From arne@mango.mef.ki.se Mon Jan 11 12:41:46 1993 From: arne@mango.mef.ki.se (Arne Elofsson) Message-Id: <9301111241.AA03503@mango.mef.ki.se> To: CHAMH@INDSVAX1.INDSTATE.EDU Subject: Re: Upgrading AIX on the RS/6000 Date: Mon, 11 Jan 93 12:41:46 +0000 I have one recomendation. When we tried upgrading from 3.1.5 to 3.2.1 It was necessary to run the tape including the new operative system twice, All files where not found the first time. I think it always is important to upgrade a system, to not do so will only make the upgrade process worse when it will be necessary to do so. arne From bio320@cvx12.inet.dkfz-heidelberg.de Mon Jan 11 14:53:51 1993 Date: Mon, 11 Jan 1993 13:53:51 +0100 From: Friedrich Rippmann Message-Id: <199301111253.AA26018@cvx12.inet.dkfz-heidelberg.de> To: CHEMISTRY@ccl.net Subject: summary: energy contribution of hbonds Some time ago I put this question to the net: >>>>Original posting<<<< I try to find some references for an apparently simple problem: What is the free energy contribution of an hbond (eg. of a peptide inhibitor in a protease)? I know that there is considerable dispute in the literature about the energy contribution, but I can't find appropriate references. What I would like to do is to correlate qualitatively a difference in binding energy with the ratio of two binding constants. Any references/comments most welcome. - Friedrich - ------------------------------------------------------------------------------- Dr. Friedrich Rippmann work: c/o E.MERCK home: Pha Fo Chem, Drug Design Schroederstrasse 72 6100 Darmstadt 6900 Heidelberg 1 POBox 4119 +49-6221-413366 +49-6151-726290 Email: bio320@cvx12.inet.dkfz-heidelberg.de Fax ... 710757 -------------------------------------------------------------------------------- >>>>End original posting<<<< Thanks a lot to all who replied. Here comes the summary: Rebecca Wade (wade@embl-heidelberg.de) writes: Just saw your question on the comp. chem. network! I have lots of refs giving energies of h-bonds from 0.0 to 6+ kcal/mol. An interesting, although maybe out of date ref is: Fersht,A. (87) TIBS 12 p301. There are many subsequent papers. The energetics depend on the chemical nature of the donors and acceptors, the h-bond geometry and whether solvent compensation can occur or not. The last factor means that most binding energy is probably achieved through hydrophobic groups binding and specificity is provided by h-bonds. But methods like GRID and LUDI stress h-bonding for binding energy and specificity. (incidently, you could use the GRID energy and h-bond functions if you want to estimate your h-bond energy difference). ( I have refs for this if you are interested). From: mes@atlas.chemistry.uakron.edu (mary ellen scott) Not so simple huh? I'm doing hydrogen bondong studies between sorbitol and sorbitol dehydrogenase. Lots of papers by Steven Withers- . My approach is kinetics then use homology model of SDG.pdb to look at active sight. modeling approach; Minimization energy of protein " protein + cofactor " protein + cofactor + substrate " protein + cofactor + analogues different substrate analogues substrate polyol all OH - haccept + hdonate polyol substitute F for OH at each position - haccept polyol substitute H for OH " - neither kinetics: deltadelta G# = RT ln( (Vm/Km)subst/(Vm/Km)unsub) These values represent the minimum hbond strengths at each position in the transition state. For ground state analysis or binding, need to design and synthesize inhibitors which are not substrates. REF: Fluorinated Carbohydrates: Chemical and Biochemical Aspects ACS Symposium Series,#374: ed N.F. Taylor, 1988 ISBN 0-8412-1492-1, Steve Withers has more papers in Biochemistry 1992 Percival, M.D. and Withers, S., Biochemistry, # 31 pp 498-505, 1992. Hope this helps in your research. I am writing my thesis now and would like to critique this approach. So if you have any suggestions let me know and would you share with me any responses you receive from your querry? Thanks. Sincerely Mary Ellen From tropsha@gibbs.oit.unc.edu Wed Jan 6 20:05:57 1993 We apply the free energy simulations technique to address the problems of relative binding free energy of different inhibitors (Tropsha&Hermans, Protein Engineering, 1992, v.5, p.29-55. Similar research was done by P. Kollman group (J.Med.Chem.,1991,v.34,p.2654-2659. The role of H-bonds in binding is addressed in such studies implicitely if the inhibitors differ in an H-bond making group. I will be happy to go into further discussion of the approach if you so desire. Sincerely, Alexander Tropsha, Ph.D. Assistant Professor, Director The Laboratory for Molecular Modeling School of Pharmacy UNC-Chapel Hill Chapel Hill, NC 27599 From: Wolfgang Sauer ein Artikel, der mir spontan zu Ihrer Frage einfiel, ist D.H.Williams: "The Molecular Basis of Biological Order" Aldrichim. Acta _24_(3), 71-80 (1991) mit einem Addendum in Aldrichim. Acta _25_(1), 9 (1992). Wolfgang Sauer. -- +======================================+=====================================+ | Wolfgang Sauer | | | Institut fuer Organische Chemie I | "You have to be three standard | | Henkestr. 42, D-8520 Erlangen, FRG | deviations away from a normal | | | personality to like UNIX." | | sauer@organik.uni-erlangen.de | | | Tel.: 49/0 - 9131 - 85 - 2952 | Morris Jones (C&T) | | Fax: - 9132 | | +======================================+=====================================+ From topper@haydn.chm.uri.edu Mon Jan 11 04:20:38 1993 Date: Mon, 11 Jan 93 09:20:38 -0500 From: topper@haydn.chm.uri.edu (Robert Q. Topper) Message-Id: <9301111420.AA21951@haydn.chm.uri.edu> To: CHEMISTRY@ccl.net Subject: force constants Thanks to everyone who wrote and asked for a preprint! I would like to say that the paper was done with several coauthors, and that the vast majority of the perturbation theory work was done by my coworker, Qi Zhang, with important contributions also made by Yi-Ping Liu, and all with the support, guidance, and expertise of Don Truhlar. The other thing I'd like to mention is that this preprint does NOT explicitly give transformations between normal and the usual "internal" coordinates; the only transformation which is explicitly given is between Cartesians and Jacobis (an internal coordinate system loved by us physical chemists, and developed many moons ago). However, it does point to references which would be helpful to someone trying to come to grips with coordinate transformations for the first time. Just a caveat so that no one's hopes are too high.... :-) Best to all, Robert ******************************** * Robert Q. Topper * * Department of Chemistry * * University of Rhode Island * * Kingston, RI 02881 * ******************************** * rtopper@chm.uri.edu OR * * topper@haydn.chm.uri.edu * * (401) 792-2597 [office] * * (401) 792-5072 [FAX] * ******************************** From evi@tiberius.tc.cornell.edu Mon Jan 11 05:05:39 1993 Message-Id: <9301111505.AA88497@tiberius.tc.cornell.edu> To: chemistry@ccl.net Subject: Physics Computing '93 Date: Mon, 11 Jan 93 10:05:39 -0500 From: Evi Goldfield PHYSICS COMPUTING '93 CONFERENCE May 31 - June 4, 1993 Albuquerque Convention Center Albuquerque, New Mexico Sponsored by The APS Division of Computational Physics and AIP Computers in Physics PRELIMINARY ANNOUNCEMENT Physics Computing '93, including the Fifth International Congress on Computational Physics and the bi-annual meeting of the APS Division of Computational Physics, is an occasion for practitioners of computational physics to meet, share ideas, and interact with each other and other members of the computational science community. It combines lectures by renowned scientists presenting research results, technical sessions highlighting the latest innovations in computational methodology, and tutorials conducted by working scientists. A major feature of the conference will be an exhibit by leading hardware and software companies demonstrating state of the art computing technologies. The Hyatt Regency Albuquerque has been designated as the headquarters hotel. TECHNICAL SESSIONS Numerical Algorithms and Methods Finite Elements Finite Differences Adaptive Systems Multigrid Acceleration Algorithms Particle Methods Fast Transforms Lagrangian Methods Eigenvalue Solvers Networks and Databases Information Retrieval Future Directions in Networking Computers in Physics Education Visualization Virtual Reality Digital Image Processing Scientific Visualization Experimental Physics Applications Real-time computing Experimental Techniques Language and Architecture Developments Parallel Languages Parallel Architectures Symbolic Computation Physics Applications Quantum Monte Carlo Quantum Monte Carlo Molecular Dynamics (Electronic Structure) Molecular Dynamics/Monte Carlo Monte Carlo Methods in Statistical Physics Density Functional Theory Basic Computation of Energetic Material s Ab Initio and Fundamental Structure Calculations (Atomic, Nuclear) Fluids Plasmas Turbulence Few Body Problems Chemical Dynamics: Reactive Scattering N-body Calculations Fractal Growth Neural Networks Cellular Automata Chaos Macromolecules and Protein Folding Climate and Pollution Modeling Mesoscopic Simulations of Solids and Fluids with Microstructure Numerical Relativity Special Session Schluter Memorial Symposium TUTORIAL SUBJECTS "Particle Simulation Methods" - -- James W. Eastwood, AEA Technology, Culham Laboratory, UK "Monte Carlo Methods for Radiative Transfer in Astrophysics" - -- Barbara Whitney, Harvard University "Quantum Monte Carlo Methods for Continuum Systems" - -- D. M. Ceperley, University of Illinois, Urbana-Champagne "Advances in Flux-Corrected Transport Algorithms: A Lazy Person's Approach to High-Resolution CFD." - -- Jay Boris, Laboratory for Computational Physics and Fluid Dynamics "Introduction to Mathematica" - -- Nancy Blachman, Variable Symbols Co. "Introduction to Maple" - -- Nancy Blachman, Variable Symbols Co. "Programming in High Performance FORTRAN" - -- Chuck Koelbel, Rice University "Modular FORTRAN: A Language for Building Large Parallel Programs" - -- Ian Foster, Argonne National Laboratory "Requirements for High Performance Scientific Distributed Computing" - -- David W. Forslund, Los Alamos National Laboratory "High Performance Computing Trends, or Massively Parallel Computing Comes of Age" - -- Mark Seager, Lawrence Livermore National Laboratory "Introduction to the Finite Element Method: A Physicist's Approach -- with Applications to Quantum Mechanics" - -- L. R. Ram-Mohan, Worcester Polytechnic Institute "2D Moving Finite Elements: An Adaptive Grid Method for Computational Fluid Dynamics" - -- Alan H. Glasser, Los Alamos National Laboratory "The Conjugate Gradient Method" - -- Steven Ashby, Lawrence Livermore National Laboratory "A Survey of Available Third Party Software for Applications in Physics, Chemistry, Engineering, and Mathematics" - -- Suslarla Murty, Lawrence Livermore National Laboratory SUBMISSION OF ABSTRACTS Abstracts of contributed papers must be received by MARCH 5, 1993. Abstracts must conform to the riles and guidelines for submission of abstracts as published in the monthly APS News. All abstracts should be sent to: Executive Secretary, The American Physical Society 335 East 45th Street New York, NY 10017 FURTHER INFORMATION Further details about the plenary session, registration information, and the site are available by anonymous ftp to pinet.aip.org in directory "pc93". ------- End of Forwarded Message From scsupham@reading.ac.uk Mon Jan 11 17:54:05 1993 From: scsupham@reading.ac.uk Date: Mon, 11 Jan 93 17:54:05 GMT Message-Id: <25233.9301111754@scsscsc3> To: chemistry@ccl.net Subject: DMol questions ---------- X-Sun-Data-Type: text X-Sun-Data-Description: text X-Sun-Data-Name: text X-Sun-Content-Lines: 9 Hi, Are there any employees from Biosym out there able to answer questions on DMol (or in fact any non-employees for that matter) ? john upham John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%susssys1.rdg.ac.uk@uk.ac (BITnet), scsupham@rdg.susssys1 (Janet) Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 ---------- X-Sun-Data-Type: default X-Sun-Data-Description: default X-Sun-Data-Name: .signature X-Sun-Content-Lines: 3 John Upham, Dept. of Chemistry, University of Reading, Berks., RG6 2AD, UK. Email: scsupham%susssys1.rdg.ac.uk@uk.ac (BITnet), scsupham@rdg.susssys1 (Janet) Voice: +44 734 875123 x7441 (day), Fax: +44 734 311610 From WILLIAMS%XRAY2@ulkyvx.louisville.edu Mon Jan 11 09:33:00 1993 Date: Mon, 11 Jan 1993 14:33 EST From: WILLIAMS%XRAY2@ulkyvx02.louisville.edu Subject: PD Net Atomic Charges and Multipoles To: chemistry@ccl.net Message-Id: <01GTE9FNVKMO8WW9PZ@ulkyvx.bitnet> Program PDM93, Potential Derived Multipoles, is now available. The following is a brief description of this program. Molecules interact with each other via their electric potential. PDM93 finds optimized net atomic charges and other site multipole representations of the molecular electric potential based on a variety of models. The program is easy to use, flexible and powerful. Results are obtained in a single iteration and a complete error treatment is made which includes estimated standard deviation and correlation of variables. The program is written in Fortran 77 and runs on Unix, Vax, and other computers with F77 capability. Program PDM93 has a unique combination of features: o general sites, not necessarily at atomic locations o each site may have any combination of monopole, dipole, or quadrupole o bond dipole model is supported o restricted (along the bond direction) bond dipole model is supported o provision for site dipole vectors in sp2 or sp3 directions o selected fixed atomic charges o selected groups of atoms with fixed charge o atomic charge equalities or symmetry relations o rotational invariance of site charges o provision for optional foreshortening of X-H bonds o comparison with Mulliken charges and Mulliken electric potential o direct input from Gaussian-92 o generalized input from other quantum mechanics programs o automatic generation of electric potential grid points o provision for custom generation of grid points o on-line program manual o comprehensive examples are provided For further information contact Dr. Donald E. Williams, Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA. Tel: (502)588-5975 Fax: (502)588-8149 E-mail: dewill01@ulkyvx.bitnet