From chemistry-request@ccl.net Mon Feb 10 03:26:11 1992 Date: Mon, 10 Feb 92 00:02 PST From: Subject: mopac automation To: CHEMISTRY@ccl.net Status: R Thanks to all who replied to my question on MOPAC automation. I was surprised at the number and variety of responses, and all that I tried in unix worked! Thanks again! Andrew A. Mundt WSU Department of Biochemistry f0418950@jaguar.csc.wsu.edu From chemistry-request@ccl.net Mon Feb 10 08:06:31 1992 From: Mark Forster Date: Mon, 10 Feb 92 11:46:37 GMT To: CHEMISTRY Status: R Subject: AMSOL on UNIX platforms. 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, I am interested in the AMSOL package for incorporating solvent effects into semi-empirical calculations (AM1). The package is described in J. Amer. Chem. Soc. vol 113, 8552 (1991) and vol 113, 8305 (1991). I have e-mailed QCPE and the one of the authors Chris Cramer. AMSOL is a CRAY program but I would like to run it on a Silicon Graphics or SUN/SPARC workstation. Has anyone out their ported AMSOL to a more general UNIX platform. Chris Cramer has pointed out the following possible problems. >The only barriers are getting all of the >double precision function calls and double precision type variables to >agree (since the Cray is a 32 bit machine, we compile with double >precision disabled, and the problem is avoided). This is tedious, but >very straightforward. Additionally, one or two matrix manipulation >subroutines (e.g. one called MXM) have to be added to replace the >Cray library routines. These are again fairly straightforward. If anyone has achieved the port and are willing to distribute it would they kindly let me know ? It would also be nice to let QCPE distribute the ported version and make AMSOL available to a wider audience. Best Wishes Mark J. Forster p.s. sending message to CHEMISTRY%ccl.net@uk.ac.nsfnet-relay From chemistry-request@ccl.net Mon Feb 10 12:35:12 1992 Date: Mon, 10 Feb 92 17:05:33 GMT From: James P. Schmidt To: CHEMISTRY@ccl.net Subject: amsol Status: R In response to Mark J.Forster's inquiry anout amsol: I have cut Crahmer and Truhlar's solvation code into the Unix version of MOPAC 6.0 which we are running on SGI platforms. This code is available by anonymous ftp at crocus.medicine.rochester.edu and can be found in the directory jones as MOSOL.tar.z. No guarantees are made about the performance of this code. I have observed it to give answers agreeable with the test jobs provided with the QCPE version of AMSOL and have been using for about month. The tests and instructions are not currently included in tar, nor are the modifications fully commented. The tests and instructions can be obtained from the QCPE distribution of AMSOL with the modification that the DERINU keyword is not to be specified since MOPAC does derivitives numerically by default. If anyone takes this code and uses it, I would appreciate feedback on any problems that you encounter for my own edification. Since this is not my original code, and I am aware that others are working on the incorporation of the code into Mopac, this code may at some future point be made unavailable if the original authors release an official version. Again I point out, no guarantees or representations as to the performance or quality of this code are made by me or any others at this site. The code appears to run fine but has not been through rigorous testing with CI or reaction coordinates, etc. PS- I have been informed while writing this posting that there is a yet un- released program which may be named mosol and has nothing to do with Mopac or SM1/SM1a, if this is the case the name of the tar on crocus may be changed to avoid confusion with this program. Jim Schmidt University of Rochester jims@duce.rochester.edu From chemistry-request@ccl.net Mon Feb 10 13:57:05 1992 Date: Mon, 10 Feb 92 13:32:47 EST From: Lynn Baird Subject: Summer Undergraduate Program at Cornell University To: chemistry@ccl.net Status: R Below is an announcement for a summer program for undergraduates. There are a number of chemistry projects--so if you know any undergraduate students who might be interested, please feel free to forward this mail! *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* Supercomputing Program for Undergraduate Research June 8 - August 14, 1992 Cornell University Ithaca, New York The Cornell Theory Center's Cornell National Supercomputer Facility is pleased to announce the 1992 Supercomputing Program for Undergraduate Research (SPUR), which offers undergraduate students the opportunity to pursue a computational science research project while developing skills in the use of high performance computing technologies. Students may apply to work on a specific research project under the guidance of a faculty or staff member at Cornell University (see list of projects below). The proposed projects explore current research problems in areas such as chemistry, physics, environmental engineering, geology, electrical engineering, and mathematics. Several of the projects include a strong visualization component. Successful applicants will attend a 10-week research program at Cornell University and will pursue the research projects using the computing resources of the Cornell National Supercomputer Facility (CNSF), including the use of vector and parallel processing, large memory, visualization tools, and distributed processing. Students will also receive a $2,000 stipend, travel allowance, and room and board (shared dorm rooms) during the 10-week program. Several of the best students will be invited to present poster sessions at national conferences (expenses paid). ------------------------ Eligibility Requirements ------------------------ - Relevant coursework for research area - Coursework or programming experience in FORTRAN or C - Graduation date not before December 1992 - U.S. Citizen, U.S. National, or permanent resident Women, minorities, and persons with disabilities are strongly encouraged to apply. Students from four-year colleges with limited research facilities are also encouraged to apply. ------------ Project List ------------ One applicant will be selected to work on each of the research projects listed below. During the first two weeks of the program, students will receive intensive training in the use of supercomputers and other high performance computing resources. For the remaining eight weeks, each student will focus on the specific research problem under the guidance of the research advisor. Weekly seminars on research topics will be presented throughout the 10 weeks, and CNSF technical consultants will be available to provide technical support on the use of computing tools and technologies. By the end of the program, each student will prepare a final written report and give an oral presentation of his or her research accomplishments to peers, faculty, invited scientists, and Theory Center staff. Seismic Imaging of the Subsurface: Parallelization Across Multiple Workstations Dr. Larry Brown, Geological Sciences Linear Algebra Algorithms R&D on a Cluster of RISC System/6000's Dr. Adolfy Hoisie, Cornell Theory Center The Mechanism of Hydroboration. An Ab initio Study of the Reaction of Ethylene With Boranes Dr. Charles Wilcox, Chemistry Time-Dependent Quantum Mechanical Study of the Photodissociation of HCO via a Renner-Teller Mechanism Dr. Evelyn Goldfield, Cornell Theory Center Applications of Simulated Annealing Algorithm to the Analysis of High Resolution Spectra Dr. Laura A. Philips, Chemistry Modeling and Visualization of Magnetohydrodynamics Dr. Steve Lantz, Cornell Theory Center The Sudden Cardiac Death Syndrome Dr. Niels Otani, Electrical Engineering Why Does the Sun have a Magnetic Field? Dr. Niels Otani, Electrical Engineering A Computational View Into Cytochrome c Dr. Atsuo Kuki, Chemistry Visualization of High-Dimensional Quantum Mechanical Systems Dr. Bruce Land and Dr. Malvin Kalos, Cornell Theory Center Vectorial Decomposition of a Reaction Coordinate Dr. Barry Carpenter, Chemistry -------- To Apply -------- Applicants must submit a completed application form, two faculty letters of recommendation, and college transcript(s). Applications must be received by March 6, 1992. Students will be notified of their acceptance no later than April 1. For more information or an application (including all forms and project descriptions), contact: Judith Eastman Workshop Coordinator Telephone 607-254-8686 Fax 607-254-8888 judy@theory.tc.cornell.edu ======================================================================== It is anticipated that this program will be sponsored by the National Science Foundation; the program is dependent upon approval of funding through the Research Experiences for Undergraduates Program. From chemistry-request@ccl.net Mon Feb 10 16:05:02 1992 Date: Mon, 10 Feb 92 20:30:04 GMT From: James P. Schmidt To: CHEMISTRY@ccl.net Subject: correction Status: R In my earlier posting I incorrectly reported my e-mail address as jims@duce.rochester.edu. The correct address is below. Jim Schmidt jims@duce.medicine.rochester.edu From chemistry-request@ccl.net Mon Feb 10 16:05:25 1992 Date: Mon, 10 Feb 92 12:37 PST From: Subject: mopac automation answers To: CHEMISTRY@ccl.net Status: R Here's a summary of the answers I got to my MOPAC question. I've cut to the chase and just put the 'meat' of the answers here. The one that worked very well for my situation was the csh shell script given in the 1st and 3rd answers. The names of those who gave the answers are given to give credit where credit is due and also to direct those with questions to the source. Andrew. This is dependent on the type of system you're using, but if all your input files are named according to some pattern, you can set up a csh script such as foreach inp (*.inp) mopac $inp end and run this in batch or "nohupped". Is this what you're looking for? -- David J. Heisterberg (djh@ccl.net) The value of philosopy is, in fact, to be The Ohio Supercomputer Center sought largely in its very uncertainty. Columbus, Ohio -- Bertrand Russell Mike Cooledge at the Seiler Research Lab at the USAF Academy has written a set of very nice scripts for setting up a queue that will run jobs one after the other. You can add jobs to the list or remove them also. The problem is that I have missplaced his e-mail address. You should be able to get in touch with a (719) 472-2655. KURTZH@MEMSTVX1.BITENT Try the equivalent of the following UNIX C shell script: #! /bin/csh foreach f (*.dat) mopac `basename $f .dat` end where the "basename" command removes the '.dat' file extension (our version of the MOPAC script wants just the root file name). Mike. system@alchemy.chem.utoronto.ca In our UNIX (GENIX5.3) system all you have to do is to invoke MOPAC filename1 filename 2 filename3 ... & On UNIX systems the & puts the jobs in the background where they run merrily without anyone knowing about them. When they are done the flassk MOPAC DONE will appear on the screen. This does not amuse anyone who is doing something else so we preface our MOPAC call with nohup. the messages from mopac are then in a file called nohup.out. The entire procedure looks like this on our AEON system NOHUP MOPAC filenmae1 filename2 filename3... & The.dat extenders are not needed. K.R.Fountain/ sc18@NEMOMUS This may not help you but there is a great method of automating MOPAC (or any other type of molecular modelling calculation or operation) in the CHEM-X modelling package. You can set up the type of calculation required, run the batch of molecules and even get CHEM-X to save the results you want into a molecular spreadsheet ready to do statistics on. CHEM-X is relatively inexpensive (compared with its competition) . You can contact Chemical Design Ltd (Oxford) by fax on 44-861-250-270. Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. dave@carbon.chem.csiro.au If I were running MOPAC on a Vax I would use the "SYNCHRONIZE" DCL command. Surely there is something similar in UNIX? SYNCHRONIZE lets you submit multiple batch jobs that won't start until the previously "synchronized" one completes. This works great on a Vax, but I don't know if there is something similar under UNIX. Greg Durst DowElanco Indpls, IN DURST_GREGORY_L@LILLY.COM store all what you do usually to run mopac in a command file for example : cp toto1.dat FOR005 mopac cp FOR006 toto1.results rm FOR005 cp toto2.dat FOR005 mopac cp FOR006 toto2.results etc .... you can run this file by the command batch or at if you work on a unix work station ------ Francois BAYARD | e-mail bayard@chitheo1.univ-lyon1.fr UNIVERSITE CLAUDE BERNARD LYON 1 | tel (+33) 72 44 82 79 43 Bd du 11 Novembre 1918 | fax (+33) 72 44 08 03 F-69622 VILLEURBANNE - FRANCE | -------------------------------------------------------------------------- From chemistry-request@ccl.net Mon Feb 10 16:06:11 1992 Date: Mon, 10 Feb 1992 14:10 CST From: BROWNK@sask.usask.ca Subject: Product operator calculations To: chemistry@ccl.net Status: R Is anyone familiar with O.W. Sorensen's product operator formalism for calculating the results of nmr pulse sequences? I am reading his original paper on the subject (Prog. NMR Spec., 16, 163-192, 1983) and have become desperately hung-up on a stated result. Specifically, the transformation from equation 49 to equation 50 is the puzzler. The upshot of the whole thing is that one can describe a pi/2 - t - pi - t - pi/2 pulse sequence as a bilinear rotation about the x or y axis in the rotating frame. However, I do not understand how he manages the transformation. Any help would be appreciated. Keith Brown University of Saskatchewan Saskatoon, Saskatchewan From chemistry-request@ccl.net Mon Feb 10 16:34:40 1992 Date: Mon, 10 Feb 92 14:34:55 EST From: "Dr./CPT Christopher J. Cramer" To: chemistry@ccl.net Subject: AMSOL and MOPAC Status: R Netters, The message attached below describes a chimeric MOPAC version modified by inclusion of the subroutines from AMSOL which calculate aqueous free energies of solvation. AMSOL is Cramer and Truhlar's modification of AMPAC 2.1. I must point out that this simple transfer of subroutines is doomed because of the way in which the two programs calculate derivatives with respect to nuclear motion, i.e. geometry optimization. AMSOL requires use of the keyword 'DERINU'. It is unfortunate that this keyword 'appears' to be a request for derivatives calculated numerically. In fact, the default optimization techniques for both AMPAC and MOPAC calculate derivatives numerically. Moreover, the gradients are calculated as the sum of all pairwise contributions from every unique two-atom pair where one of the atoms HAS BEEN MOVED. Without getting bogged down in the details, this is a pleasantly fast procedure because the energy calculations involve rather small matrices -- at most 8 by 8. However, the theory underpinning AMSOL does not allow this decomposition to be made -- ALL pairwise interactions are affected by the movement of a single atom, specifically the Coulomb radii used in the calculation of G(ENP) are changed purely as a result of the new geometry. Moreover, the movement of any one atom may cause a significant change in both the density and Fock matrices as a result of charge redistribution, and the above approach does not permit the Coulomb radii to relax accordingly. It is thus deficient in two significant respects. To arrive at true stationary points, gradients must be calculated using the full Fock and density matrices. This is what 'DERINU' accomplishes. From my perusal of MOPAC 6.0 such an option is not incorporated into that code (indeed, the AMPAC code makes it clear that this is regarded as somewhat archaic, but with solvation effects turned on it can not be avoided). Thus, structures optimized by the modified MOPAC are NOT true stationary points, although they may be quite close depending on the molecule in question. In general, however, molecules which are either highly polarizable or incorporate atoms with large partial charges will not be treated well by the pairwise-summation approach. We are not advocating AMPAC over MOPAC (or vice versa) in any way. It would not be terribly difficult to modify the MOPAC subroutine DCART.f to permit the equivalent gradient calculations to be performed. However, the latest version of MOPAC does not come so equipped, and that is one of the chief reasons we chose to create AMSOL as opposed to "MOSOL". Chris Cramer Date: Mon, 10 Feb 92 17:05:33 GMT From: James P. Schmidt To: CHEMISTRY@ccl.net Subject: amsol Date: Mon, 10 Feb 92 16:58:11 EST From: kpc23%CAS.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU (Kevin P. Cross Ext. 3192 Room 2209B) Subject: Useful Numeric Property Data To: CHEMISTRY@ccl.net.bitnet Status: R Dear netters: Chemical Abstracts Service is interested in the types of numeric data you would like to see associated with structures and how you would use such data. This could be data for molecular modeling, computational chemistry, etc. In particular, we are interested in useful types of data that could be calculated for large numbers of structures that users might find beneficial when searching in conjuction with structures. We welcome any and all suggestions! Sincerely, ~ Kevin P. Cross, Ph.D. Research Chemical Abstracts Service 2540 Olentangy River Road P.O. Box 3012 Columbus, OH 43210 ~ kpc23@cas.org Internet kpc23@cas Bitnet From chemistry-request@ccl.net Mon Feb 10 17:34:17 1992 From: Dan Severance Subject: Gaussian basis sets for Iodine and Bromine To: CHEMISTRY@ccl.net Date: Mon, 10 Feb 92 17:03:16 EST Organization: Laboratory for Computational Chemistry Status: R Hi, Does anyone know of reliable ab initio basis sets for iodine and/or bromine? I know of a few out there, but I'd like to know which ones are the most reliable in other's experience? Thanks in advance! Dan Severance dan@omega.chem.yale.edu From chemistry-request@ccl.net Mon Feb 10 17:58:47 1992 Date: Mon, 10 Feb 92 22:37:37 GMT From: James P. Schmidt To: CHEMISTRY@ccl.net Subject: amsol Status: R I appreciate C.Cramer pointing out the defiency in my 'chimeric' mosol code. I cannot at this time remove the code from the ftp site it is at, so I request that noone take it until the problem is fixed unless they wish to undertake corrective measures themselves. Jim Schmidt jims@duce.medicine.rochester.edu From chemistry-request@ccl.net Mon Feb 10 19:17:29 1992 Date: Mon, 10 Feb 92 18:38:04 EST From: alper@zohar.bms.com To: chemistry@ccl.net Status: R if anyone knows the whearabouts of rob rosenberg, please e-mail me at alper@zohar.bms.com (internet) thanks howard alper From chemistry-request@ccl.net Mon Feb 10 22:34:35 1992 Date: Tue, 11 Feb 1992 14:12:54 +1100 From: apa@ccadfa.cc.adfa.oz.au (Alan P Arnold) To: chemistry@ccl.net Subject: ESP 'version' of AMPAC ?? Status: R Dear colleagues, for a while now I have been using a version of MOPAC 6.0 which allows the fitting of atom-centered point-charges to the calculated molecular electrostatic potential. If I remember correctly, it originated from Brent Besler (sorry if I have acknowledged the wrong person...). In light of recent postings about AMSOL (vs MOSOL), can someone tell me whether there is an AMPAC version which allows ESP-fitting of point charges? PS What are the pros and cons of AMPAC vs MOPAC?? (That should generate some friendly discussion ;-) .