From chemistry-request@ccl.net Tue Feb 11 07:10:37 1992 From: Mark Forster Date: Tue, 11 Feb 92 11:13:47 GMT To: CHEMISTRY Status: R Subject: 1992 annual meeting of Molecular Graphics Society, Bath UK. MAIL FROM Mark .J. Forster, Informatics Laboratory, National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Hertfordshire, EN6 3QG, UK. Tel (0707) 54753 Fax (0707) 46730 e-mail from within the u.k. use forster@uk.ac.nibsc.computing rest of the world uses the reverse order system. forster@computing.nibsc.ac.uk Dear netters, Here is some information (free advertising) regarding the forthcoming Molecular Graphics Society (MGS) annual Meeting. VENUE: University of Bath, Bath, United Kingdom. DATES: 13th-16th April 1992. THEME: Focus will be on Membrane proteins, Small molecule structure-activity, Novel algorithms. COST: Registration fee MGS member: 80 pounds sterling (148 US dollars) non-member: 105 pounds sterling (195 US dollars) student member: 30 pounds sterling (55 US dollars) student non-member: 43 pounds sterling (80 US dollars) Accomodation: 78 pounds sterling (145 US dollars) Conference dinner: 25 pounds sterling (47 US dollars) Lunch 13th April: 7 pounds sterling (13 US dollars) Lunch 16th April: 7 pounds sterling (13 US dollars) Registration forms and payment to: Molecular Graphics Conference C/O Dr D.J.Osguthorpe, School of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK. e-mail: D.J.Osguthorpe@uk.ac.bath phone: (44)-225-826116 FAX: (44)-225-826231 Invited speakers. John Findlay, University of Leeds. "3D molecular modelling using protein chemistry data" Leo Herbette, University of Connecticut Health Centre, "Molecular basis for drug and peptide interactions with biological membranes: experimental databases and computer simulations." Tim Clark, Erlangen University. "Neural Networks and other tricks that improve AM1" Dan Dolata, University of Arizona, Tucson. "MOUSE: A learning program for conformational analysis" John Moult, CARB, Rockville. "Comparison of monte carlo and genetic algorithm approach to determining peptide conformation" Hans-Peter Weber, Sandoz, Basle. "Drug design by COMPA: Comparative molecular potential analysis" D.G.Burder, 3D-images "Stereo 3D visualisation" Events: Conference reception, Monday night April 13th at roman baths in the centre of Bath. Conference dinner Wednesday April 15th in the 18th century assembly rooms. Exhibition by hardware and software vendors during the conference. Best Wishes Mark J. Forster p.s. sending message to CHEMISTRY%ccl.net@uk.ac.nsfnet-relay From chemistry-request@ccl.net Tue Feb 11 11:15:25 1992 Date: Tue, 11 Feb 92 09:02:20 EST From: Kurt.Hillig@um.cc.umich.edu To: Chemistry@ccl.net Status: R I've been trying to get Dan Severance's PSI88 package working on an SGI 4D/360 GTX, and run into a snag which I hope someone can help with. The PSI88 distribution comes with subroutine libraries to generate Calcomp, HPGL, PostScript and GKS plots. Unfortunately, what I need most are libraries for Tektronix 4010/4014 and/or SGI GL, and while I've seen these at some other sites (as binaries, and not on SGI machines) I haven't been able to find the sources. If anyone can point me toward these I (and some of our post-docs) would be grateful. Kurt Hillig Department of Chemistry University of Michigan Ann Arbor, MI Kurt.Hillig@um.cc.umich.edu From chemistry-request@ccl.net Tue Feb 11 12:50:43 1992 Date: Tue, 11 Feb 92 16:48:26 GMT From: James P. Schmidt To: CHEMISTRY@ccl.net Subject: mosol Status: R The problem regarding the use of full SCF derivatives in adapting Cramer and Truhlar's solvation methods to MOPAc 6.0 turns out to be relatively simple to correct. The tar on crocus.medicine.rochester.edu cannot be modifeied at the moment however as the owner of that machine is out of town for the week. The following patch will correct the problem: To the segment deriv.f the following 2 lines need to be added after line 168 SLOW = (INDEX(KEYWRD,'AQUO') + 1 INDEX(KEYWRD,'ENVAQ') .NE. 0) To put in context, the code should look like thsi after being patched: 110 GNORM=GNORM+GRAD(I)**2 GNORM=SQRT(GNORM) SLOW=.FALSE. NOANCI=.FALSE. IF(HALFE) THEN NOANCI=(INDEX(KEYWRD,'NOANCI').NE.0 .OR. NOPEN.EQ.NORBS) SLOW=(NOANCI.AND.(GNORM .LT. GRLIM .OR. SCF1)) ENDIF SLOW = (INDEX(KEYWRD,'AQUO') + 1 INDEX(KEYWRD,'ENVAQ') .NE. 0) IF(NDEP.NE.0) CALL SYMTRY CALL GMETRY(GEO,COORD) C C COORD NOW HOLDS THE CARTESIAN COORDINATES C This modification will force the use of full SCF derivatives if the keyword AQUO or ENVAQ are specified. I cannot comment on whther this code runs faster or slower than amsol since I never got the original Amsol cray code to run on our systems, but I can say that using full SCF derivatives slows down convergence by an order of magnitude. I wonder whether it might not be useful to adapt the code to only switch to full derivatives after nearing the stationary point. This admittedly may cause problems for large polar molecules where the error is great but for the uncharged molecules in the test suite the error was never more than a few hundreths of a Kcal while using the improper derivative scheme. Thanks again to Chris Cramer for pointing out the error and for his advice in setting things aright. If anyone uses this code I would appreciate any comments or observations they have as I am using this code in my own work and would like to catch any further problems as soon as possible. Jim Schmidt jims@duce.medicine.rochester.edu From jkl@ccl.net Tue Feb 11 15:37:24 1992 Date: Tue, 11 Feb 1992 15:37:17 -0500 From: jkl@ccl.net To: chemistry@ccl.net Subject: Re: FAB-MS Status: R Forwarding to chemistry@ccl.net ---------- Begin Forwarded Message ---------- >From VKUMAR@UCONNVM.UCONN.EDU Tue Feb 11 15:16:19 1992 Date: Tue, 11 Feb 92 15:09:37 EST From: vkumar Subject: FAB-MS To: chemistry-request@ccl.net Status: R Hi, I am trying to collect information on Fast-Atom-Bombardment Mass Spectra. Any recent review article 1988-present is most welcome, especially articles dealing with the fragmentation patterns involved, and the use of FAB-MS in structure elucidation. Please send replies to VKUMAR@UCONNVM.BITNET Thanks Vivek Kumar PS: Any recent Books?? ----------- End Forwarded Message ----------- From chemistry-request@ccl.net Tue Feb 11 20:12:24 1992 Date: Tue, 11 Feb 92 16:13:34 -0800 From: ross@zeno.mmwb.ucsf.EDU To: chemistry@ccl.net Subject: email addr: SW Homans, U. Dundee, Scotland Status: R Does anyone have an email address for S. W. Homans of the Dept. Biochemistry, U. of Dundee, Scotland? Bill Ross UC San Francisco From chemistry-request@ccl.net Wed Feb 12 11:07:52 1992 Date: Wed, 12 Feb 92 10:12:15 -0500 From: moncrief@ds6.scri.fsu.edu (David Moncrieff) To: chemistry@ccl.net Subject: Workshop on Molecular Mechanics and Molecular Mechanics Status: R ****************************************************************************** Workshop on Molecular Mechanics and Molecular Dynamics III at Florida State University ****************************************************************************** The Supercomputer Computations Research Institute at Florida State University will sponsor a workshop on Molecular Mechanics and Molecular Dynamics in Tallahassee, Florida from March 30-April 3, 1992. Cost to register is $300 before February 28, $325 after February 28, or $200 if your contributed talk or poster is accepted, $100 for students. The fee includes reception, 4 breakfasts, 3 lunches and a banquet. The conference hotel is the Radisson, 425 North Monroe Street, Tallahassee, FL 32301, Tel: (904) 224-6000. Room rates are $79 single or double. Please call Delos DeTar at (904) 644-3709 for program information. Respond by e-mail to: mol_dyn@scri.fsu.edu You may fax your registration directly to the conference center at (904) 644-2589. Please make checks payable to Florida State University. PRELIMINARY PROGRAM =================== [SCHEDULE as of February 10, 1992] MAR 30 Mon 6:30-8:30 PM Reception MAR 31 Tue 8:00 Continental Breakfast 9:00 Welcome: Dale Lick introduced by Joe Lannutti 9:10 Preliminary Comments: DeLos F. DeTar 9:15 Harold A. Scheraga The Multiple-Minima Problem in Calculations of Protein Conformation 10:15 Coffee 10:30 Wayne C. Guida Computational Approaches for Determining the Conformational Preferences of Inhibitors Bound to Thermolysin and Purine Nucleoside Phosphorylase 11:00 Paul Bash 11:30 Carol Venanzi Molecular Dynamics Simulations of Amiloride Analogues 12:00 Adi Treasurywala Recent Developments in the Design of Antipicoraviral Agents 12:30 Lunch 1:45-4:30 Contributed talks, posters, exhibits APR 1 Wed 8:00 Continental Breakfast Edwin F. Hilinski, chair 9:00 Normal L. Allinger Recent Work in Molecular Mechanics 10:00 Coffee 10:15 Curt M. Breneman The Development and Use of Transferable Atom Equivalents in Molecular Modeling 10:45 Bastiaan van de Graaf Development and Applications of a Consistent Force Field for Zeolites 11:15 Leonard F. Lindoy Molecular Mechanics Calculations - Transition and Post Transition Metal Complexes 11:45 Angelo Vedani Directionality and Charge Transfer: The Keys for Modeling Metal Centers in Macromolecules? 12:15 Lunch chair 1:30 Paul Mller Application of Molecular Mechanics Calculations to Steric Effects on Rate and Equilibrium Constants 2:30 Joseph A. Halgren The New Merck Molecular Force Field: Scope, Structure, and Performance. What It Does, How It Does It, How It Does 3:30 Richard D. Cramer Methods for implementing an Open Force Field Policy 4:00 Hagai Meirovitch Energy Simulation of the Entropy of Peptides using the Local States Method 4:30 High tea and exhibits APR 2 Thu 8:00 Continental Breakfast Paul Bash, chair 9:00 Kenneth B. Wiberg Calculation of Solvent Effects on Equilibria 10:00 Coffee 10:15 Gnter Hfelinger Basis Set Dependence and Accuracy of ab Initio Optimizations of Molecular Structures of Organic Compounds 10:45 Samuel Krimm Molecular Mechanics Energy Functions from ab Initio Vibrational Force Fields and Structures 11:15 Jerzy Cioslowski Endohedral Complexes of the C60 Cluster: A Challenge to Molecular Mechanics 11:45 Jan L. M. Dillen Least Squares Optimization of Force Fields. PEFF: A Program for the Development of Force Fields 12:15 Lunch chair 1:30 Eiji Osawa Reservoir-Filling Algorithm: an Efficient Method for Searching Conformational Space of Large and Flexible Molecules 2:00 Jay Ponder Modeling of Protein Structures 2:30 Martin Saunders Stochastic Search Methods for Seeking Conformers of Flexible Molecules 3:00 Load buses for trip to Wakulla Springs APR 3 Fri 8:00 Continental Breakfast DeLos F. DeTar, chair 9:00 Terry R. Stouch Lipid Bilayers and the Lipid-Water Interface: Atomic Level Simulations of Structures and Dynamics 10:00 Coffee 10:15 Joseph Andose AMF - The Merck Molecular Modeling System 10:45 James P. Snyder Molecular Design of Small Molecules at Ill-Defined Biological Receptors 11:15 Andr Michelle 11:45 Clark R. Landis New Approaches to Force Field Descriptions of Complex Molecular Shapes 12:15 Workshop ends From chemistry-request@ccl.net Wed Feb 12 11:11:06 1992 Date: Wed, 12 Feb 1992 09:33 CST From: Andy Holder Subject: AMPAC vs. MOPAC To: CHEMISTRY@ccl.net Status: R Let me preface my remarks on this discussion with the caveat that I am a recent "graduate" of the Dewar group, so am a bit biased. You will pro- bably need to filter my input with this in mind. I will endeavor to be as fair and impartial as possible, though. MOPAC and AMPAC originated with the same set of FORTRAN code. This was a compendium of a number of different programs that was brought together and linked via a common interface. After this, the codes have diverged along different paths and philosophies. They are now quite distiguishable. We recently tried a set of speed trials to see which program was "faster". This set of trials was carried out on several platforms, with both vector and nonvector architectures. The results were inconclusive, as so much has changed in the way things are implemented that you might as well compare to SINDO. All of this goes to say that the programs are DIFFERENT. Be aware. One of the primary differences is an almost complete recoding of certain sections of the code by Daniel Liotard around 1987-1989. This was done in conjunction with the port to the CRAY. Daniels' efforts have vastly improved the performance of AMPAC. In addition, Daniel added a substantial set of tools to the program that have largely changed the way studies (especially transition state loc- ation) are carried out. These include the excellent CHAIN method which is a vast improvement over SADDLE (which I don't recommend using). Listed below are a set of keywords/methods which are present in AMPAC but not in MOPAC: CHAIN (See above) LTRD (Gradient minimization with full Hessian at each step.) NEWTON (Energy minimzation alternative to DFP/BFGS) POWELL (Rapid gradient minimization routine.) PATH (Eigenvector following routine.) UVABS (*** TEST *** Computes the energy of electronic promotion.) LTRD is also useful in that the force constants from this calculation come out in INTERNAL rather than CARTESIAN coordinates. This makes analysis of the frequencies and movement along eigenvectors vastly easier. The POWELL keyword has become almost standard in the "hunt- and-peck" approach to transition state location due to its speed. PATH is an excellent approach to determining what will happen if a particular transition vector is followed. Also good for elimin- ating those pesky second and third negative eigenvalues in the Hessian. I feel that, in general AMPAC is a bit more advanced that MOPAC and contrary to popular thought, more robust. (Opinion showing through.) There are a significant number of computational chemists who feel just the opposite. (I even respect some of these people. :) ) In the interest of fairness, listed below are some of the features of MOPAC not present in AMPAC: IRC - Intrisic reaction coordinate following routine. ESP - Electrostatic potential fitting for point charges. EF - Eigenvector following optimization method. Note that I did not include the PM3 computational method as a "feature" of MOPAC. My opinion is that it is a disadvantage to have this avail- able. There are sound scientific reasons for this, but that is a discussion for another message that is too long. Also note that some items are implemented differently in MOPAC and AMPAC. Two notable examples are the configuration interaction (CI) routines and the polarizability. AMPAC's CI stuff was recoded completely by Daniel Liotard and is much more efficient and robust than the older stuff, which I believe is still included in MOPAC. The MOPAC polarizability approach is quite frankly superior to that in AMPAC. So, both programs have strengths and weaknesses, advantages and disad- vantages. Where you come down depends on your history and the work you need to get accomplished. Just a few points in closing: 1. AMPAC 2.1 is available from QCPE or anonymous ftp here at UMKC. It is in the subdirectory AHOLDER.AMPAC. Note that this is a homegrown version of the VAX/VMS program. 2. My information indicates that the newest version of MOPAC will soon be marketed and will not be available in a public domain format. Hope that this is helpful. (I have also wrapped my terminal in asbestos and have a fire extinguisher handy.) Enjoy..... Andy Holder =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER Assistant Professor of Computational/Organic Chemistry Department of Chemistry || BITNET Addr: AHOLDER@UMKCVAX1 University of Missouri - Kansas City || Internet Addr: aholder@vax1.umkc.edu Spencer Chemistry, Room 502 || Phone Number: (816) 235-2293 Kansas City, Missouri 64110 || FAX Number: (816) 235-1717 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@ccl.net Wed Feb 12 11:19:13 1992 Date: Wed, 12 Feb 1992 09:47 CST From: BROWNK@sask.usask.ca Subject: Product Operator Calculations To: chemistry@ccl.net Status: R I should have been somewhat more specific about my problem. My apologies. Part of the trouble is that the original paper uses plenty of Greek symbols so its difficult to reproduce them on the screen. Hmmm .... here is what I'll do. Let 'pi' stand for Greek lower case pi, 'Sig' stand for Greek upper case sigma, 'sig' stand for Greek lower case sigma and 'ta' stand for Greek lower case tau. The k's, l's, x's, y's and z's are subscripts. Now, the (to me) offending equations and text are: --------------------------------------------------------------------- 3/2pi Sig Ikx Sig piJkl2ta2IkzIlz pi/2 Sig Ikx sig(t_) --------------> --------------------> --------------> sig(t+2ta) (49) This can be simplified to: Sig piJkl2taIkyIly sig(t_) --------------------> sig(t+2ta) (50) --------------------------------------------------------------------- This is as close to the original text as I can manage on my terminal. I understand that IkyIly is the analog of IkzIlz and how to use it but I am puzzled at how the simplification from equation (49) to equation (50) is made. It is very likely something quite trivial that I am missing but I would certainly appreciate some illumination. ============================================================================== Keith Brown Department of Chemistry Magnetic Resonance Laboratory University of Saskatchewan Saskatoon, Saskatchewan BROWNK@SASK.USASK.CA