@MHS> To: CHEMISTRY@ccl.net Subject: Liquid Simulators ... can you help me ? Does anyone have simulated highly concentrated solutions of ammonium sulphate and / or ammonium acetate in water ? I would like to do so, but I do not know which programs are capable of accomplish it. I would really appreciate ANY SUGGESTION, but please do not just tell me to read the book of Allen ... because I did it allready ! looking forward your help !!!! best regards Luca I.G. TOLDO Institute of Molecular Biology and Biophysics HPM F 11 ETH-Honggerberg CH-8093 Zuerich, Switzerland. email:luca@aeolus.ethz.ch From mrigank@imtech.ernet.in Mon Sep 13 19:54:34 1993 Message-Id: <9309131655.AA12208@ern.doe.ernet.in> Date: Mon, 13 Sep 93 14:24:34 +0530 From: Dr. Mrigank To: chemistry@ccl.net Subject: parameters for beta-gly and beta-ala Hi chem folks I want to model some peptides containing beta-alanine and beta-glycine * I want to know any computayional work doen on them ? * Has any one worked out non-bonded parameters ? * If i use c-beta'(in back bone ) as usual tetrahedran in a chain will it be OK ? * Any otehr relavent information ? Thanks in advance Mrigank ---- Dr. Mrigank Phone: +91 172 45004 x216 Institute of Microbial Technology Email: mrigank@imtech.ernet.in P O Box 1304, Sector 39A UUCP: Chandigarh 160 014 India. ...!uunet!sangam!vikram!imtech!mrigank ==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+ -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From stc@MIT.EDU Mon Sep 13 10:50:09 1993 From: stc@MIT.EDU Message-Id: <9309131850.AA02894@m66-080-10.MIT.EDU> To: CHEMISTRY@ccl.net, calculation@MIT.EDU, using@MIT.EDU, ewald@MIT.EDU, Subject: pressure Date: Mon, 13 Sep 93 14:50:09 EDT I would appreciate it if someone could suggest references for calculating the pressure when using the Ewald sum method in molecular dynamics simulation? Thanks. Shengting Cui From bunge@sysul1.ifisicacu.unam.mx Mon Sep 13 07:51:33 1993 From: bunge@sysul1.ifisicacu.unam.mx (Carlos F. Bunge Molina) Message-Id: <9309131951.AA00574@sysul1.ifisicacu.unam.mx> Subject: Roothaan-Hartree-Fock To: chemistry@ccl.net Date: Mon, 13 Sep 1993 13:51:33 -0600 (CST) Mexico, 13 September 1993 Dear colleagues, You may be interested to know about a new compilation of atomic Roothaan-Hartree-Fock wave functions for He through Xe, of numerical accuracy, which appeared in Atomic Data and Nuclear Data Tables 53,113-162(1993); see also Physical Review A46,3691-3696(1992). An ascii file named RHF.TABLES containing all numerical information can be obtained via anonymous ftp 132.248.7.2 from the directory /pub/tables. Carlos F. Bunge . From mail Mon Sep 13 15:50:42 1993 Date: Mon, 13 Sep 93 15:56:47 EDT From: "George J. Maalouf" Message-Id: <9309131956.AA01376@proline.rowland.org> To: CHEMISTRY@ccl.net Subject: geminal coupling constants Dear Netters, I am iteratively fitting simulated to experimental 1D proton NMR spectra using newly developed code. For small peptides I am obtaining geminal, vincinal, and long range coupling constants to very high precision. Has anyone tabulated or can anyone point me to a tabulation of geminal coupling constants verses the H-C(IV)-H angle (determined experimentally by x-ray for example)? "Advances in Magnetic Resonance" vol. 1 has a nice compilation of geminal coupling constants for small molecules, for example, but no comparison against experimental structure. Also, does anyone know of accurate theoretical derivations relating the geminal coupling constant to the angle? Thanks in advance, George Maalouf maalouf@proline.rowland.org From msjones@whale.st.usm.edu Tue Sep 14 42:47:58 1993 From: msjones@whale.st.usm.edu (Michael Sean Jones) Message-Id: <9309132231.AA14924@whale.st.usm.edu> Subject: HyperChem Parameters To: CHEMISTRY@ccl.net (chemlist) Date: Mon, 13 Sep 1993 17:31:58 +22304916 (CDT) Dear Netters, I am a student at the University of Southern Mississippi using HyperChem to model a 99 residue peptide. I am attempting to find its conformation of lowest energy. I attempted the minimization using the AMBER force field doing a geometry optimization using distance dependent options. Is this the best method to use to minimize the structure? If anyone knows more about this please let me know. I am anxiously trying many different methods to no avail. Please send any suggestion to me at my address below. Thanks in advance. Mike msjones@wave.st.usm.edu From X0ZHAO01@ULKYVX.LOUISVILLE.EDU Mon Sep 13 16:14:17 1993 Date: Mon, 13 Sep 1993 21:14:17 -0500 (EST) From: LIU JIANLING Subject: csd To: chemistry@ccl.net Message-Id: <01H2WWPF08R68WX89R@ULKYVX.LOUISVILLE.EDU> dear netters: I have access to Cambridge Structure Database , but have no manual or user's guide etc.... with me. Can anyone tell me how to get those information or how to contact the CSD headquarter? BIG THANX! From ilya@lisboa.ks.uiuc.edu Mon Sep 13 12:26:24 1993 From: Ilya Logunov Message-Id: <9309140230.AA00384@lisboa.ks.uiuc.edu> Date: Mon, 13 Sep 93 17:26:24 -0500 To: chemistry@ccl.net Subject: MOPAC on SGI Could somebody tell me where I can get the version of MOPAC running on SGI? ********************************************************* Ilya Logunov University of Illinois at U-C ilya@lisboa.ks.uiuc.edu *********************************************************