From ndaisy@cobra.ordata.com Tue Feb 28 02:43:58 1995 Received: from ordata.com for ndaisy@cobra.ordata.com by www.ccl.net (8.6.9/930601.1506) id CAA00744; Tue, 28 Feb 1995 02:15:17 -0500 Received: from pppndaisy.ordata.com by ordata.com with smtp (Smail3.1.28.1 #2) id m0rjM7Y-0002cxC; Mon, 27 Feb 95 23:13 PST Date: Mon, 27 Feb 95 22:56:55 PST From: "Nick K. Daisy" Subject: FFT flters To: chemistry@ccl.net X-Mailer: Chameleon - TCP/IP for Windows by NetManage, Inc. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII We are developing intrinsic viscosity data from an old system to justify future capitol investment in new equipment. The major drawback currently is reducing the pump pulsation from the data stream. A fft treatment would seem proper, and although our programmer is able to transform the data stream to a fft transform and back, we lack the knowledge of how to implement a filter. Any help would be appreciated. NKD From kreidler@hp817s.rz.uni-duesseldorf.de Tue Feb 28 05:42:56 1995 Received: from hp817s.rz.uni-duesseldorf.de for kreidler@hp817s.rz.uni-duesseldorf.de by www.ccl.net (8.6.9/930601.1506) id FAA01545; Tue, 28 Feb 1995 05:01:26 -0500 Message-Id: <199502281001.FAA01545@www.ccl.net> Received: by hp817s.rz.uni-duesseldorf.de (1.37.109.14/16.2) id AA063935699; Tue, 28 Feb 1995 11:01:39 +0100 From: Kay Kreidler Subject: microscopic dissociation To: chemistry@ccl.net (Theochem Liste) Date: Tue, 28 Feb 95 11:01:38 MEZ Mailer: Elm [revision: 70.85.2.1] Dear colleagues! Did any one of you try to calculate microscopic dissociation constants by any kind of computational chemistry method? Did you have any success? Are there hints in the literature? Any kind of advice will be useful. I will summarise the result to the mailing list. Thanks in advance Kay Kreidler Institut fuer Anorganische Chemie und Strukturchemie I Heinrich-Heine-Universitaet Duesseldorf Universitaetsstr. 1 40225 Duesseldorf Email: kreidler@uni-duesseldorf.de From wdi@ccl.net Tue Feb 28 07:42:56 1995 Received: from schiele for wdi@ccl.net by www.ccl.net (8.6.9/930601.1506) id HAA02130; Tue, 28 Feb 1995 07:02:00 -0500 Received: by schiele (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@ccl.net id MAA11111; Tue, 28 Feb 1995 12:58:20 +0100 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9502281258.ZM11109@schiele> Date: Tue, 28 Feb 1995 12:58:17 +0100 Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: GDCh-CIC Mailing List Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Due to some convoluted problems involving access permissions, nfs crossmounts and a non-standard mail system there were some problems from Saturday to Tuesday morning (local time) with the mailing list manager for the GDCh-CIC mailing list. Please check if you were a victim: The sympton is a compete loss of mail sent from some places when trying to subscribe to the GDCh-CIC mailing list via majordomo@eros.ccc.uni-erlangen.de with 'subscribe gdch-cic' in the mail body. So please if you did not receive any answer (i.e. a message indicating success or failure of subscription and the info file) subscribe again. We apologize for the inconvenience. Once more the info file for the mailing list: *************************************************************************** Diese Mailing-Liste mit dem Namen 'gdch-cic' befindet sich unter der Adresse 'eros.ccc.uni-erlangen.de' im Computer-Chemie-Centrum der Universitaet Erlangen-Nuernberg. Sie ist ein elektronisches Diskusssionsforum der Fachgruppe 'Chemie Information Computer' (CIC) in der GDCh, der Gesellschaft Deutscher Chemiker. 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Bitte senden Sie Ihre Meldungen an 'gdch-cic@eros.ccc.uni-erlangen.de', nicht an 'majordomo'. Die 'majordomo' Adresse dient auschliesslich zum An- und Abmelden und fuer weitere Serviceleistungen. Benutzen Sie bitte eine aussagekraeftige 'Subject:' Zeile im Mailheader. Vor diese Zeile wird automatisch 'GDCH-CIC:' eingefuegt, so dass Meldungen aus dieser Quelle leicht in den Mailboxen der Empfaenger zu finden sind. Zur Zeit werden alle Nachrichten archiviert. Wir koennen keine unbegrenzte Aufbewahrung garantierten, aber es stehen auf jeden Fall die Nachrichten der letzten Wochen fuer Spaeteinsteiger zum nachtraeglichen Studium zur Verfuegung. Um diese gespeicherten Nachrichten zu erhalten, schicken Sie bitte das Kommando 'get gdch-cic aktuell' im Hauptteil der Nachricht an 'majordomo@eros.ccc.uni-erlangen.de'. An die Liste angekoppelt ist ein Archiv aktueller Dokumente, die die CIC betreffen, zum Beispiel Protokolle und Reports. Eine Uebersicht erhalten Sie mit dem Kommando 'index gdch-cic' im Hauptteil einer Nachricht an 'majordomo@eros.ccc.uni-erlangen.de'. Auch diese Texte stehen Ihnen ueber ein 'get' Kommando zur Verfuegung. Wenn Sie techische Fragen haben oder Probleme mit dem Bezug der Liste oder der Verbreitung Ihrer Meldungen, wenden Sie sich bitte an 'gdch-cic-owner@eros.ccc.uni-erlangen.de'. Erlangen, 24.2.95 -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 From thep@risc1.lrm.fi.cnr.it Tue Feb 28 09:48:38 1995 Received: from risc1.lrm.fi.cnr.it for thep@risc1.lrm.fi.cnr.it by www.ccl.net (8.6.9/930601.1506) id JAA01345; Tue, 28 Feb 1995 09:16:59 -0500 Received: by risc1.lrm.fi.cnr.it (AIX 3.2/UCB 5.64/4.03) id AA24404; Tue, 28 Feb 1995 14:32:47 +0100 From: thep@risc1.lrm.fi.cnr.it (Pornthep Sompornpisut) Message-Id: <9502281332.AA24404@risc1.lrm.fi.cnr.it> Subject: Chianti Workshop on Magnetic Resonance To: chemistry@ccl.net Date: Tue, 28 Feb 1995 14:32:47 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 3912 ******************************************************************************** 6th CHIANTI WORKSHOP ON MAGNETIC RESONANCE: NUCLEAR AND ELECTRON RELAXATION ******************************************************************************** SAN MINIATO (PISA), ITALY, MAY 27 - JUNE 2, 1995 CHAIRPERSONS: I. BERTINI (Univ. Florence), Conference Chairman K. MOEBIUS (Free Univ. Berlin), Program Chairman ORGANIZERS: R. BASOSI (Univ. Siena), C. LUCHINAT (Univ. Bologna), C.A. VERACINI (Univ. Pisa) The present Workshop, in the spirit of the series of the Chianti Workshops, aims at bringing together scientists involved in theoretical and experimental aspects of nuclear and electron spin relaxation to study the structure and dynamics of molecules. The main topics to be discussed by NMR and EPR scientists will deal with: structure determination of biomolecules, spin polarization phenomena and processes, relaxation in paramagnetic systems, quasi-ordered phases, spin imaging, new methodologies. The program will consist of invited lectures and poster presentations. At the moment the following scientists have accepted an invitation to present a lecture: L. Banci (Florence), G. Bodenhausen (Tallahassee), R.D. Britt (Davis), R. Bruschweiler (Zurich), M. Brustolon (Padova), D.A. Case (La Jolla), V. Chizhik (St. Petersburg), K.P. Dinse (Darmstadt), R.Y. Dong (Brandon), J.W. Emsley (Southampton), C. Forte (Pisa), J.H. Freed (Ithaca), E. Gaggelli (Siena), G. Giacometti (Padova), D. Goldfarb (Rehovot), C. Griesinger (Frankfurt/M.), R.G. Griffin (Cambridge, MA), E.J.J. Groenen (Leiden), B. Halle (Lund), A.J. Hoff (Leiden), B.M. Hoffman (Evanston), P. Hore (Oxford), W.L. Hubbell (Los Angeles), M. Huber (Berlin), J. Huttermann (Homburg), J.S. Hyde (Milwaukee), R. Ishima (Tsukuba), T.L. James (San Francisco), G. Kothe (Freiburg), J. Kowalewski (Stockholm), Ya.S. Lebedev (Moscow), H. Levanon (Jerusalem), W. Lubitz (Berlin), G.R. Luckhurst (Southampton), Z. Luz (Rehovot), M.W. Makinen (Chicago), K.A. McLauchlan (Oxford), A.E. Merbach (Lausanne), G. Navon (Tel Aviv), A. Pines (Berkeley), T.F. Prisner (Berlin), K.M. Salikhov (Kazan), S. Schlick (Detroit), R. Sharp (Ann Arbor), H.W. Spiess (Mainz), D. Stehlik (Berlin), U.E. Steiner (Konstanz), S. Styring (Stockholm), W.H. Thomann (Annandale), R.R. Vold (San Diego), L. Weiner (Rehovot), L. Werbelow (Marseille), P.O. Westlund (Umea). Participants intending to present posters on work related to the topics of the Workshop are asked to submit an abstract (max. 1 page A4 format typed single-spaced) of the proposed communication not later than April 15, 1995. Since the total number of participants is limited, acceptance will be on a "first come first served" basis. There is a registration fee of 250,000 Italian Lira for active participants and 120,000 Italian Lira for accompanying persons. The cost of the accommodation, based on sharing a twin-bedded room, plus all meals (including Chianti wine!) will be 700,000 Italian Lira per person. For further information, please contact: Prof. Riccardo Basosi, Dept. of Chemistry, Univ. of Siena, Pian dei Mantellini, 44, 53100 Siena, Italy,TEL. 39/577 298040,FAX 39/577 280405 Prof. Claudio Luchinat,c/o Dept. of Chemistry,Univ. of Florence Via G.Capponi, 7, 50121 Florence, Italy, TEL. 39/55 2757563, FAX 39/55 2757555 Prof. Carlo A.Veracini, Dept. of Chemistry, Univ. of Pisa Via Risorgimento, 35, 56100 Pisa, Italy, TEL. 39/50 918266, FAX 39/50 918260 or the Program Chairman: Prof. Klaus Moebius, Dept. of Physics, Free Univ. of Berlin, Arnimallee 14 D-14195 Berlin, Germany, TEL. 49/30 8382770, FAX 49/30 8386046 ############################################################################# For the REGISTRATION FORM please contact Giacomo Parigi giacomo@risc1.lrm.fi.cnr.it ############################################################################# From shubin@email.unc.edu Tue Feb 28 10:48:36 1995 Received: from email.unc.edu for shubin@email.unc.edu by www.ccl.net (8.6.9/930601.1506) id KAA03403; Tue, 28 Feb 1995 10:36:52 -0500 Received: by email.unc.edu (AIX 3.2/UCB 5.64/4.03) id AA257869; Tue, 28 Feb 1995 10:36:17 -0500 Date: Tue, 28 Feb 1995 10:36:17 -0500 (EST) From: Shubin Liu X-Sender: shubin@isisa.oit.unc.edu To: chemistry@ccl.net Cc: chemistry@ccl.net Subject: CCL:Density matrix and pair function from Gaussian 92 In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all CCLers: Can one obtain the density matrix (1st-order) and the pair function (giving a reference point) from Gaussian 92 output directly? I will give a summary here if there is any response. Shubin ............................................................................. Shubin Liu Department of Chemistry Email: shubin@email.unc.edu University of North Carolina sliu@mulliken.chem.unc.edu Chapel Hill, NC 27599-3290 Tel : (919) 962-0150(O) ............................................................................. From fant@bioc.rice.edu Tue Feb 28 11:48:28 1995 Received: from moe.rice.edu for fant@bioc.rice.edu by www.ccl.net (8.6.9/930601.1506) id KAA03765; Tue, 28 Feb 1995 10:50:10 -0500 Received: from babs.rice.edu by moe.rice.edu (JAA05028); Tue, 28 Feb 1995 09:50:07 -0600 Received: by babs.rice.edu (931110.SGI/) (for chemistry@ccl.net) id AA23500; Tue, 28 Feb 95 09:52:17 -0600 From: "Andrew Fant" Message-Id: <9502280952.ZM23498@babs.rice.edu> Date: Tue, 28 Feb 1995 09:52:16 -0600 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Results of Multi search Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Last week I asked if anyone could tell me where to find Multi. The current version can be found at ftp://kamakazi.niehs.nih.gov/pub/MULTI/MULTI-3.1 . Thanks to everyone that helped. Andy -- Andrew Fant | fant@bioc.rice.edu | "A Libertarian is someone Departmental Geek | (713)527-4774 | who wants police Biochemistry & Cell Biology | I disclaim, | protection from their Rice University | therefore I am | slaves" - K.S. Anderson From ANTHONY@admis.med.usf.edu Tue Feb 28 13:04:18 1995 Received: from pharm1.pharm.med.usf.edu for ANTHONY@admis.med.usf.edu by www.ccl.net (8.6.9/930601.1506) id MAA01020; Tue, 28 Feb 1995 12:48:30 -0500 Received: from admis.med.usf.edu ([131.247.70.101]) by pharm1.pharm.med.usf.edu (8.6.5/8.6.5) with SMTP id MAA11073 for ; Tue, 28 Feb 1995 12:48:25 -0500 Message-Id: <199502281748.MAA11073@pharm1.pharm.med.usf.edu> Received: from COM_ADM/MERCURY-MAIL by admis.med.usf.edu (Mercury 1.1); Tue, 28 Feb 95 12:46:36 +1100 To: Chemistry@ccl.net From: "Anthony Lemus" Organization: USF College of Medicine Date: Tue, 28 Feb 1995 12:46:24 EST Subject: Results of Graduate Programs query X-pmrqc: 1 Priority: normal X-mailer: WinPMail v1.0 (R1) I am posting the results of my query of PhD programs in computational chemistry for all those who requested this information. Thanks to all those who replied and sorry for the delay in compiling this data: ======================================================== Quantum Theory Project, University of Florida at Gainesville. The Quantum Theory Project is the home of ZINDO, ACESII, AMPAC, FLIMMSY, etc. and such luminaries as Michael Zerner, Rod Bartlett, and Nigel Richards, etc. Quantum Theory Project, Williamson Hall, University of Florida, Gainesville FL 32611 ----------------------------------------------------------------------------------------------------------------- There is a comp. chem. program here at UC Berkeley. And I believe that Stanford, Cornell, Madison WI, Caltech, and UCLA also have good programs. Clayton Springer ---------------------------------------------------------------------------------------------------------------- Consider Rutgers University in New Jersey. They have several professors there working on various aspects of theoretical chemistry. You may also want to look at the University of Georgia. Jeff Nauss ---------------------------------------------------------------------------------------------------------------- The Univ. of Houston has the chemical physics program joint by physics and engineering departments. The professors in computatinal area are: B.M. Pettitt, D.J. Kouri, T.A. Albright, etc.. ---------------------------------------------------------------------------------------------------------------- There is a program at Bryn Mawr College (near Philadelphia in Pennsylvania). Michelle M. Francl Associate Professor of Chemistry Bryn Mawr College Bryn Mawr, PA 19010 ----------------------------------------------------------------------------------------------------------------- The ACS sells a CD-ROM called Directory of Graduate Research. This is a chemical science directory of all colleges and universities offering chemistry curriculums. I can send you a brochure on it if you like? Just met me know. Nan Butterworth ---------------------------------------------------------------------------------------------------------------- I received a forwarded message from Dr. Jim Gano of our department that you were interested in graduate studies in computational chemistry. Dr. Hua Guo of our department is a nationally recognized computational physical chemist. If you would like information on his research, our graduate program in chemistry, please send me your address and I will have the information mailed to you. Jon Kirchhoff Chairman, Graduate Admissions Committee The University of Toledo ---------------------------------------------------------------------------------------------------------------- I don't know if there is a degree in comp. chem. anywhere, but William Jorgensen at Yale is well known in the field. In practice, you get your degree in either Physical chemistry or organic chemistry (or perhaps a more bio related field) depending on your major interests. This is true with most people in the field. (I got my degree from Bill). In addition, there is Peter Kollman at USCF pharmacy school, Ken Houk at UCLA, Andy McCammon at UCSD, all having somewhat different focuses within the field of computational chemistry. There are quite a few more, but those are most of the big names (Martin Karplus at Harvard) as a starting point. Take care, Dan ======================================================== Cheers! -ANT ______________________________________________________________________ Anthony Lemus (813) 974-3427 -Systems Analyst University of South Florida Anthony@admis.med.usf.edu College of Medicine ______________________________________________________________________ From windemut@cumbnd.bioc.columbia.edu Tue Feb 28 14:04:17 1995 Received: from cumbnd.bioc.columbia.edu for windemut@cumbnd.bioc.columbia.edu by www.ccl.net (8.6.9/930601.1506) id NAA02543; Tue, 28 Feb 1995 13:38:00 -0500 Received: from sirius by cumbnd.bioc.columbia.edu (NX5.67d/NX3.0M) id AA24600; Tue, 28 Feb 95 13:37:53 -0500 From: Andreas Windemuth Message-Id: <9502281837.AA24600@cumbnd.bioc.columbia.edu> Received: by sirius.bioc.columbia.edu (NX5.67d/NX3.0X) id AA25968; Tue, 28 Feb 95 13:37:54 -0500 Date: Tue, 28 Feb 95 13:37:54 -0500 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: chemistry@ccl.net Subject: Parallel Molecular Dynamics with full Coulomb interactions Cc: windemut@cumbnd.bioc.columbia.edu For those interested in parallel and scalable molecular dynamics simulation of biological macromolecules: Version 0.9 of the program PMD has been made available. This is an experimental program that uses the Greengard/ Rokhlin fast multipole algorithm (FMA) in conjunction with a constant force multiple timestep method to permit the efficient simulation of large biological macromolecules without cutting off the long range forces. For more details, see "http:/tincan.bioc.columbia.edu/pmd" or the README file from the distribution reproduced below. --- Andreas Windemuth +-------------------------------------------------------------------- |Columbia University, Department of Biochemistry and Biophysics |630 West 168th St. BB-221 | tel: (212)-305-6884, fax: 6926, NeXTmail |New York, NY 10032 | email: windemut@cumbnd.bioc.columbia.edu +-------------------------------------------------------------------- This is an experimental version of PMD, Version 0.9, release Feb 28, 1995, all rights reserved. PMD is a scalable, parallel program for the simulation of the dynamics of biological macromolecules. PMD utilizes the Greengard/Rokhlin Fast Multipole Algorithm to allow the simulation of very large biological macromolecular systems without sacrificing the important long-range Coulomb interactions. The force field implemented by PMD is compatible to programs such as CHARMM, X-PLOR, GROMOS, Discover and others. Residue topology and parameter files suitable for X-PLOR can be used with PMD. Particularly, PMD can fully implement the CHARMM19 CHARMM22 force fields. PMD is also intrinsically and transparently parallel and suitable for running on a wide variety of parallel architectures, both shared memory and message passing. The most salient features of PMD are: - Use of the Fast Multipole Algorithm allows for the calculation of the full long range electrostatic interactions in linear (of order N) time. - The Distance Class Algorithm reduces the calculation time further to make full-range calculations faster than conventional cutoff methods. - PMD is designed to be completely scalable, i.e. arbitrarily large systems (millions of atoms) can be simulated as long as enough processing nodes are available. Memory use is minimal, compared to other programs. - PMD runs without changes on a large number of UNIX workstations and can easily be adapted to others. Parallel implementations exist for the CM-5, the Intel Paragon, the Cray T3D and workstation networks. - Parallel instructions are limited to a small set of commands that are easily implemented in any machine specific or portable (TCGMSG, PVM, Linda) parallel processing interface. PMD is work in progress. Expect plenty of changes of all kinds in future versions. This program is made available to encourage researchers to add features they need and in the hope that some of these improvements find their way back into future versions. A mailing list has been established to foster discussion among users and contributors. Please direct inquiries to join the mailing list to "pmd-request@cumbnd.bioc.columbia.edu". The source code is being made available under the condition that any additions, improvements or changes will be sent to the author (windemut@cumbnd.bioc.columbia.edu) for inclusion into the distribution. No restrictions different from those on PMD itself may be put on such contributions. PMD or parts of it may not be used or distributed for non-disclosed corporate research or commercially without prior consent of the author. If either the program or ideas from its code are used in a publication, it is asked that the following references be cited: J.A. Board Jr., J.W. Causey, J.F. Leathrum Jr., A. Windemuth, and K. Schulten. Accelerated molecular dynamics simulation with the parallel fast multipole algorithm. Chem. Phys. Lett. 198:89--94, 1992. A. Windemuth and K. Schulten. Molecular dynamics on the Connection Machine. Molecular Simulation, 5:353--361, 1991. A. Windemuth. Advanced Algorithms for Molecular Dynamics Simulation: The Program PMD. in "Parallel Computing in Computational Chemistry" (Timothy G. Mattson, ed.), ACS Books, 1995, in press. Installation: cd zcat pmd.tar.Z | tar xvf - Demo run: cd pmd/demo make SYS= (one of next hpux dec iris aix sun paragon) Parallel demo run: [install TCGMSG and customize bin/par.] cd demo make SYS= PSYS=tcgmsg This will start a simulation of Pancreatic Trypsin Inhibitor (PTI), starting from the original PDB file, adding hydrogens, equilibrating with harmonic constraints and a minimizing. Look at "demo/makefile" and "src/make.sim" to see how the run is controlled and how you might modify it to run your own molecules. First, try changing the line "SYS=next" to reflect the machine you are actually using. Then, try "make MOL=mb" to run the solvated myoglobin setup that is frequently used as a benchmark for CHARMM. Finally, try "make mutant" to generate a Ile 3 -> Tyr mutant of T4 phage lysozyme (2lzm). Some of these simulation will take quite some time if not interrupted. It is suggested to run them in the background using the ampersand ("&") character, i.e. "make mutant &". The link "demo/log" will always point to the newest simulation log. Try "tail -f log" to check on the simulation progress. Some other sample molecules are available in "demo". Their topology is described in files "*.str", their atom coordinates in files "*.pdb". It is quite straightforward to make your own "*.str" files, once you study the sample files and "src/make.sim". If you wish to run PMD in parallel, make sure that you have TCGMSG or PVM installed and that there is a directory or link "tcgmsg" or "pvm" in your home directory pointing to your system's TCGMSG or PVM root directory. Edit "makefile" and change the line "PSYS=serial" to one of the supported parallel interfaces (tcgmsg, pvm, pvm-t3d). You also will have to edit a startup script that sets up processes on the network. The script has the name "par-$(SYS)-$(PSYS)" and it is located in "bin". Some examples are provided, but you will almost certainly have to adapt one of them to your own environment. TCGMSG can be obtained from "ftp.tcg.anl.gov". See the file "README.TCGMSG" for more information. Information on PVM can be obtained at "http://www.epm.ornl.gov/pvm/pvm_home.html" on the World-Wide Web. For information on the Cray T3D refer to "http://pscinfo.psc.edu/machines/cray/t3d/t3d.html". Documentation: This file, some scattered comments in makefiles and scripts, and the World Wide Web pages. Main features: Fast multipole algorithm Linear scaling enables simulation of extremely large systems Full long range interactions with no cut-off Distance class algorithm Accounts for full long-range interaction while providing performance better than conventional cut-off calculations Scalable parallel implementation on Workstation networks (with TCGMSG or PVM) Cray T3D (PVM) Convex Exemplar (TCGMSG) Intel Paragon (TCGMSG) Thinking Machines CM-5 (slow, no vector units, no longer supported) Parsytec GC (initial implementation, no longer supported) Now implemented: Growing of hydrogens Mutation (Growing of sidechains) Building solvation shells Superposition and RMS-values Solvent accessible surface (no forces, yet) Harmonic constraints Stochastic boundary (friction and random fluctuations) Restart files and DCD trajectories Main limitations: FMA and atom reassignment not fully scalable (yet) No vectorization Not enough features Forthcoming: (no guarantees, of course :-) ) Advanced solvent treatment Generalized Born potential Hydrophobic forces and continuum electrostatics with forces FMA and atom reassignment Improved scalable versions Periodic boundary conditions Other features Containment fields for closed boundary Pretty pictures (ray-tracing and movies) Adapting PMD to other parallel systems: All machine-specific parallel communication commands have been isolated into one file, called the adaptor. The adaptors in the current release are "tcgmsg.c": for the TCGMSG public domain parallel programming Interface, "pvm.c": for the PVM public domain parallel programming Interface, "cm5.c": for the Connection Machine 5 with CMMD-3.0, "pvm-t3d.c" for the restricted set of PVM used on the Cray T3D, and "serial.c": for non-parallel workstation implementations. With TCGMSG or PVM PMD can be run on a wide variety of platforms, such as workstation networks, the Intel Paragon and the Convex Exemplar. Other adaptors are expected to become available as work progresses. Changes from 0.8: - Much improved makefiles and compilation - Simplified parallel execution - Parallel output is now much faster and should always work - new trajectory format, with PDB and DCD conversion utility - PVM and the Cray T3D are now supported - Numerous bugs corrected. - Everything else also improved. Have fun! Andreas Windemuth +-------------------------------------------------------------------- |Columbia University, Dept. of Biochemistry and Biophysics, BB-221 |630 West 168th St. | tel: (212)-305-6884, fax: 6926, NeXTmail |New York, NY 10032 | email: windemut@cumbne.bioc.columbia.edu +-------------------------------------------------------------------- From feaster@tessa.iaf.uiowa.edu Tue Feb 28 15:22:43 1995 Received: from ns-mx.uiowa.edu for feaster@tessa.iaf.uiowa.edu by www.ccl.net (8.6.9/930601.1506) id OAA03284; Tue, 28 Feb 1995 14:05:16 -0500 Received: from tessa.iaf.uiowa.edu by ns-mx.uiowa.edu (8.6.8.2/19950217.1) on Tue, 28 Feb 1995 13:05:14 -0600 id NAA13295 with SMTP Received: by tessa.iaf.uiowa.edu (920330.SGI/891024) on Tue, 28 Feb 95 12:57:06 -0600 id AA03795 Date: Tue, 28 Feb 1995 12:50:12 -0600 (CST) From: shawn feaster Subject: Fe(0) complex modeling To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all computational chemists, Does anyone know of a method for modeling transition metal complexes. For example, Fe(0) and carbon tetrachloride? I believe at this moment that most canned programs do not have this capability. I think that "Cerius" may be able to do some very rough modeling, but the modeling assumes very approximate geometries. Is this true? If there is a solution to my problem I would very much like to hear from you. My email address is feaster@tessa.iaf.uiowa.edu. Thanks, Shawn Feaster From windemut@cumbnd.bioc.columbia.edu Tue Feb 28 15:22:53 1995 Received: from cumbnd.bioc.columbia.edu for windemut@cumbnd.bioc.columbia.edu by www.ccl.net (8.6.9/930601.1506) id OAA03651; Tue, 28 Feb 1995 14:26:44 -0500 Received: from sirius by cumbnd.bioc.columbia.edu (NX5.67d/NX3.0M) id AA25240; Tue, 28 Feb 95 14:26:21 -0500 From: Andreas Windemuth Message-Id: <9502281926.AA25240@cumbnd.bioc.columbia.edu> Received: by sirius.bioc.columbia.edu (NX5.67d/NX3.0X) id AA25999; Tue, 28 Feb 95 14:26:22 -0500 Date: Tue, 28 Feb 95 14:26:22 -0500 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: chemistry@ccl.net Subject: Re: Parallel Molecular Dynamics with full Coulomb interactions Cc: windemut@cumbnd.bioc.columbia.edu Unfortunately the URL was misspelled in my last message on PMD. This is the (hopefully) correct spelling: http://tincan.bioc.columbia.edu/pmd/ Note the double slash in front and the trailing slash ... Sorry. --- Andreas Windemuth +-------------------------------------------------------------------- |Columbia University, Department of Biochemistry and Biophysics |630 West 168th St. BB-221 | tel: (212)-305-6884, fax: 6926, NeXTmail |New York, NY 10032 | email: windemut@cumbnd.bioc.columbia.edu +-------------------------------------------------------------------- From lim@rani.chem.yale.edu Mon Feb 27 23:20:19 1995 Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by www.ccl.net (8.6.9/930601.1506) id XAA17904; Mon, 27 Feb 1995 23:20:17 -0500 Received: by rani.chem.yale.edu; Mon, 27 Feb 95 23:20:12 -0500 From: Dongchul Lim Message-Id: <9502280420.AA18868@rani.chem.yale.edu> Subject: conformational isomers To: chemistry@ccl.net (Computational Chemistry) Date: Mon, 27 Feb 95 23:20:12 EST X-Mailer: ELM [version 2.3 PL11] Status: RO Here's a summary of the articles posted on the CCL and I received personally. I thank all who replied to my question. I chopped off signatures severely to save space. I hope you don't mind. --- original posting --- Is there a simple way of testing if two given conformational isomers are equivalent? E.g., how can you know the gauche (+) conformer of n-butane is equivalent to the gauche (-) conformer? My idea is 1) superimpose the two conformers. 2) if they are not superimposed, superimpose the one conformer and the mirror image of the other. __________________________________________________________________________ >From jordi@stark.udg.es Tue Feb 21 07:26:38 1995 There is a simple way of testing if two conformers are equivalent. You can know it just calculating the corresponding molecular self-similarity measures (MSM). Two equivalent conformers will have the same electronic density distribution, thus, their MSM value will be the same. Since calculation of the exact MSM value is not computationally feasible for large molecules, here you have some recent references on several approximations to evaluate the MSM for large systems: * J.Comp.Chem. 1994, 15, 1113-1120 * J.Am.Chem.Soc. 1994, 116, 5909-5915 * J.Chem.Inf.Comp.Sci. 1994, 34, 1047-1053 * Scientia gerundensis 1995, 21, xxx (in press) __________________________________________________________________________ >From MARTIN@cmda.abbott.com Tue Feb 21 09:07:35 1995 An easier way is to calculate the interatomic distances since that is invariant to reflection. We consider 0.3A tolerance to be the cut-off if two conformers are different. __________________________________________________________________________ >From Karl.F.Moschner@urlus.sprint.com Tue Feb 21 10:37:02 1995 Sounds about right to me, but, if your program doesn't do so already, you should first provide a "standard" orientation such as placing the origin at the center of mass and orienting the molecule along the principal moment axes or dipoles, if you include charges. But, depending on your code, you may still have to consider reversed orientation, i.e., check if x1(a) = x1(b) or x1(a) = -x1(b), if the latter, reverse the orientation, ditto for y and z. Besides exact superposition, quick screens are the total energy, dipole (if you include charges), and moments. For larger molecules, end-to-end or selected interatomic distances afford quick checks. And, if you're checking a series of molecules, molecular weight or elemental composition are effective screens. It's suprising that some/many molecular mechanics packages do not support/generate "standard" orientations since it would be helpful not only for your problem but also as a start for CoMFA alignments. However, you could easily write your own starting from MOPAC or GAMESS subroutines, if you have them. There may also be a program/subroutine available from QCPE which you could modify. A few years ago I had modified the GAMESS subroutine for determining the principal moments to generate standard orienetations for Tripos "*.mol" files. It was very fast, requiring only a several seconds to reorient lysozyme on an SGI 4D/35. Unfortunately I no longer have the code and would be prohibited from redistributing it even if I did. My original interest was to subsequently compute the 3 principal cross-sectional areas, and/or solvent cross-sectioanl areas, to try to relate them to diffusivities but I didn't get that far. __________________________________________________________________________ >From polowin@hyper.hyper.com Tue Feb 21 09:17:43 1995 Depends on what you mean by "equivalent", and how you're doing the superimposition. In molecular modelling, for example, even structures with the "same" conformation can differ significantly as a result of a slight shift in a torsional angle near the middle of a large system. If you were checking for "equivalence" by something like RMS deviation of atomic positions, you'd take them to be completely different. If you were checking bond angles and torsional angles, they'd probably appear to be pretty similar. __________________________________________________________________________ >From hendrick@agouron.com Tue Feb 21 12:26:39 1995 Hi The way this was done in MacroModel was to identify equilavent atoms and then check for identical conformers by doing rms superimposition with the equilivalent atoms. For example in your n-butane case (C1-C2-C3-C4), if you made atom one equivalent to atom four, and atom two equivalent to atom three and then do the rms superpositions, you would find the redundant conformers. Tom Hendrickson __________________________________________________________________________ From: lnl@novo.dk (Leif Norskov) > Is there a simple way of testing if two given conformational isomers > are equivalent? > E.g., how can you know the gauche (+) conformer of n-butane is > equivalent to the gauche (-) conformer? > My idea is [ to superimpose the conformers ]... If speed is a problem (and it could well be - consider for example the matching of the protons in butane) then it might be advantageous to first compare the moments of inertia, which of course are invariant to atom labelling and rotation/translation, before proceeding with superpositioning. __________________________________________________________________________ From: "E. Lewars" Dongchul Lim asked how one can tell if two conformers are the same. This is a special case of how to tell if two isomers are really the same species. It seems to me a simple approach is (after looking to see that they are not obviously different) to have your program (MOPAC, GAUSSIAN etc) calculate the total internuclear repulsions. Two species that look the same and have the same internuclear repulsions (to 6 or more decimals--Hartrees) are, I would think, extremely unlikely not to be the same. Many comp. chem programs calculate internucl. repulsions; if a check job wn't give that number, then ask for a single-point calc. using a fast method like a semiempirical routine. The actual internuclear repulsin calc. is trivial. Errol Lewars __________________________________________________________________________ From: peon@medchem.dfh.dk (Per-Ola Norrby) Your proposal is of course the only final test, but there are some ways to do a quick screening to avoid having to test a lot of conformations by superimposition. If your structures are output from some calculation, several commonly calculated criteria have to be equal for the two conformers. Two simple ones are calculated energy (only if you have fair convergence) and moment of inertia (very sensitive to conformational changes). You only need to superimpose structures that differ "very little" in these two test. __________________________________________________________________________ From: (sandeep kumar) I think one way to test the conformational equivalence esp. for small structures like n-butane is to calculate or measure the energies of the two isomers. For example, in case of n-butane both g+ and g- have almost equal energies i.e. both of them are almost equally stable while trans isomer has lower energy than any of the two and is much more stable than any of the two. I restrict myself to recomend its usage with small organic molecules with simple geometries only. for further disscussion on the matter please refer to organic chemistry text book by Morrison and Boyd. yours' cordially sandeep kumar san@mbu.iisc.ernet.in P.S. I shall be grateful to you if you summarize what you find. __________________________________________________________________________ From: Garcia Edgardo About the conf. isomers question of Dongchul Lim, my opinion is that first we should ask if we want to compare IDENTICAL or EQUIVALENT isomers (concerning energy for example). In the first case a simple superpossition will probably work. In the second we can make a non-bonding energy calculation and compare the energies or compare the distance matrix of the structures (or some kind of invariant of them) within some allowed range of values. __________________________________________________________________________ From: polowin@hyper.hyper.com (Joel Polowin) > From: "E. Lewars" > Subject: CCL:TELLING IF TWO CONFORMERS ARE IDENTICAL > > Dongchul Lim asked how one can tell if two conformers are the same. This is > a special case of how to tell if two isomers are really the same species. > It seems to me a simple approach is (after looking to see that they are > not obviously different) to have your program (MOPAC, GAUSSIAN etc) > calculate the total internuclear repulsions. Two species that look the same > and have the same internuclear repulsions (to 6 or more decimals--Hartrees) > are, I would think, extremely unlikely not to be the same. Many comp. > chem programs calculate internucl. repulsions; if a check job wn't give > that number, then ask for a single-point calc. using a fast method like > a semiempirical routine. The actual internuclear repulsin calc. is > trivial. I don't think the situation is quite so simple -- possibly depending on what is meant by conformers being "the same". If I have a large structure and alter a torsional angle in the middle by a fraction of a degree, it's probably still "the same structure". If the structure was energy- optimized before, it's very likely that trying to optimize it again won't do much to change it back unless there are other steric effects. But the atoms at the ends of this large structure will probably move a *lot* as the result of that tiny bend in the middle, and the internuclear repulsions are likely to change significantly too. Maybe only a little, or maybe some other local minimum would be found, but I don't think the internuclear repulsions would likely be the same to 6 or more decimals. I think that the matter depends critically on: What sort of structures are you trying to compare, and what do you mean by "the same"? Regards, Joel __________________________________________________________________________ From: valery-g@dcl.co.il (Dr. Golender Valery) Dear Lim, You asked on CCL how one can tell if two conformers are the same. I already saw some responses on the net advising to solve the problem from the molecular modeling point of view. In fact, there exist a strict mathematical formulation of this problem called isomorphism of 3D objects. It is a common problem arising in a number of applications including 3D database search, ligand design, spanning of conformational space and etc. A number of different algorithms and programs were proposed to solve this problem. Simple superposition suggested in the original posting is not working because of molecular symmetry. We recently developed an efficient algorithm incorporated into the conformer clustering utility of Apex-3D activity prediction system marketed by Biosym. I can provide more detailed information if you are interested in this functionality. __________________________________________________________________________ From: Karl.F.Moschner@urlus.sprint.com Sounds about right to me, but, if your program doesn't do so already, you should first provide a "standard" orientation such as placing the origin at the center of mass and orienting the molecule along the principal moment axes or dipoles, if you include charges. But, depending on your code, you may still have to consider reversed orientation, i.e., check if x1(a) = x1(b) or x1(a) = -x1(b), if the latter, reverse the orientation, ditto for y and z. Besides exact superposition, quick screens are the total energy, dipole (if you include charges), and moments. For larger molecules, end-to-end or selected interatomic distances afford quick checks. And, if you're checking a series of molecules, molecular weight or elemental composition are effective screens. It's suprising that some/many molecular mechanics packages do not support/generate "standard" orientations since it would be helpful not only for your problem but also as a start for CoMFA alignments. However, you could easily write your own starting from MOPAC or GAMESS subroutines, if you have them. There may also be a program/subroutine available from QCPE which you could modify. A few years ago I had modified the GAMESS subroutine for determining the principal moments to generate standard orienetations for Tripos "*.mol" files. It was very fast, requiring only a several seconds to reorient lysozyme on an SGI 4D/35. Unfortunately I no longer have the code and would be prohibited from redistributing it even if I did. My original interest was to subsequently compute the 3 principal cross-sectional areas, and/or solvent cross-sectioanl areas, to try to relate them to diffusivities but I didn't get that far. Good luck! __________________________________________________________________________ From: Mick Kappler > Is there a simple way of testing if two given conformational isomers > are equivalent? Yes. The Stereochemical Extended Morgan Algorithm (SEMA) developed by Wipke and Dyott provides a stereochemical canonical name. Comparison of the structure SEMA names is straight forward. __________________________________________________________________________ From: marvin@biosym.com (Marvin Waldman) > Is there a simple way of testing if two given conformational isomers > are equivalent? This is, in fact, quite a difficult and subtle question. The SEMA algorithm which Mick Sappler proposed can be used to detect if two CONFIGURATIONAL isomers are equivalent (ie. they have the same or different stereochemistry). However, it will not detect if the same configurational isomers are equivalent or not in a CONFORMATIONAL sense. SEMA cannot detect the difference between the gauche and trans forms of n-butane. These are CONFORMATIONAL isomers. The issue of the equivalence of two conformations is further complicated by the problem of topological symmetry. This makes an RMS comparison of atoms problematic for detecting equivalent conformations. For example, if I do an RMS comparison of corresponding atoms between two conformers in which the hydrogens of a methyl group are rotated by 120 degrees, I will detect an RMS difference because I am now comparing the wrong set of atoms. One needs to compare all combinations of topologically equivalent atoms in the molecule to see if they have a (virtually) zero RMS. If one proposes to do an RMS comparison of heavy atoms only, then you only need to replace the methyl group with a t-butyl group, and the problem remains. If one proposes to compare only energies (and not RMS), then, of course, the symmetry will be correctly handled for the energy, and you only need to worry about the somewhat unlikely case of two different conformers having (almost?) the same energy. Since these conformers are likely to come from some energy optimization procedure, roundoff error and tolerances used for the minimization implies that one needs to use some kind of tolerance in comparing energies, which always leads to the (remote?) possibility that nearly equal energies may not correspond to the same conformer. The larger the molecule and the more conformational flexibility (and therefore conformers) it has, the more likely that this somewhat theoretical problem may manifest itself in a real example. The ideal/correct solution would be to compare both the energy as well as all combinations of RMS comparisons of topologically equivalent atoms until the RMS difference found for a given comparison pair fell below some threshold. I am not aware of a software package that has actually implemented such an algorithm, and would be very interested to hear about one that does. So, the bottom line answer to the question, is: No, I don't think there is a SIMPLE way to do this. __________________________________________________________________________ From: "E. Lewars" When I suggested using the internuclear repulsion E to check if two isomers are identical, I should have pointed out that enantiomers have precisely the same energies--internuclear, electronic, etc (in the absence of a chiral perturbation; physicists may quibbl, too, that the negation of parity by the weak nuclear force causes a miniscule difference in enantiomer E's). Joel Polowin of HyperChem pointed out that as a practical matter identity isn't an all-or-nothing phenomenon: how similar do two species have to be for a chemist to call them the same thing? As several people said, there are sophisticated algorithms for matching up two molecules and looking at, e.g., RMS differences in geometric parameters. I think the widely- used MM program PCModel can do something like this; one or two other programs were mentioned. Joel's idea about a small tweak in one part of a molecule causing a ratcheting effect that's amplified elsewhere (cf. allosteric effects in enzymes?) is interesting. Errol Lewars =============================== Regarding internucl rep.--one could calc it for some test cases, alter these geometries slightly, and see if it might be useful for the problem at hand. =============== __________________________________________________________________________ From: "CBAS25 ::P_BLADON ::CBAS25" Dear Dongchul Lim, With regard to the conparisons of conformers. There are several points to consider. (1) If the problem involves small molecules like butane where the number of stable conformers is known, then simply superimposing the "unknown" structure on each of the "known" conformers in turn will give an answer. The rms deviation of atom positions or some other figure of merit will afford an answer even when an exact match is not achieved. (2) If the structures are more complex, perhaps involving large membered rings, then the number of conformers could be large. But suppose that you have a set of such structures, and wish to test which of them your "unknown" most resembles. You would still get an answer. If the "unknown" were a crystal structure and the "knowns" derived >from a conformer generating program, you would not expect a good match necessarily. What you could do then is to take the pair of best matched structures and refine them with your favourite MM or MO package, and see if they both decend into the same energy well. (3) To do the matching you could use atom to atom matching, or alternatively use the icosahedral matching algorithm in programs like COMPARISONS or CORRELATE. The first of these programs will match an "unknown" against a series of "unknowns", while the second would allow the correlation of a whole series of conformers. The matching of mirror-image forms is taken care of. Both programs are available from QCPE as part of the INTERCHEM package. __________________________________________________________________________ From: "Victor M. Rosas Garcia" Some people have mentioned algorithms for comparison of conformers and evidently the solution to this problem is far from simple. The best implementation I have seen to solve this problem is in the program GMMX, a global minimum search utility by Serena Software. As I understand it, the program calculates the RMS of the conformers by using identical numbering in the atoms of both conformers and, if necessary, checks for planes of symmetry and for the so-called numerical isomers. The idea is that making the atoms distinguishable by numbering them will introduce artificial conformers that differ only in the numbering but that are really "the same" conformer e.g. a product of a rotation or reflection or some other symmetry operation. __________________________________________________________________________ From: graham@sentex.net (Graham Hurst) >> Is there a simple way of testing if two given conformational isomers >> are equivalent? [good stuff deleted] >The ideal/correct solution would be to >compare both the energy as well as all combinations of RMS comparisons >of topologically equivalent atoms until the RMS difference found >for a given comparison pair fell below some threshold. I am not >aware of a software package that has actually implemented such >an algorithm, and would be very interested to hear about one that >does. The Conformational Search module of the ChemPlus set of extensions for HyperChem uses energy and RMS compairisons of topologically equivalent atom pairings. I've been following this discussion with some interest. When I wrote the Conformational Search module of ChemPlus, I implemented the following tests to compare for equivalent conformations that might result from the search. The comparisons available are (in the order that the program can optionally execute them) are: 1. Changed chirality (R or S) of chiral centers with 4 bonded neighbours. (Chiral centers are determined by HyperChem.) 2. Energy (from HyperChem) within a user adjustable range. 3. Varied torsions within a user adjustable range. This test is turned off by default, since it doesn't handle topologically equivalent dihedral angles. 4. R.M.S. deviation for a least-squares overlay of atoms. As Marvin Waldman pointed out, one needs to compare with all topologically equivalent permutations of atom order and this option (discussed further below) is available in ChemPlus. A subset of atoms can also be specified for the comparision. I initially included an option for comparison of inertial moments (suggested earlier by Leif Norskov ) but I abandoned it because it seemed too sensitive a measure, with suitable tolerances varying widely with the number of atoms. If the option to use equivalent atoms in the RMS comparison is turned on, the program generates all equivalent atom order permutations. The algorithm I used for this is basically brute force, O(N!) at worst, but being able to compare element type and number of bonds for each topological "node" allows considerable trimming of the paths. Further trimming results from only considering a subset of atoms (eg. no hydrogens or only backbone atoms) so that permutations of ignored atoms are unnecessary (assuming equivalent sets are either all included or all excluded). >So, the bottom line answer to the question, is: No, I don't think >there is a SIMPLE way to do this. I agree! It took me about a month to puzzle out and implement an algorithm for generating equivalent atom orders! As Valery Golender pointed out, the conformational isomer problem is a specific instance of isomorphism of 3D objects. Cheers, Graham P.S. If you want more ChemPlus or HyperChem product info, please send email to info@hyper.com, not to me because I don't work there anymore. __________________________________________________________________________ From: Matt Stahl Greetings, The problem of duplicate conformer removal certainly is challenging, especially to anyone doing extensive conformational searches. The "easy" method of detection is to compare a unique identifier based on atomic coordinates. Shape descriptors such as the sum of interatomic distances, or the sum of all triangles in a molecule provide a single number to identify a conformation. In this sense, energy is also a "shape descriptor" because it is simply a function operated on a set of coordinates. As pointed out by Dr. Waldman, there is always the possibility of ambiguity when using this kind of descriptor. I have seen cases in larger bicyclo alkanes where very different conformations had the same mechanics energy to the 5th or 6th decimal place! There are several matters that must be addressed with regard to comparing conformations. Rms fitting may not be the best measure of similarity when comparing long acyclic chains because of the 'torque' effect. Torsional comparisons certainly have valid applications. In general, rms fits work well with the exception of the problems of automorphism and enantiomeric coordinates. Generating enantiomers is trivial. Simply multiply all of the x, y, or z coordinates by -1 to generate the mirror image. Automorphisms can be more of a problem. They can be discovered by connectivity matrix manipulations (see balasubramanian in j. chem. inf. comp. sci. may/june 1994). A much quicker approach is to effectively do an atom-by-atom max common substructure search using comparisons of atom types. Once the automorphisms are discovered they can be used in both torsional and rms comparisons. Pat Walters and i have written a program called Padre (Population Analysis and Duplicate REmoval) that will read multi-structure files, automatically generate the automorphisms (and enantiomers if desired), and do rms or torsional comparisons and identify duplicate conformers. It will also map rings onto each other and compare all possible overlays. Padre is FAR from completion, but the features currently implemented are solid. Please contact me directly if you are interested in this software. __________________________________________________________________________ From: Mick Kappler > Is there a simple way of testing if two given conformational isomers > are equiva lent? This question can be interpreted in two ways, as Joel Polowin indicated. On Wed, 22 Feb 95 10:29:54 -0500, Joel Polowin wrote: > I don't think the situation is quite so simple -- possibly depending on > what is meant by conformers being "the same". If one is interested in structural equivalency independent of conformation, the SEMA algorithm (JACS, 96, 4834, 1974) is a solution. If one is interested in structural equivalency dependent of conformation, the solution is more complex, as Marvin Waldman pointed out. On Wed, 22 Feb 1995 14:47:42 -0800, Marvin Waldman wrote: > This is, in fact, quite a difficult and subtle question. The SEMA > algorithm which Mick Sappler proposed can be used to detect if > two CONFIGURATIONAL isomers are equivalent (ie. they have the > same or different stereochemistry). However, it will not detect > if the same configurational isomers are equivalent or not in > a CONFORMATIONAL sense. SEMA cannot detect the difference between > the gauche and trans forms of n-butane. These are CONFORMATIONAL > isomers. This is correct. The ultimate solution to the structural equivalency dependent of conformation problem will depend on analytical features of the two structures only. On Thu, 23 Feb 1995 01:47:29 EST, CBAS25 ::P_BLADON ::CBAS25 wrote: > There are several points to consider. > > (1) If the problem involves small molecules like butane where the number > of stable conformers is known... We can not assume we have anything but the two conformations that we wish to compare. Given a hypothetical structure, who knows the set of stable conformers? > (2) If the structures are more complex... then the number of conformers > could be large. But suppose that you have a set of such structures... Again, let's not assume we know. > (3) To do the matching you could use atom to atom matching... This could take a long time, considering the size of the set of structures to compare. Is time an issue? I imagine it is if you have a large set of structures to compare. On Wed, 22 Feb 1995 23:36:21 -0800, Victor M. Rosas Garcia wrote: > ...The best implementation I have seen to solve this problem is in the > program GMMX, a global minimum search utility by Serena Software. If this works for you, this is great. Unfortunately, this technique is only as good as the software and comparison of conformation A by software X to conformation B by software Y is impossible. Hence, comparisons between research groups may be a problem. This is not to mention the multiple minima problem, as E. Lewars pointed out. On Wed, 22 Feb 1995 17:10:28 -0500, E. Lewars wrote: > ...enantiomers have precisely the same energies... On Wed, 22 Feb 1995 23:32:59 -0500, Graham Hurst wrote: > The Conformational Search module of the ChemPlus set of extensions > for HyperChem uses energy and RMS compairisons of topologically > equivalent atom pairings. RMS comparisons look promising at first. Unfortunately, before the comparison can be made, the conformations need to be superimposed, which is independent of the conformation itself. Although the superimposition can be solved analytically, it is sometimes solved iteratively, and can be a source of contention. Can we solve this problem indepedent of transformation? I would love to hear more from experts in this field. This is an interesting problem and this discussion has increased our interest in publishing our latest work relating to conformational comparisons. __________________________________________________________________________ From: Ramesh Gopalaswamy I have been working with steroid conformational analysis in connection with receptor modeling. I have generated several (typically 100) structures (conformers) for each steroid using DGEOM program. Now I need to pick out those conformers that are unique. (DGEOM generated structures might converge to same minimum upon minimization). Any ideas on how to do that using commercial modeling software or other shareware programs? Also, how to run minimizations (for 100 or so structures) as a background job, instead of having to read in each structure on to the graphics interface? I have access to Quanta, Cerius2 and Sybyl. Thanks a lot. Ramesh (rameshg@umich.edu) __________________________________________________________________________ From: Harold Helson Hi DC, I hope you are well! If I remember Wipke & Dyott's paper on SEMA ("Stereochemically extended Morgan algorithm") correctly, they propose some modifications to treat conformers. Here is an idea that's not too carefully thought out, and would take more time than you probably want to invest, but -- hell, it's an interesting problem. Canonicalization algorithms, which deliver a unique description of a molecule, incorporate some representation of a given bond's environment. In topological algorithms, this may merely be the bond order. In con- figurational algorithms, it is more complex, also including cis/trans and chiral parity information. What you would do is append additional configurational information, such as dihedral relationships along the path being grown. This might be all there is to this problem. So you would perform conventional canonicalization, using the more detailed bonding representation. You end up with one or more paths of equal priority, the presence of more than one reflecting automor- phisms (symmetry). The power in SEMA is that it is a trivial operation to enumerate all the enantiomers and geometric isomers. I expect that you would similarly be able to trivially enu- merate all the conformations, provided (and it's a big proviso) that you limited the dihedral angles to, say, multiples of thirty degrees, or whatever number is small enough to be a good approximation, but large enough so that the number of possible conformations does not go rapidly to infinity. This is certainly a valid approximation in the gauche butane example you cite. You would be able to tell a mirror image because its stereochemical parity table (see Wipke & Dyott) would contain an inversion, but the extra, appended conformational table would be the same for both structures. You could tell configurational isomers because their stereochemical tables would be identical, but their conformational tables would differ. __________________________________________________________________________ From kreidler@hp817s.rz.uni-duesseldorf.de Tue Feb 28 05:01:31 1995 Received: from hp817s.rz.uni-duesseldorf.de for kreidler@hp817s.rz.uni-duesseldorf.de by www.ccl.net (8.6.9/930601.1506) id FAA01545; Tue, 28 Feb 1995 05:01:26 -0500 Message-Id: <199502281001.FAA01545@www.ccl.net> Received: by hp817s.rz.uni-duesseldorf.de (1.37.109.14/16.2) id AA063935699; Tue, 28 Feb 1995 11:01:39 +0100 From: Kay Kreidler Subject: microscopic dissociation To: chemistry@ccl.net (Theochem Liste) Date: Tue, 28 Feb 95 11:01:38 MEZ Mailer: Elm [revision: 70.85.2.1] Status: R Dear colleagues! Did any one of you try to calculate microscopic dissociation constants by any kind of computational chemistry method? Did you have any success? Are there hints in the literature? Any kind of advice will be useful. I will summarise the result to the mailing list. Thanks in advance Kay Kreidler Institut fuer Anorganische Chemie und Strukturchemie I Heinrich-Heine-Universitaet Duesseldorf Universitaetsstr. 1 40225 Duesseldorf Email: kreidler@uni-duesseldorf.de p2623.spt.new 1168 -rw-r--r-- 1 osu683 597892 Feb 27 19:14 stg2.out 1152 -rw-r--r-- 1 osu037 589824 Feb 27 07:07 FFRGD2 1152 -rw-r--r-- 1 osu037 372736 Feb 27 07:07 SCRTC1 1152 -rw-r--r-- 1 osu037 364544 Feb 27 07:07 TAPE12 984 -rw-r--r-- 1 osu683 503517 Feb 27 19:14 sbout 920 -rw-r--r-- 1 osu683 471040 Feb 27 19:14 b10 920 -rw-r--r-- 1 osu683 471040 Feb 27 19:14 B10 904 -rw-r----- 1 osu714 458759 Feb 28 00:47 t0006820 896 -rw-r--r-- 1 osu037 274432 Feb 27 07:11 SCRTC7 856 -rw-r--r-- 1 osu683 438272 Feb 27 19:14 b07 856 -rw-r--r-- 1 osu683 438272 Feb 27 19:14 B07 856 -rwxr-xr-x 1 osu683 436088 Feb 27 19:14 premx 832 -rw-r----- 1 osu714 425984 Feb 28 00:50 v0006820 832 -rw-r----- 1 osu714 425984 Feb 28 00:49 u0006820 832 -rw-r--r-- 1 osu037 278528 Feb 27 06:19 DIISPOLD 832 -rw-r--r-- 1 osu683 254656 Feb 27 19:14 prempro.o 808 -rw-r--r-- 1 osu683 413696 Feb 27 19:14 b06 808 -rw-r--r-- 1 osu683 413696 Feb 27 19:14 B06 616 -rw-r--r-- 1 osu683 315392 Feb 27 19:14 b11 616 -rw-r--r-- 1 osu683 315392 Feb 27 19:14 B11 608 -rw-r--r-- 1 osu683 310099 Feb 27 19:14 stg2.pre 584 -rw-r--r-- 1 osu683 295480 Feb 27 19:14 stglib.o 512 -rw-r--r-- 1 osu683 261335 Feb 27 19:14 stg1.pre 488 -rw-r--r-- 1 osu683 247080 Feb 27 19:14 f26.23.qnt 480 -rw-r--r-- 1 osu683 244790 Feb 27 19:14 sb2623 456 -rw-r--r-- 1 osu683 233248 Feb 27 19:14 stglib.pre 456 -rw-r--r-- 1 osu683 232995 Feb 27 19:14 stglib.pre.1 448 -rw-r--r-- 1 osu683 229376 Feb 27 19:14 b08 448 -rw-r--r-- 1 osu683 229376 Feb 27 19:14 B08 448 -rw-r--r-- 1 osu683 229376 Feb 27 19:14 B01 440 -rw-r--r-- 1 osu683 225280 Feb 27 19:14 STG1.DAT 416 -rw-r--r-- 1 osu683 212992 Feb 27 19:14 b14 416 -rw-r--r-- 1 osu683 212992 Feb 27 19:14 B14 376 -rw-rw---- 1 osu1017 189877 Feb 27 14:02 vwind 368 -rw-rw---- 1 osu1017 187518 Feb 27 14:02 uwind 352 -rw-r--r-- 1 osu683 179613 Feb 27 19:14 sb2623.qnt.new.2 344 -rw-r--r-- 1 osu683 176128 Feb 27 19:14 b03 344 -rw-r--r-- 1 osu683 176128 Feb 27 19:14 B03 344 -rw-r--r-- 1 osu683 173016 Feb 27 19:14 f2625.sgt 336 -rw-r--r-- 1 osu683 172032 Feb 27 19:14 b05 336 -rw-r--r-- 1 osu683 172032 Feb 27 19:14 B05 304 -rw-r--r-- 1 osu683 155648 Feb 27 19:14 b09 304 -rw-r--r-- 1 osu683 155648 Feb 27 19:14 B09 280 -rwxrwxrwx 1 osu683 140436 Feb 27 19:14 zsspnl 272 -rw-r--r-- 1 osu683 136473 Feb 27 19:14 stgf.pre 264 -rw-r--r-- 1 osu683 135168 Feb 27 19:14 b12 264 -rw-r--r-- 1 osu683 135168 Feb 27 19:14 B12 240 -rw-r--r-- 1 osu683 122880 Feb 27 19:14 b15 240 -rw-r--r-- 1 osu683 122880 Feb 27 19:14 B15 224 -rw-r--r-- 1 osu683 114688 Feb 27 19:14 b04 224 -rw-r--r-- 1 osu683 114688 Feb 27 19:14 B04 216 -rw-r--r-- 1 osu683 108090 Feb 27 19:14 stgbf.pre 216 -rw-r--r-- 1 osu683 108090 Feb 27 19:14 premin 216 -rw-r--r-- 1 osu683 108067 Feb 27 19:14 prempro 192 -rw-r--r-- 1 osu683 97168 Feb 27 19:14 prempro.test 192 -rw-r--r-- 1 osu683 96721 Feb 27 19:14 stgh.pre 176 -rw-r----- 1 osu683 88742 Feb 27 19:14 stgb 144 -rw-r--r-- 1 osu683 73365 Feb 27 19:14 stgb.pre 144 -rw-rw---- 1 osu1017 69996 Feb 27 14:02 outsp.sfc 144 -rw-rw---- 1 osu1017 69996 Feb 27 14:02 outsp.mas 144 -rw-rw---- 1 osu1017 69996 Feb 27 14:02 outnp.mas 136 -rw-r--r-- 1 osu683 69632 Feb 27 19:14 b13 136 -rw-r--r-- 1 osu683 69632 Feb 27 19:14 B13 120 -rw-r--r-- 1 osu683 57657 Feb 27 19:14 f2623.spt.new 120 drwxr----- 2 osu714 57344 Feb 28 01:53 88636 112 -rw-r--r-- 1 osu683 57344 Feb 27 19:14 b18 112 -rw-r--r-- 1 osu683 57344 Feb 27 19:14 B18 96 -rw-r--r-- 1 osu683 49152 Feb 27 19:14 nf00 88 -rw-r--r-- 1 osu683 45056 Feb 27 19:14 b19 88 -rw-r--r-- 1 osu683 45056 Feb 27 19:14 b16 88 -rw-r--r-- 1 osu683 45056 Feb 27 19:14 B19 88 -rw-r--r-- 1 osu683 45056 Feb 27 19:14 B16 80 -rw-r--r-- 1 osu683 40571 Feb 27 19:14 stgbb.pre 80 -rw-r--r-- 1 osu037 39689 Feb 27 06:52 TAPE13 80 -rw-r--r-- 1 osu037 39503 Feb 27 06:52 TAPE27 72 -rw-r--r-- 1 osu037 36864 Feb 27 06:51 TAPE36 72 -rw-rw---- 1 osu1017 34998 Feb 27 16:56 tren.dat 72 -rw-r--r-- 1 osu683 34434 Feb 27 19:14 prebf.pre 64 -rw-r--r-- 1 osu683 32768 Feb 27 19:14 b22 64 -rw-r--r-- 1 osu683 32768 Feb 27 19:14 F00 64 -rw-r--r-- 1 osu683 32768 Feb 27 19:14 B22 64 -rw-r--r-- 1 osu683 31397 Feb 27 19:14 stgb.out 56 -rw-r--r-- 1 osu683 28672 Feb 27 19:14 b02 56 -rw-r--r-- 1 osu683 28672 Feb 27 19:14 B02 56 -rw-r--r-- 1 osu683 27119 Feb 27 19:14 stg1.out 56 -rw-r--r-- 1 osu683 26809 Feb 27 19:14 sb2623.qnt.new 48 -rw-r--r-- 1 osu683 24576 Feb 27 19:14 b01 48 -rw-r----- 1 osu1017 24107 Feb 27 14:02 cap.f 48 -rw-r----- 1 osu1017 23786 Feb 27 16:35 trenberth.f 48 -rw-r--r-- 1 osu683 20644 Feb 27 19:14 i2623.tpt 40 drwxr----- 2 osu714 20480 Feb 28 01:53 91812 32 -rw-r--r-- 1 osu683 14808 Feb 27 19:14 rdf00.o 32 -rw-r--r-- 1 osu683 14023 Feb 27 19:14 stgf.out 32 -rw-r--r-- 1 osu037 12928 Feb 27 06:33 TAPE32 24 -rw-r--r-- 1 osu683 12288 Feb 27 19:14 b23 24 -rw-r--r-- 1 osu683 12288 Feb 27 19:14 b17 24 -rw-r--r-- 1 osu683 12288 Feb 27 19:14 B23 24 -rw-r--r-- 1 osu683 12288 Feb 27 19:14 B17 24 -rw-r--r-- 1 osu683 11464 Feb 27 19:14 i2623.qnt 24 -rw-r--r-- 1 osu683 11014 Feb 27 19:14 id 24 -rw-rw---- 1 osu1017 10610 Feb 27 14:02 togaprocess.f 24 -rw-r--r-- 1 osu683 10077 Feb 27 19:14 elev 24 -rw-rw---- 1 osu1017 9042 Feb 27 14:02 tape.msg 16 -rw-r--r-- 1 osu683 8192 Feb 27 19:14 b00 16 -rw-r--r-- 1 osu683 8192 Feb 27 19:14 B00 16 -rw-r--r-- 1 osu683 5458 Feb 27 19:14 i2623.qnt.new 16 -rw-r--r-- 1 osu683 5458 Feb 27 19:14 i2623 16 -rw-r----- 1 osu1017 5291 Feb 27 14:02 convert2.f 16 -rw-r----- 1 osu1017 4682 Feb 27 14:02 convert.f 16 -rw-r--r-- 1 osu683 4586 Feb 27 19:14 id.tpt.1 16 -rw-r--r-- 1 osu683 4212 Feb 27 19:14 i2623.spt 8 drwxr-xr-- 2 osu937 4096 Feb 28 01:53 junk 8 drwxr-x--- 25 osu937 4096 Feb 28 01:53 wrk 8 drwxr-x--- 6 osu937 4096 Feb 28 01:53 rpm 8 drwxr-x--- 5 osu937 4096 Feb 28 01:53 nh3 8 drwxr-x--- 4 osu937 4096 Feb 28 01:53 c8-dzp-qrhf 8 drwxr-x--- 4 osu937 4096 Feb 28 01:53 c6-rohf 8 drwxr-x--- 4 osu937 4096 Feb 28 01:53 buta 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 o2min_beta 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 o2_min 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 o2_beta 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 o2 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 lib 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 h2o_uhf 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 h2o 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 c9-dzp-qrhf 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 c7-dzp-rohf 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 c5-rohf 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 c5- 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 c4-uhf 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 c4-rohf 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 c4-qrohf 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 c4-dzp-uhf 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 c4-dzp-qrohf 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 c3- 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 c2h4_ohrn 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 c2h4_hak_fs 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 c2h4 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 c2-qrhf 8 drwxr-x--- 2 osu937 4096 Feb 28 01:53 c2- 8 -rw-r--r-- 1 osu683 4096 Feb 27 19:14 b27 8 -rw-r--r-- 1 osu683 4096 Feb 27 19:14 b26 8 -rw-r--r-- 1 osu683 4096 Feb 27 19:14 b25 8 -rw-r--r-- 1 osu683 4096 Feb 27 19:14 b24 8 -rw-r--r-- 1 osu683 4096 Feb 27 19:14 b21 8 -rw-r--r-- 1 osu683 4096 Feb 27 19:14 b20 8 -rw-r--r-- 1 osu683 4096 Feb 27 19:14 D00.DAT 8 -rw-r--r-- 1 osu683 4096 Feb 27 19:14 B27 8 -rw-r--r-- 1 osu683 4096 Feb 27 19:14 B26 8 -rw-r--r-- 1 osu683 4096 Feb 27 19:14 B25 8 -rw-r--r-- 1 osu683 4096 Feb 27 19:14 B24 8 -rw-r--r-- 1 osu683 4096 Feb 27 19:14 B21 8 -rw-r--r-- 1 osu683 4096 Feb 27 19:14 B20 8 -rw-r--r-- 1 osu037 4096 Feb 27 02:58 TAPE85 8 -rw-r--r-- 1 osu037 4092 Feb 27 07:09 logfile 8 -rw-r----- 1 osu1017 3798 Feb 27 14:02 merge.f 8 -rw-r--r-- 1 osu683 3601 Feb 27 19:14 stg2.inp.fe3.tpt 8 -rwxrwxrwx 1 osu683 3578 Feb 27 19:14 stgh.inp.tpt.1 8 -rw-r--r-- 1 osu683 3488 Feb 27 19:14 stg2.inp.fe3.sgt 8 -rw-r--r-- 1 osu683 3473 Feb 27 19:14 s2infe3.sgt 8 -rw-r--r-- 1 osu683 3429 Feb 27 19:14 stg2.inp.fe3.qnt 8 -rw-r--r-- 1 osu683 3404 Feb 27 19:14 stg2.inp.tpt 8 -rw-r--r-- 1 osu683 3377 Feb 27 19:14 diff.stglib 8 -rw-r--r-- 1 osu683 3328 Feb 27 19:14 stg2.inp 8 -rw-r--r-- 1 osu683 3233 Feb 27 19:14 stg2.inp.fe3.sgt.2 8 -rw-rw---- 1 osu1017 3077 Feb 27 14:02 average.f 8 -rwxrwxrwx 1 osu683 3066 Feb 27 19:14 stgh.inp.fe3.tpt 8 -rw-r--r-- 1 osu683 2904 Feb 27 19:14 stg2.inp.fe3.spt 8 -rw-r--r-- 1 osu683 2471 Feb 27 19:14 qsbfx.o44450 8 -rw-r--r-- 1 osu683 2446 Feb 27 19:14 qsbfx.o43954 8 -rwx------ 1 osu1017 2388 Feb 27 16:53 caprun 8 -rw-r--r-- 1 osu683 2304 Feb 27 19:14 stg2.inp.tpt.all 8 -rwxrwxrwx 1 osu683 2088 Feb 27 19:14 stgh.inp.sgt.2 8 -rwx------ 1 osu1017 2025 Feb 27 14:02 conv2run 8 -rw-r--r-- 1 osu683 1989 Feb 27 19:14 stgbf.out 8 -rw-r--r-- 1 osu683 1989 Feb 27 19:14 qsbfx.o47337 8 -rw-r--r-- 1 osu683 1923 Feb 27 19:14 premout 8 -rw-r--r-- 1 osu683 1821 Feb 27 19:14 qsbfx.o46143 8 -rw-r--r-- 1 osu683 1804 Feb 27 19:14 qsbfx.o46022 8 -rw-r--r-- 1 osu683 1792 Feb 27 19:14 packout 8 -rw-r--r-- 1 osu683 1785 Feb 27 19:14 t26.23 8 -rwxrwxrwx 1 osu683 1689 Feb 27 19:14 stgh.inp.fe3.qnt 8 -rwxrwxrwx 1 osu683 1689 Feb 27 19:14 stgh.inp 8 -rwx------ 1 osu1017 1688 Feb 27 14:02 mergerun 8 -rwx------ 1 osu1017 1687 Feb 27 14:02 convrun 8 -rw-r--r-- 1 osu683 1664 Feb 27 19:14 rdf00 8 -rwxrwxrwx 1 osu683 1637 Feb 27 19:14 stgh.inp.tpt.2 8 -rwxrwxrwx 1 osu683 1637 Feb 27 19:14 stgh.inp.tpt 8 -rwxrwxrwx 1 osu683 1408 Feb 27 19:14 stgh.inp.sgt 8 -rw-r--r-- 1 osu683 1328 Feb 27 19:14 stgb.inp.tpt 8 -rw-r--r-- 1 osu683 1260 Feb 27 19:14 t2623.tpt 8 -rw-r--r-- 1 ysu002 1145 Feb 27 21:23 g92-91158.int-inp 8 -rwx------ 1 osu1017 1014 Feb 27 14:02 upectrun 8 -rw-r--r-- 1 osu683 1010 Feb 27 19:14 sbin.tpt 8 -rw-r--r-- 1 osu683 982 Feb 27 19:14 sbin.fe3.tpt 8 -rw-r--r-- 1 osu683 884 Feb 27 19:14 sbbinfe3.tpt 8 -rwxr-xr-x 1 osu683 853 Feb 27 19:14 stgb.inp.fe3.qnt 8 -rw-r--r-- 1 osu683 853 Feb 27 19:14 stgb.inp.all 8 -rw-r--r-- 1 osu683 853 Feb 27 19:14 sbin 8 -rw-r--r-- 1 osu683 747 Feb 27 19:14 stgbb.inp.fe3.qnt 8 -rw-r--r-- 1 osu683 747 Feb 27 19:14 stgbb.inp 8 -rw-r--r-- 1 osu683 742 Feb 27 19:14 stgbf.inp.all 8 -rwxr-xr-x 1 osu683 657 Feb 27 19:14 stgb.inp.fe3.spt 8 -rw-r--r-- 1 osu683 657 Feb 27 19:14 sbin.fe3.spt 8 -rw-r--r-- 1 osu683 657 Feb 27 19:14 ELEV 8 -rw-r--r-- 1 osu683 650 Feb 27 19:14 t2623.qnt 8 -rw-r--r-- 1 osu683 650 Feb 27 19:14 t2623 8 -rw-r--r-- 1 osu683 567 Feb 27 19:14 qsbfx.e46143 8 -rwxrwxrwx 1 osu683 560 Feb 27 19:14 stgbb.inp.fe3.spt 8 -rw-r--r-- 1 osu683 542 Feb 27 19:14 qsbfx.e44450 8 -rw-r--r-- 1 osu683 542 Feb 27 19:14 qsbfx.e43954 8 -rw-r--r-- 1 osu683 497 Feb 27 19:14 stgbf.inp.keep 8 -rwxrwxrwx 1 osu683 482 Feb 27 19:14 stgh.inp.fe3.spt 8 -rwxr-xr-x 1 osu683 384 Feb 27 19:14 psall 8 -rw-r--r-- 1 osu683 340 Feb 27 19:14 sfinfe3.tpt 8 -rwxrwxrwx 1 osu683 336 Feb 27 19:14 stgf.inp.fe3.spt 8 -rw-r--r-- 1 osu683 333 Feb 27 19:14 stgf.inp 8 -rw-r--r-- 1 osu683 333 Feb 27 19:14 enin 8 -rwxr-xr-x 1 osu683 320 Feb 27 19:14 psall.op 8 -rw-r--r-- 1 osu683 315 Feb 27 19:14 stgf.inp.fe3.tpt 8 -rwxrwxrwx 1 osu683 308 Feb 27 19:14 stgf.inp.fe3.qnt 8 -rwxr-xr-x 1 osu683 290 Feb 27 19:14 psone 8 -rwx------ 1 osu1017 264 Feb 27 14:02 exe 8 -rw-r--r-- 1 osu037 226 Feb 27 06:52 AMOLINPUT 8 -rw-r--r-- 1 osu683 168 Feb 27 19:14 ft3 8 -rw-r--r-- 1 osu683 156 Feb 27 19:14 datprm 8 -rw-r--r-- 1 osu683 153 Feb 27 19:14 datprm2.tpt 8 -rw-r--r-- 1 osu683 153 Feb 27 19:14 datprm.1 8 -rw-r--r-- 1 osu683 146 Feb 27 19:14 stgbf.inp.slc 8 -rw-r--r-- 1 osu683 145 Feb 27 19:14 stgbf.inp.tpt 8 -rw-r--r-- 1 osu683 144 Feb 27 19:14 dimmi 8 -rw-r--r-- 1 osu683 144 Feb 27 19:14 datpasp 8 -rw-r--r-- 1 osu683 135 Feb 27 19:14 dimmi.op 8 -rw-r--r-- 1 osu683 125 Feb 27 19:14 stgb.inp 8 -rw-r--r-- 1 osu683 103 Feb 27 19:14 stgbb.inp.fe3.tpt 8 -rw-r--r-- 1 osu683 100 Feb 27 19:14 stg1.inp 8 -rw-r--r-- 1 osu683 96 Feb 27 19:14 sbfinfe2.dbl 8 -rwxr-xr-x 1 osu683 91 Feb 27 19:14 psrm 8 -rw-r--r-- 1 osu683 89 Feb 27 19:14 qsbfx 8 -rwxr-xr-x 1 osu683 87 Feb 27 19:14 runf00 8 -rw-r--r-- 1 osu683 70 Feb 27 19:14 sbfin.pt 8 -rwxr-xr-x 1 osu683 63 Feb 27 19:14 psop 8 -rwxr-xr-x 1 osu683 63 Feb 27 19:14 psas 8 -rw-r--r-- 1 osu683 57 Feb 27 19:14 stgbf.inp 8 -rwxr-xr-x 1 osu683 52 Feb 27 19:14 orcp 8 -rwxr-xr-x 1 osu683 43 Feb 27 19:14 psone.2 8 -rwxr-xr-x 1 osu683 40 Feb 27 19:14 psone.1 8 -rwxrwx--- 1 osu1017 28 Feb 27 14:02 upect.in 8 -rw-r--r-- 1 osu683 25 Feb 27 19:14 qsbfx.e47337 8 -rw-r--r-- 1 osu683 25 Feb 27 19:14 qsbfx.e46022 8 -rw-r--r-- 1 osu683 21 Feb 27 19:14 endln 8 -rw-r--r-- 1 osu683 17 Feb 27 19:14 enln 8 -rw-r--r-- 1 osu683 11 Feb 27 19:14 packin total 6946336 total 4051776 total 3932496 total 32 total 184 total 160 total 16 total 13144016 total 11080912 /tmp/rich: /tmp/osu937: /tmp/osu937/rpm: /tmp/osu937/rpm/wrk: /tmp/osu714: /tmp/osu714/88636: /tmp/nqs.+++++0C4H: /tmp/nqs.+++++0BpN: /tmp/iron3: 0 -rw-r--r-- 1 ysu002 0 Feb 27 19:21 g92-91159.int 0 -rw-r--r-- 1 ysu002 0 Feb 27 19:21 g92-91159.d2e 0 -rw-r--r-- 1 osu037 0 Feb 27 07:05 DUMFIL38 0 -rw-r--r-- 1 osu037 0 Feb 27 03:02 TAPE87 0 -rw-r--r-- 1 osu037 0 Feb 27 03:02 TAPE86 0 -rw-r--r-- 1 osu037 0 Feb 27 03:02 TAPE84 0 -rw-r--r-- 1 osu037 0 Feb 27 03:02 TAPE83 0 -rw-r--r-- 1 osu037 0 Feb 27 03:02 TAPE82 0 -rw-r--r-- 1 osu037 0 Feb 27 03:02 TAPE81 0 -rw-r--r-- 1 osu037 0 Feb 27 03:02 TAPE77 0 -rw-r--r-- 1 osu037 0 Feb 27 03:01 FKEY21 0 -rw-r--r-- 1 osu037 0 Feb 27 02:58 SINFO 0 -rw-r--r-- 1 osu037 0 Feb 27 02:58 IINFO ***** OSCA: 43577616 disk blocks in 2179 files ***** Checking Users over limits in /tmp File system: /tmp User: ysu002, Id: 1016 ** User warning time: Thu Oct 27 14:04:47 1994 File blocks Inodes User Quota: 200000* (434.2%) Unlimited* ** LIMIT Warning: 180000* (482.4%) None ** WARNING Usage: 868306 11 User: osu037, Id: 1189 ** User warning time: Tue Jan 18 15:36:57 1994 File blocks Inodes User Quota: 200000* (260.0%) Unlimited* ** LIMIT Warning: 180000* (288.9%) None ** WARNING Usage: 520074 37 User: osu683, Id: 3202 ** User warning time: Tue Jan 18 15:05:48 1994 File blocks Inodes User Quota: 200000* (976.9%) Unlimited* ** LIMIT Warning: 180000* (***.*%) None ** WARNING Usage: 1953722 1240 User: osu714, Id: 3365 ** User warning time: Thu Jan 20 17:42:34 1994 File blocks Inodes User Quota: 200000* (335.7%) Unlimited* ** LIMIT Warning: 180000* (373.0%) None ** WARNING Usage: 671438 2202 User: osu772, Id: 3470 ** User warning time: Tue Jan 18 16:07:24 1994 File blocks Inodes User Quota: 200000* (406.2%) Unlimited* ** LIMIT Warning: 180000* (451.3%) None ** WARNING Usage: 812345 243 User: osu826, Id: 3601 ** User warning time: Fri Apr 15 11:30:21 1994 File blocks Inodes User Quota: 200000* (117.7%) Unlimited* ** LIMIT Warning: 180000* (130.7%) None ** WARNING Usage: 235338 57 User: osu937, Id: 3893 ** User warning time: Tue Jan 18 15:49:10 1994 File blocks Inodes User Quota: 200000* (442.9%) Unlimited* ** LIMIT Warning: 180000* (492.1%) None ** WARNING Usage: 885827 191 User: osu996, Id: 4029 ** User warning time: Tue Jan 18 18:09:43 1994 File blocks Inodes User Quota: 200000* (128.6%) Unlimited* ** LIMIT Warning: 180000* (142.9%) None ** WARNING Usage: 257221 53 User: osu1017, Id: 4069 ** User warning time: Wed Feb 1 13:58:10 1995 File blocks Inodes User Quota: 200000* (692.5%) Unlimited* ** LIMIT Warning: 180000* (769.4%) None ** WARNING Usage: 1384923 203 User: osu1288, Id: 4666 ** User warning time: Sun Jan 23 18:47:33 1994 File blocks Inodes User Quota: 200000* (149.1%) Unlimited* ** LIMIT Warning: 180000* (165.6%) None ** WARNING Usage: 2981From MAILER-DAEMON@ccl.net Tue Feb 28 08:50:01 1995 Received: for MAILER-DAEMON@ccl.net by www.ccl.net (8.6.9/930601.1506) id IAA00361; Tue, 28 Feb 1995 08:50:01 -0500 Date: Tue, 28 Feb 1995 08:50:01 -0500 From: Message-Id: <199502281350.IAA00361@www.ccl.net> Apparently-To: ccl@ccl.net From thep@risc1.lrm.fi.cnr.it Tue Feb 28 09:17:33 1995 Received: from risc1.lrm.fi.cnr.it for thep@risc1.lrm.fi.cnr.it by www.ccl.net (8.6.9/930601.1506) id JAA01345; Tue, 28 Feb 1995 09:16:59 -0500 Received: by risc1.lrm.fi.cnr.it (AIX 3.2/UCB 5.64/4.03) id AA24404; Tue, 28 Feb 1995 14:32:47 +0100 From: thep@risc1.lrm.fi.cnr.it (Pornthep Sompornpisut) Message-Id: <9502281332.AA24404@risc1.lrm.fi.cnr.it> Subject: Chianti Workshop on Magnetic Resonance To: chemistry@ccl.net Date: Tue, 28 Feb 1995 14:32:47 +0100 (NFT) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 3912 Status: R ******************************************************************************** 6th CHIANTI WORKSHOP ON MAGNETIC RESONANCE: NUCLEAR AND ELECTRON RELAXATION ******************************************************************************** SAN MINIATO (PISA), ITALY, MAY 27 - JUNE 2, 1995 CHAIRPERSONS: I. BERTINI (Univ. Florence), Conference Chairman K. MOEBIUS (Free Univ. Berlin), Program Chairman ORGANIZERS: R. BASOSI (Univ. Siena), C. LUCHINAT (Univ. Bologna), C.A. VERACINI (Univ. Pisa) The present Workshop, in the spirit of the series of the Chianti Workshops, aims at bringing together scientists involved in theoretical and experimental aspects of nuclear and electron spin relaxation to study the structure and dynamics of molecules. The main topics to be discussed by NMR and EPR scientists will deal with: structure determination of biomolecules, spin polarization phenomena and processes, relaxation in paramagnetic systems, quasi-ordered phases, spin imaging, new methodologies. The program will consist of invited lectures and poster presentations. At the moment the following scientists have accepted an invitation to present a lecture: L. Banci (Florence), G. Bodenhausen (Tallahassee), R.D. Britt (Davis), R. Bruschweiler (Zurich), M. Brustolon (Padova), D.A. Case (La Jolla), V. Chizhik (St. Petersburg), K.P. Dinse (Darmstadt), R.Y. Dong (Brandon), J.W. Emsley (Southampton), C. Forte (Pisa), J.H. Freed (Ithaca), E. Gaggelli (Siena), G. Giacometti (Padova), D. Goldfarb (Rehovot), C. Griesinger (Frankfurt/M.), R.G. Griffin (Cambridge, MA), E.J.J. Groenen (Leiden), B. Halle (Lund), A.J. Hoff (Leiden), B.M. Hoffman (Evanston), P. Hore (Oxford), W.L. Hubbell (Los Angeles), M. Huber (Berlin), J. Huttermann (Homburg), J.S. Hyde (Milwaukee), R. Ishima (Tsukuba), T.L. James (San Francisco), G. Kothe (Freiburg), J. Kowalewski (Stockholm), Ya.S. Lebedev (Moscow), H. Levanon (Jerusalem), W. Lubitz (Berlin), G.R. Luckhurst (Southampton), Z. Luz (Rehovot), M.W. Makinen (Chicago), K.A. McLauchlan (Oxford), A.E. Merbach (Lausanne), G. Navon (Tel Aviv), A. Pines (Berkeley), T.F. Prisner (Berlin), K.M. Salikhov (Kazan), S. Schlick (Detroit), R. Sharp (Ann Arbor), H.W. Spiess (Mainz), D. Stehlik (Berlin), U.E. Steiner (Konstanz), S. Styring (Stockholm), W.H. Thomann (Annandale), R.R. Vold (San Diego), L. Weiner (Rehovot), L. Werbelow (Marseille), P.O. Westlund (Umea). Participants intending to present posters on work related to the topics of the Workshop are asked to submit an abstract (max. 1 page A4 format typed single-spaced) of the proposed communication not later than April 15, 1995. Since the total number of participants is limited, acceptance will be on a "first come first served" basis. There is a registration fee of 250,000 Italian Lira for active participants and 120,000 Italian Lira for accompanying persons. The cost of the accommodation, based on sharing a twin-bedded room, plus all meals (including Chianti wine!) will be 700,000 Italian Lira per person. For further information, please contact: Prof. Riccardo Basosi, Dept. of Chemistry, Univ. of Siena, Pian dei Mantellini, 44, 53100 Siena, Italy,TEL. 39/577 298040,FAX 39/577 280405 Prof. Claudio Luchinat,c/o Dept. of Chemistry,Univ. of Florence Via G.Capponi, 7, 50121 Florence, Italy, TEL. 39/55 2757563, FAX 39/55 2757555 Prof. Carlo A.Veracini, Dept. of Chemistry, Univ. of Pisa Via Risorgimento, 35, 56100 Pisa, Italy, TEL. 39/50 918266, FAX 39/50 918260 or the Program Chairman: Prof. Klaus Moebius, Dept. of Physics, Free Univ. of Berlin, Arnimallee 14 D-14195 Berlin, Germany, TEL. 49/30 8382770, FAX 49/30 8386046 ############################################################################# For the REGISTRATION FORM please contact Giacomo Parigi giacomo@risc1.lrm.fi.cnr.it ############################################################################# From mmccar@postman.essex.ac.uk Tue Feb 28 09:48:58 1995 Received: from postman.essex.ac.uk for mmccar@postman.essex.ac.uk by www.ccl.net (8.6.9/930601.1506) id JAA02371; Tue, 28 Feb 1995 09:48:41 -0500 Received: from postman.essex.ac.uk by postman.essex.ac.uk with SMTP (PP) id <19104-0@postman.essex.ac.uk>; Tue, 28 Feb 1995 14:47:16 +0000 From: Mccarron M Date: Tue, 28 Feb 95 14:47:13 GMT Message-Id: <15056.9502281447@solb1.essex.ac.uk> To: chemistry Subject: CHARMM Status: R Has anyone out there carried out amino acid mutations using BLOCK If so do you know how to get around the problem of having interactions between three blocks (blocks 2 and 3 containing different side chains) thanks in advance Matthew mmccar@essex.ac.uk From shubin@email.unc.edu Tue Feb 28 10:36:59 1995 Received: from email.unc.edu for shubin@email.unc.edu by www.ccl.net (8.6.9/930601.1506) id KAA03403; Tue, 28 Feb 1995 10:36:52 -0500 Received: by email.unc.edu (AIX 3.2/UCB 5.64/4.03) id AA257869; Tue, 28 Feb 1995 10:36:17 -0500 Date: Tue, 28 Feb 1995 10:36:17 -0500 (EST) From: Shubin Liu X-Sender: shubin@isisa.oit.unc.edu To: chemistry@ccl.net Subject: CCL:Density matrix and pair function from Gaussian 92 In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: R Dear all CCLers: Can one obtain the density matrix (1st-order) and the pair function (giving a reference point) from Gaussian 92 output directly? I will give a summary here if there is any response. Shubin ............................................................................. Shubin Liu Department of Chemistry Email: shubin@email.unc.edu University of North Carolina sliu@mulliken.chem.unc.edu Chapel Hill, NC 27599-3290 Tel : (919) 962-0150(O) ............................................................................. From fant@bioc.rice.edu Tue Feb 28 10:50:12 1995 Received: from moe.rice.edu for fant@bioc.rice.edu by www.ccl.net (8.6.9/930601.1506) id KAA03765; Tue, 28 Feb 1995 10:50:10 -0500 Received: from babs.rice.edu by moe.rice.edu (JAA05028); Tue, 28 Feb 1995 09:50:07 -0600 Received: by babs.rice.edu (931110.SGI/) (for chemistry@ccl.net) id AA23500; Tue, 28 Feb 95 09:52:17 -0600 From: "Andrew Fant" Message-Id: <9502280952.ZM23498@babs.rice.edu> Date: Tue, 28 Feb 1995 09:52:16 -0600 X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@ccl.net Subject: Results of Multi search Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Status: R Last week I asked if anyone could tell me where to find Multi. The current version can be found at ftp://kamakazi.niehs.nih.gov/pub/MULTI/MULTI-3.1 . [157.98.8.47] Thanks to everyone that helped. Andy -- Andrew Fant | fant@bioc.rice.edu | "A Libertarian is someone Departmental Geek | (713)527-4774 | who wants police Biochemistry & Cell Biology | I disclaim, | protection from their Rice University | therefore I am | slaves" - K.S. Anderson From ANTHONY@admis.med.usf.edu Tue Feb 28 12:48:32 1995 Received: from pharm1.pharm.med.usf.edu for ANTHONY@admis.med.usf.edu by www.ccl.net (8.6.9/930601.1506) id MAA01020; Tue, 28 Feb 1995 12:48:30 -0500 Received: from admis.med.usf.edu ([131.247.70.101]) by pharm1.pharm.med.usf.edu (8.6.5/8.6.5) with SMTP id MAA11073 for ; Tue, 28 Feb 1995 12:48:25 -0500 Message-Id: <199502281748.MAA11073@pharm1.pharm.med.usf.edu> Received: from COM_ADM/MERCURY-MAIL by admis.med.usf.edu (Mercury 1.1); Tue, 28 Feb 95 12:46:36 +1100 To: Chemistry@ccl.net From: "Anthony Lemus" Organization: USF College of Medicine Date: Tue, 28 Feb 1995 12:46:24 EST Subject: Results of Graduate Programs query X-pmrqc: 1 Priority: normal X-mailer: WinPMail v1.0 (R1) Status: R I am posting the results of my query of PhD programs in computational chemistry for all those who requested this information. Thanks to all those who replied and sorry for the delay in compiling this data: ======================================================== Quantum Theory Project, University of Florida at Gainesville. The Quantum Theory Project is the home of ZINDO, ACESII, AMPAC, FLIMMSY, etc. and such luminaries as Michael Zerner, Rod Bartlett, and Nigel Richards, etc. Quantum Theory Project, Williamson Hall, University of Florida, Gainesville FL 32611 ----------------------------------------------------------------------------------------------------------------- There is a comp. chem. program here at UC Berkeley. And I believe that Stanford, Cornell, Madison WI, Caltech, and UCLA also have good programs. Clayton Springer ---------------------------------------------------------------------------------------------------------------- Consider Rutgers University in New Jersey. They have several professors there working on various aspects of theoretical chemistry. You may also want to look at the University of Georgia. Jeff Nauss ---------------------------------------------------------------------------------------------------------------- The Univ. of Houston has the chemical physics program joint by physics and engineering departments. The professors in computatinal area are: B.M. Pettitt, D.J. Kouri, T.A. Albright, etc.. ---------------------------------------------------------------------------------------------------------------- There is a program at Bryn Mawr College (near Philadelphia in Pennsylvania). Michelle M. Francl Associate Professor of Chemistry Bryn Mawr College Bryn Mawr, PA 19010 ----------------------------------------------------------------------------------------------------------------- The ACS sells a CD-ROM called Directory of Graduate Research. This is a chemical science directory of all colleges and universities offering chemistry curriculums. I can send you a brochure on it if you like? Just met me know. Nan Butterworth ---------------------------------------------------------------------------------------------------------------- I received a forwarded message from Dr. Jim Gano of our department that you were interested in graduate studies in computational chemistry. Dr. Hua Guo of our department is a nationally recognized computational physical chemist. If you would like information on his research, our graduate program in chemistry, please send me your address and I will have the information mailed to you. Jon Kirchhoff Chairman, Graduate Admissions Committee The University of Toledo ---------------------------------------------------------------------------------------------------------------- I don't know if there is a degree in comp. chem. anywhere, but William Jorgensen at Yale is well known in the field. In practice, you get your degree in either Physical chemistry or organic chemistry (or perhaps a more bio related field) depending on your major interests. This is true with most people in the field. (I got my degree from Bill). In addition, there is Peter Kollman at USCF pharmacy school, Ken Houk at UCLA, Andy McCammon at UCSD, all having somewhat different focuses within the field of computational chemistry. There are quite a few more, but those are most of the big names (Martin Karplus at Harvard) as a starting point. Take care, Dan ======================================================== Cheers! -ANT ______________________________________________________________________ Anthony Lemus (813) 974-3427 -Systems Analyst University of South Florida Anthony@admis.med.usf.edu College of Medicine ______________________________________________________________________ From windemut@cumbnd.bioc.columbia.edu Tue Feb 28 13:38:02 1995 Received: from cumbnd.bioc.columbia.edu for windemut@cumbnd.bioc.columbia.edu by www.ccl.net (8.6.9/930601.1506) id NAA02543; Tue, 28 Feb 1995 13:38:00 -0500 Received: from sirius by cumbnd.bioc.columbia.edu (NX5.67d/NX3.0M) id AA24600; Tue, 28 Feb 95 13:37:53 -0500 From: Andreas Windemuth Message-Id: <9502281837.AA24600@cumbnd.bioc.columbia.edu> Received: by sirius.bioc.columbia.edu (NX5.67d/NX3.0X) id AA25968; Tue, 28 Feb 95 13:37:54 -0500 Date: Tue, 28 Feb 95 13:37:54 -0500 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: chemistry@ccl.net Subject: Parallel Molecular Dynamics with full Coulomb interactions Cc: windemut@cumbnd.bioc.columbia.edu Status: R For those interested in parallel and scalable molecular dynamics simulation of biological macromolecules: Version 0.9 of the program PMD has been made available. This is an experimental program that uses the Greengard/ Rokhlin fast multipole algorithm (FMA) in conjunction with a constant force multiple timestep method to permit the efficient simulation of large biological macromolecules without cutting off the long range forces. For more details, see "http://tincan.bioc.columbia.edu/pmd/" or the README file from the distribution reproduced below. --- Andreas Windemuth +-------------------------------------------------------------------- |Columbia University, Department of Biochemistry and Biophysics |630 West 168th St. BB-221 | tel: (212)-305-6884, fax: 6926, NeXTmail |New York, NY 10032 | email: windemut@cumbnd.bioc.columbia.edu +-------------------------------------------------------------------- This is an experimental version of PMD, Version 0.9, release Feb 28, 1995, all rights reserved. PMD is a scalable, parallel program for the simulation of the dynamics of biological macromolecules. PMD utilizes the Greengard/Rokhlin Fast Multipole Algorithm to allow the simulation of very large biological macromolecular systems without sacrificing the important long-range Coulomb interactions. The force field implemented by PMD is compatible to programs such as CHARMM, X-PLOR, GROMOS, Discover and others. Residue topology and parameter files suitable for X-PLOR can be used with PMD. Particularly, PMD can fully implement the CHARMM19 CHARMM22 force fields. PMD is also intrinsically and transparently parallel and suitable for running on a wide variety of parallel architectures, both shared memory and message passing. The most salient features of PMD are: - Use of the Fast Multipole Algorithm allows for the calculation of the full long range electrostatic interactions in linear (of order N) time. - The Distance Class Algorithm reduces the calculation time further to make full-range calculations faster than conventional cutoff methods. - PMD is designed to be completely scalable, i.e. arbitrarily large systems (millions of atoms) can be simulated as long as enough processing nodes are available. Memory use is minimal, compared to other programs. - PMD runs without changes on a large number of UNIX workstations and can easily be adapted to others. Parallel implementations exist for the CM-5, the Intel Paragon, the Cray T3D and workstation networks. - Parallel instructions are limited to a small set of commands that are easily implemented in any machine specific or portable (TCGMSG, PVM, Linda) parallel processing interface. PMD is work in progress. Expect plenty of changes of all kinds in future versions. This program is made available to encourage researchers to add features they need and in the hope that some of these improvements find their way back into future versions. A mailing list has been established to foster discussion among users and contributors. Please direct inquiries to join the mailing list to "pmd-request@cumbnd.bioc.columbia.edu". The source code is being made available under the condition that any additions, improvements or changes will be sent to the author (windemut@cumbnd.bioc.columbia.edu) for inclusion into the distribution. No restrictions different from those on PMD itself may be put on such contributions. PMD or parts of it may not be used or distributed for non-disclosed corporate research or commercially without prior consent of the author. If either the program or ideas from its code are used in a publication, it is asked that the following references be cited: J.A. Board Jr., J.W. Causey, J.F. Leathrum Jr., A. Windemuth, and K. Schulten. Accelerated molecular dynamics simulation with the parallel fast multipole algorithm. Chem. Phys. Lett. 198:89--94, 1992. A. Windemuth and K. Schulten. Molecular dynamics on the Connection Machine. Molecular Simulation, 5:353--361, 1991. A. Windemuth. Advanced Algorithms for Molecular Dynamics Simulation: The Program PMD. in "Parallel Computing in Computational Chemistry" (Timothy G. Mattson, ed.), ACS Books, 1995, in press. Installation: cd zcat pmd.tar.Z | tar xvf - Demo run: cd pmd/demo make SYS= (one of next hpux dec iris aix sun paragon) Parallel demo run: [install TCGMSG and customize bin/par.] cd demo make SYS= PSYS=tcgmsg This will start a simulation of Pancreatic Trypsin Inhibitor (PTI), starting from the original PDB file, adding hydrogens, equilibrating with harmonic constraints and a minimizing. Look at "demo/makefile" and "src/make.sim" to see how the run is controlled and how you might modify it to run your own molecules. First, try changing the line "SYS=next" to reflect the machine you are actually using. Then, try "make MOL=mb" to run the solvated myoglobin setup that is frequently used as a benchmark for CHARMM. Finally, try "make mutant" to generate a Ile 3 -> Tyr mutant of T4 phage lysozyme (2lzm). Some of these simulation will take quite some time if not interrupted. It is suggested to run them in the background using the ampersand ("&") character, i.e. "make mutant &". The link "demo/log" will always point to the newest simulation log. Try "tail -f log" to check on the simulation progress. Some other sample molecules are available in "demo". Their topology is described in files "*.str", their atom coordinates in files "*.pdb". It is quite straightforward to make your own "*.str" files, once you study the sample files and "src/make.sim". If you wish to run PMD in parallel, make sure that you have TCGMSG or PVM installed and that there is a directory or link "tcgmsg" or "pvm" in your home directory pointing to your system's TCGMSG or PVM root directory. Edit "makefile" and change the line "PSYS=serial" to one of the supported parallel interfaces (tcgmsg, pvm, pvm-t3d). You also will have to edit a startup script that sets up processes on the network. The script has the name "par-$(SYS)-$(PSYS)" and it is located in "bin". Some examples are provided, but you will almost certainly have to adapt one of them to your own environment. TCGMSG can be obtained from "ftp.tcg.anl.gov". See the file "README.TCGMSG" for more information. Information on PVM can be obtained at "http://www.epm.ornl.gov/pvm/pvm_home.html" on the World-Wide Web. For information on the Cray T3D refer to "http://pscinfo.psc.edu/machines/cray/t3d/t3d.html". Documentation: This file, some scattered comments in makefiles and scripts, and the World Wide Web pages. Main features: Fast multipole algorithm Linear scaling enables simulation of extremely large systems Full long range interactions with no cut-off Distance class algorithm Accounts for full long-range interaction while providing performance better than conventional cut-off calculations Scalable parallel implementation on Workstation networks (with TCGMSG or PVM) Cray T3D (PVM) Convex Exemplar (TCGMSG) Intel Paragon (TCGMSG) Thinking Machines CM-5 (slow, no vector units, no longer supported) Parsytec GC (initial implementation, no longer supported) Now implemented: Growing of hydrogens Mutation (Growing of sidechains) Building solvation shells Superposition and RMS-values Solvent accessible surface (no forces, yet) Harmonic constraints Stochastic boundary (friction and random fluctuations) Restart files and DCD trajectories Main limitations: FMA and atom reassignment not fully scalable (yet) No vectorization Not enough features Forthcoming: (no guarantees, of course :-) ) Advanced solvent treatment Generalized Born potential Hydrophobic forces and continuum electrostatics with forces FMA and atom reassignment Improved scalable versions Periodic boundary conditions Other features Containment fields for closed boundary Pretty pictures (ray-tracing and movies) Adapting PMD to other parallel systems: All machine-specific parallel communication commands have been isolated into one file, called the adaptor. The adaptors in the current release are "tcgmsg.c": for the TCGMSG public domain parallel programming Interface, "pvm.c": for the PVM public domain parallel programming Interface, "cm5.c": for the Connection Machine 5 with CMMD-3.0, "pvm-t3d.c" for the restricted set of PVM used on the Cray T3D, and "serial.c": for non-parallel workstation implementations. With TCGMSG or PVM PMD can be run on a wide variety of platforms, such as workstation networks, the Intel Paragon and the Convex Exemplar. Other adaptors are expected to become available as work progresses. Changes from 0.8: - Much improved makefiles and compilation - Simplified parallel execution - Parallel output is now much faster and should always work - new trajectory format, with PDB and DCD conversion utility - PVM and the Cray T3D are now supported - Numerous bugs corrected. - Everything else also improved. Have fun! Andreas Windemuth +-------------------------------------------------------------------- |Columbia University, Dept. of Biochemistry and Biophysics, BB-221 |630 West 168th St. | tel: (212)-305-6884, fax: 6926, NeXTmail |New York, NY 10032 | email: windemut@cumbne.bioc.columbia.edu +-------------------------------------------------------------------- From feaster@tessa.iaf.uiowa.edu Tue Feb 28 14:05:18 1995 Received: from ns-mx.uiowa.edu for feaster@tessa.iaf.uiowa.edu by www.ccl.net (8.6.9/930601.1506) id OAA03284; Tue, 28 Feb 1995 14:05:16 -0500 Received: from tessa.iaf.uiowa.edu by ns-mx.uiowa.edu (8.6.8.2/19950217.1) on Tue, 28 Feb 1995 13:05:14 -0600 id NAA13295 with SMTP Received: by tessa.iaf.uiowa.edu (920330.SGI/891024) on Tue, 28 Feb 95 12:57:06 -0600 id AA03795 Date: Tue, 28 Feb 1995 12:50:12 -0600 (CST) From: shawn feaster Subject: Fe(0) complex modeling To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Status: R Dear all computational chemists, Does anyone know of a method for modeling transition metal complexes. For example, Fe(0) and carbon tetrachloride? I believe at this moment that most canned programs do not have this capability. I think that "Cerius" may be able to do some very rough modeling, but the modeling assumes very approximate geometries. Is this true? If there is a solution to my problem I would very much like to hear from you. My email address is feaster@tessa.iaf.uiowa.edu. Thanks, Shawn Feaster From andrey@atp.biochem.usyd.edu.au Tue Feb 28 19:08:32 1995 Received: from atp.biochem.usyd.edu.au for andrey@atp.biochem.usyd.edu.au by www.ccl.net (8.6.10/930601.1506) id SAA08417; Tue, 28 Feb 1995 18:16:02 -0500 Received: from nicePC.biochem.usyd.EDU.AU (nicePC [129.78.130.68]) by atp.biochem.usyd.edu.au (8.6.9/8.6.9) with SMTP id KAA17892 for ; Wed, 1 Mar 1995 10:05:51 +1100 Message-Id: <199502282305.KAA17892@atp.biochem.usyd.edu.au> From: "Andrey Bliznyuk" To: chemistry@ccl.net Date: Wed, 1 Mar 1995 10:14:38 Subject: Molecular Simulation address ? Reply-to: A.Bliznyuk@biochem.usyd.edu.au Priority: normal X-mailer: Pegasus Mail/Windows (v1.11a) Dear Netters, Would someone be so kind to send me the address and name of editor(s) of journal "Molecular Simulations" ? Thank you, Dr. Andrey Bliznyuk Department of Biochemistry University of Sydney, NSW 2006, Australia From MARYJO@neu.edu Tue Feb 28 20:08:34 1995 Received: from nuhub.dac.neu.edu for MARYJO@neu.edu by www.ccl.net (8.6.10/930601.1506) id TAA08931; Tue, 28 Feb 1995 19:13:23 -0500 From: Received: from neu.edu by neu.edu (PMDF V4.3-7 #7628) id <01HNLDX5GFPS936VKG@neu.edu>; Tue, 28 Feb 1995 19:17:11 EST Date: Tue, 28 Feb 1995 19:17:10 -0500 (EST) Subject: Grignard rxn intermediates? To: chemistry@ccl.net Message-id: <01HNLDX5I1KY936VKG@neu.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hi there, everybody. Is anyone aware of any computational work on Grignard reaction intermediates? Is there any hope of guessing at an intermediate geometry and running a calculation with any meaning whatsoever? Is there any way to get information about the electronic structure of a reaction intermediate? Any information, advice, or informed opinion will be welcomed. Thanks very much, Mary Jo Ondrechen From wdi@ccl.net Tue Feb 28 07:42:56 1995 Received: from schiele for wdi@ccl.net by www.ccl.net (8.6.9/930601.1506) id HAA02130; Tue, 28 Feb 1995 07:02:00 -0500 Received: by schiele (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@ccl.net id MAA11111; Tue, 28 Feb 1995 12:58:20 +0100 From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9502281258.ZM11109@schiele> Date: Tue, 28 Feb 1995 12:58:17 +0100 Reply-To: wdi@eros.ccc.uni-erlangen.de X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: GDCh-CIC Mailing List Status: R Due to some convoluted problems involving access permissions, nfs crossmounts and a non-standard mail system there were some problems from Saturday to Tuesday morning (local time) with the mailing list manager for the GDCh-CIC mailing list. Please check if you were a victim: The sympton is a compete loss of mail sent from some places when trying to subscribe to the GDCh-CIC mailing list via majordomo@eros.ccc.uni-erlangen.de with 'subscribe gdch-cic' in the mail body. So please if you did not receive any answer (i.e. a message indicating success or failure of subscription and the info file) subscribe again. We apologize for the inconvenience. Once more the info file for the mailing list: *************************************************************************** Diese Mailing-Liste mit dem Namen 'gdch-cic' befindet sich unter der Adresse 'eros.ccc.uni-erlangen.de' im Computer-Chemie-Centrum der Universitaet Erlangen-Nuernberg. Sie ist ein elektronisches Diskusssionsforum der Fachgruppe 'Chemie Information Computer' (CIC) in der GDCh, der Gesellschaft Deutscher Chemiker. Die Liste dient zur Zeit primaer als Koordinierungs- und Austauschstelle zur Projektierung des Informationsprojektes, das gemeinsam mit den Verbaenden der Physiker, Mathematiker und Informatiker konzipiert wird. Im Moment ist die Liste unmoderiert, d.h. jeder Bezieher der Liste kann ungefiltert Beitraege hineingeben, die sofort an alle Subskribenten weitergegeben werden. Auch die Mitgliedschaft ist frei. Es nicht nicht zwingend notwendig, Mitglied der GDCh oder der CIC zu sein, obwohl wir beides empfehlen. Wenn Sie Mitglied der CIC werden wollen und bereits GDCh Mitglied sind, schicken Sie bitte eine Nachricht an Prof. Gasteiger (gasteiger@eros.ccc.uni-erlangen.de), den Vorsitzenden der Gruppe. Wenn Sie Mitglied der GDCh werden wollen, koennen Sie dies leider noch nicht ueber elektronische Medien. Bitte fragen Sie einen Kollegen, der Mitglied ist und Sie einfuehrt. Da dies ein deutsches Forum ist, ist die bevorzugte Sprache der Meldungen Deutsch. Bitte senden Sie Ihre Meldungen an 'gdch-cic@eros.ccc.uni-erlangen.de', nicht an 'majordomo'. Die 'majordomo' Adresse dient auschliesslich zum An- und Abmelden und fuer weitere Serviceleistungen. Benutzen Sie bitte eine aussagekraeftige 'Subject:' Zeile im Mailheader. Vor diese Zeile wird automatisch 'GDCH-CIC:' eingefuegt, so dass Meldungen aus dieser Quelle leicht in den Mailboxen der Empfaenger zu finden sind. Zur Zeit werden alle Nachrichten archiviert. Wir koennen keine unbegrenzte Aufbewahrung garantierten, aber es stehen auf jeden Fall die Nachrichten der letzten Wochen fuer Spaeteinsteiger zum nachtraeglichen Studium zur Verfuegung. Um diese gespeicherten Nachrichten zu erhalten, schicken Sie bitte das Kommando 'get gdch-cic aktuell' im Hauptteil der Nachricht an 'majordomo@eros.ccc.uni-erlangen.de'. An die Liste angekoppelt ist ein Archiv aktueller Dokumente, die die CIC betreffen, zum Beispiel Protokolle und Reports. Eine Uebersicht erhalten Sie mit dem Kommando 'index gdch-cic' im Hauptteil einer Nachricht an 'majordomo@eros.ccc.uni-erlangen.de'. Auch diese Texte stehen Ihnen ueber ein 'get' Kommando zur Verfuegung. Wenn Sie techische Fragen haben oder Probleme mit dem Bezug der Liste oder der Verbreitung Ihrer Meldungen, wenden Sie sich bitte an 'gdch-cic-owner@eros.ccc.uni-erlangen.de'. Erlangen, 24.2.95 -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566