From ghammond@metz.une.edu.au Thu Apr 8 10:04:23 1993 From: Gerard Hammond Message-Id: <199304071404.AA18238@metz.une.edu.au> Subject: Has MOPAC7 Shipped Yet?? To: chemistry@ccl.net Date: Thu, 8 Apr 1993 00:04:23 +1000 (EST) Does anybody know when MOPAC7 will ship. Apparently the name will change and that it may become commercial in that businesses and academics will have to pay to play. I presume this means that everybody must get the programme though the QCPE and not by ftp. Thanks for any info. -- Gerard Hammond internet: ghammond@metz.une.edu.au Department of Chemistry Telephone: 067 - 732382 University of New England Armidale NSW 2351 Australia From markm@iris.polymer.uakron.edu Wed Apr 7 06:00:13 1993 Date: Wed, 7 Apr 93 10:00:13 -0400 From: markm@iris.polymer.uakron.edu (Mark Alan Matties) Message-Id: <9304071400.AA17613@iris.polymer.uakron.edu> To: chemistry@ccl.net Subject: dissertations via anon ftp i'm glad to see that others have been actively wondering about having dissertations available via anonymous ftp. i've recently inquired of my advisor about setting up an anonymous ftp server with the dissertations from our department. this is still in the kicking it around stage of discussion, but if there were enough interest, he would might want to expand it to also include computational type dissertations. i don't think he reads this list regularly, but he does read the neomig list. i will be VERY interested in discussing this further with any who care to do so. mark ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mark alan matties u of akron markm@iris.polymer.uakron.edu dept of polymer science "aoibheann beatha an scola/ire" akron, ohio, usa From BALLY@CFRUNI52.bitnet Wed Apr 7 11:54:20 1993 Message-Id: <199304071532.AA03353@oscsunb.ccl.net> Date: Wed, 7 Apr 93 17:31 N From: Subject: SQM force field program To: CHEMISTRY@ccl.net Dear SQM force field fans, my reply to the inquiry of Dr. El-Azhari on the subject of SQM force fields has elicited a great number of requests for both Dr. Tang's thesis and the program he has helped to develop. In the wake of this wave of requests, let me make the following three comments: 1) There is nothing magic about Dr. Tang's thesis. He has not (re)invented the wheel in any way and most of what he writes is from textbooks such as Califano's "Vibrational States" or the classical Wilson, Decius & Cross as well as from original papers available in the literature. I will have to see in what form I can distribute the parts of the text which are of general relevance. The idea with a postscript data bank sounds good! 2) I was really impressed with the apparent need of so many colleagues for an SQM force field fitting program. Again, there is nothing magic to this. We started from QCPE program #576 and added the transformation from car- tesian to internal coordinates, the Gaussian interface and other goodies here and there (for example the dipole moment derivatives El-Azhar was interested in), until the program suited our needs. However, as I said in my reply to El-Azhar, our code is barely stable enough to solve our current problems and would probably lead to great frustration in the hands of the "uninitiated". 3) In view of the situation, I am considering to invite Dr. Tang back to Fribourg to whip the program into a shape which would permit its orderly distribution. The problem is that I have to find funds, but I am working on this (perhaps some of you folks from commercial institutions have an idea how I could suceed). I am keeping a list of all colleagues who have announced interest and I promise to get back to you as soon as I know about the future of this project. However, you might have to be a bit patient, a distribution version of our program will in any event not be available before the end of the year (Tang is on a postdoc in the US until October and we have all hands full of other stuff to do). Have a nice Easter weekend! thomas ------------------------------------------------------------------------------ | Prof. Thomas Bally | E-mail: BALLY@CFRUNI52 | | Institute for Physical Chemistry | | | University of Fribourg | Tel: 011-41-37 826 489 | | Perolles | FAX: 011-41-37 826 488 | | CH-1700 FRIBOURG | | | Switzerland | | ------------------------------------------------------------------------------ From nauss@wrair-emh1.army.mil Sun Apr 7 06:00:00 1993 Message-Id: <199304071512.AA02951@oscsunb.ccl.net> Date: 7 Apr 93 11:00:00 EST From: nauss@wrair-emh1.army.mil Subject: Summary of replies about simulated annealing To: "chemistry" Good day, all - Some time ago I posed a question to the net about simulated annealing. Finally, here is a summary of responses I received. Warning: it is somewhat lengthy. Direct quotes are in parenthesis. Everything else is my edited summary. My apologies if my editing loses some of the flavor (or, God forbid, the meaning) of the responses. My thanks to all who offered opinions. My original question follows: >I am trying to refine some structural homology models of proteins. One >approach I am considering is simulated annealing. However, I want to ensure >that I understand the concept first. Please correct me if I am in error. >As I understand it, simulated annealing is simply a molecular dynamics >simulation where the protein is heated to a rather high temperature then slowly >cooled down to zero. The protein is then locked into some low energy >conformation which it was close to at the higher temperature. In order to get >accurate results, one needs to perform the simulation several times and obtain >a consensus structure. How am I doing so far? >Okay, so here are my questions. >(1) Can the procedure be implemented using the standard MSI CHARMM package or >is a special (and maybe proprietary) version needed? Has anyone a script file I >can use to learn by example? >(2) How high a temperature is needed? 300K, 600, 900, more? >(3) Any good references for learning how to use simulated annealing? >(4) Am I missing anything in my understanding of the technique? ************************************************************************************* From: Bob Funchess MOLECULAR SIMULATIONS HOTLINE SUPPORT 16 New England Executive Park Burlington, MA 01803-5297 hotline@msi.com "You are correct about simulated annealing. One thing is that you need to go to a much higher temperature such as 5000K." He also provided a much appreciated CHARMm script as an example for performing simulated annealing. I will be happy to provide the script to anyone upon request. ************************************************************************************* >From "arne" (arne@mango.mef.ki.se) "I think that you are correct in your assumptions." Some other comments are: 1. "I am quite doubtfull that a sim. annealing approach will work without any "extra" information, such as NOE constrains or something else." 2. "Temperature: I am using a 500 K temperature without any cooling period for modelling BPTI and small helical segments." 3. "references: The original paper was : Brunger, Clore et al, PNAS,83,3801-3805 (1986)" ************************************************************************************* From: David C. Doherty Computational Scientist Minnesota Supercomputer Center doherty@msc.edu "Functionally, this is correct, but usually simulated annealing involves taking monte carlo steps, and following a schedule of temperature lowering. How you design that schedule (how many steps of MC or MD to take) is something of an art." Temperature is suggested to be of 700-1000K to start. ************************************************************************************* From: Georgia B. McGaughey Computational Center for Molecular Structure and Design Department of Chemistry University of Georgia, Athens, GA 30602 georgia@Huckel.chem.uga.edu Georgia provided two references for the use of SA with NMR data. 1. James TL. Relaxation Matrix Analysis of Two-Dimensional Nuclear Overhauser Effect Spectra. "Current Opinion in Structural Biology, 1, 1042 (1991). 2. Clore GM, Nilges M, Gronenborn A. Determination of Three- Dimensional Structures of Proteins in Solution by Dynamical Simulated Annealing with Interproton Distances Derived from Nuclear Magnetic Resonance Spectroscopy. Computer-Aided Molecular Design, Richard WG, ed. 203 (1989). ************************************************************************************* From: Emil Marcus Biophysics PhD Student University at Buffalo / Roswell Cancer Institute marcus@acsu.buffalo.edu "Simulated Annealing is a Monte Carlo ("random draw", "throwing the dice") method that can be quite successful in dealing with large combinatorial optimization problems, such as finding the conformation of a protein (i.e. find the position - cartesian coordinates or dihedral angles of all, or only a targeted number of atoms, such as those which are part of the backbone or side chain). The idea underlying most conformational searches is to find a set of coordinates (cartesian or dihedral) that minimize the potential energy of the system. Unfortunately, the conformational space of a protein features (very)many local energy minima... Simulated Annealing overcomes the major inconvenient of a typical gradient(derivative) - based method: that of remaining/being trapped in a local minima. SA *samples* the conformational space, prevents being trapped in local energy minima because, due to its Monte Carlo nature it is able to "jump" from one minima to another. It does not promis/guarantee the global minimum, however, if used carefully, and in combination with other search methods (such as homology...) can provide good results: consider for instance the pentapeptides, Met- and Leu- Enkephalin." "No SA option is provided (even) in the last version of Charmm, Charmm - Version 22.0.b - April, 1991, I have recently used. Neither is it available with the Amber or Ecepp force fields." ************************************************************************************* From: Lee Herman HERMAN@ULNA.BWH.HARVARD.EDU "The heating phase is a trick to push the structure into parts of the conformational surface that are dissimilar to the starting structure. This structure is then allowed to minimize (cool) to a local minimum. This final structure can be quite different locally from the "hot" sampled structure, allow in terms of tertiary structure you're right, they're probably pretty close. "Watch out when it comes to sampling conformational space "a few times". The degrees of freedom for a structure such as protein can be enormous. Adequate sampling is essential in searching for a "global minimum" (if you think it's important, that is. It may not be.). Adequate sampling is also necessary in order to properly estimate properties. Find literature on how many samples are appropriate for the kind of system you're looking at." ************************************************************************************* From: Gerard J. Kleywegt Department of Molecular Biology Biomedical Centre Sweden rd@xray.bmc.uu.se "We use this technique often while refining protein structures against crystallographic data. In those cases, we start at 3000 or even 4000 K and do a fast-cool (steps of 50 K) or a slow-cool (steps of 25 K) down to 300 K. I don't know about CHARMm, but XPLOR (which, I think, is also sold by MSI) does a good job at it." He strongly recommended using some experimental data as constraints in the SA. ************************************************************************************* From: Chris Chen Agouron Pharmaceuticals, Inc San Diego, CA 92121 chen@tbone.agouron.com "The higher the temperature, the better the calculation theoretically. 900K is a best choose when I used MMOD to do the calcs. Another thing probably need to be mentioned. When you cool down the very high temperature, you may have to consider which way is better: stepwise annealing or contiuns annealing. That will cause different results." ************************************************************************************* From: Jim Poole, Ohio University, Dept. of Chemistry jim@quanta.phy.ohiou.edu or jpoole@oucsace.cs.ohiou.edu "You have probably already gotten lots of response but here are a few references that I have found for sim.-ann. Treutlein, et al. (1992) Biochemistry 31,12726-12733 best Nilges and Brunger (1993) Proteins:Str. Fxn. Gen. 15, 133-146 Brunger (1991) Ann. Rev. Phys. Chem. 42, 197-233 Kirkpatrick, et al. (1983) Science 220, 671-680" From tony@wucmd.wustl.edu Wed Apr 7 07:46:53 1993 Date: Wed, 7 Apr 93 12:46:53 -0500 From: tony@wucmd.wustl.edu (Tony Dueben) Message-Id: <9304071746.AA01478@wucmd> To: chemistry@ccl.net Subject: computational chemistry / undergrad I skimmed over C. Cramer's course material used in a grad level course at the U. of Minn. I wondered whether anyone had tried to put together a course in computational chemistry at the undergraduate level (Sr. yr.). This would be primarily of value for students at four-years institutions and those schools w/o graduate programs. I will be returning to such an intitution after my sabbatical here, and your responses could be useful. Please send me syllabi, supplemental info. and your evaluation of the success (and problems) of teaching a computational chemistry course at the undergraduate level. I will summarize your responses and make them available to all on the network. Anthony J. Duben Center for Molecular Design Washington University Campus Box 1099 One Brookings Drive St. Louis MO 63130 tony@wucmd.wustl.edu From jstewart@fujitsu.fai.com Wed Apr 7 07:45:52 1993 Date: Wed, 7 Apr 93 14:45:52 PDT From: jstewart@fai.com (Dr. James Stewart) Message-Id: <9304072145.AA20863@fujitsu.fai.com> To: chemistry@ccl.net Subject: MOPAC 7 and MOPAC 93 release MOPAC 7 and MOPAC 93 There has been a delay in the release of MOPAC 93 and MOPAC 7. A few copies of the program are being shipped to various sites, but the general release is being delayed for a while. I apologise for this delay, and can only commiserate with users. The cause of the delay is not obvious, and I have no control over it. The delay is not due to anything resulting from actions at the QCPE, so please do not bug Richard Counts. If you do, he will bug me, and I'm as frustrated as anyone. Jimmy Stewart From ross@cgl.ucsf.EDU Wed Apr 7 09:08:39 1993 Date: Wed, 7 Apr 93 16:08:39 -0700 Message-Id: <9304072308.AA23903@socrates.ucsf.EDU> From: ross@cgl.ucsf.edu (Bill Ross ) To: chemistry@ccl.net Subject: annealing Some comments on the comments about annealing: "Simulated Annealing is a Monte Carlo ("random draw", "throwing the dice") method The basis of annealing is the heating up and cooling of something to reach a globally lower energy. In the simulation context, Monte Carlo is one method that might be used for annealing or other purposes. The other method that I am familiar with is dynamics. In the general sense then, the high temperatures can be simulated by either random or deterministic methods. In fact, as I understand it, 'annealing' has been generalized to encompass any method in which normal conditions have been permuted temporarily to enable an energy barrier to be crossed, i.e. futzing with other things than temperature, and in contexts where temperature does not exist. In the molecular context, lowering the torsional potentials for a period and then turning them back on would be an annealing protocol. "No SA option is provided (even) in the last version of Charmm, Charmm - Version 22.0.b - April, 1991, I have recently used. Neither is it available with the Amber or Ecepp force fields." >From what I have said above, it should be clear that annealing has Some clips from the manual: This is a guide to sander, a new AMBER module which allows NMR-NOE refinement. The acronym stands for Simulated Annealing with NMR-Derived Energy Restraints. The features described below allow one to "easily" carry out refinements using NOE- derived restraint distances, torsion angle restraints, and penalty functions based on chemical shifts and NOESY volumes. Sander also offer an excellent interface to protocols such as simulated annealing, etc., ... Also in the ../dat/nmr directory is a script, mk_chir_cons, which creates constraints relating to chirality and peptide bonds. Use of these constraints will ensure that high-temperature annealing runs do not destroy chirality or flip peptide bonds. Bill Ross