From keith@kbw350.chem.yale.edu Thu Jul 18 00:18:24 1996 Received: from kbw350.chem.yale.edu for keith@kbw350.chem.yale.edu by www.ccl.net (8.7.5/950822.1) id XAA20002; Wed, 17 Jul 1996 23:18:48 -0400 (EDT) Received: by kbw350.chem.yale.edu (AIX 3.2/UCB 5.64/4.03) id AA22500; Wed, 17 Jul 1996 23:14:59 -0400 Date: Wed, 17 Jul 1996 23:14:59 -0400 From: keith@kbw350.chem.yale.edu (Todd Keith) Message-Id: <9607180314.AA22500@kbw350.chem.yale.edu> To: chemistry@www.ccl.net Subject: SCIPCM in G94 Re: > I have been having problems getting geometries (and in some cases SCF's) > to converge when using the scrf=scipcm option in G94. The higher > the dielectric constant, the more problem there seems to be. Does > anyone have any suggestions on how this problem might be cured? I > have already started with prior hessians and the molecules are simple, > so the problem seems to be the inclusion of solvent effects. > > Thanks in advance, John > This is one of a many such complaints I've seen on the CCL, so a reply (possibly long-winded) to the list might be helpful ... The problem is probably due to the multi-center surface integration procedure which, unfortunately, is used by default for SCI-PCM in G94. Often, a far superior procedure is to use the non- default single center surface integration procedure: when used appropriately, it is much faster and the surface integrals much more accurate than the default procedure. Geometry optimizations are much more stable using the single center method (a conseqence of the more accurate surface integrals). To invoke the single center integration procedure, one must enter some additional input on the input line which specifies the solvent's dielectric constant. Here is the format and a partial description of the general SCI-PCM input line for G94: Epsilon Cont NPhi NTheta ISurf Epsilon = Dielectric constant of solvent (for example: 78.3 for water). Cont = Value of isodensity surface in atomic units. 0.0004 au is recommended and the default. Molecular volumes defined by 0.0004 isodensity surfaces consistently agree fairly well with values inferred from corresponding measured pure liquid molar volumes or partial liquid molar volumes, which suggests that solute cavities by such isodensity surfaces are physically reasonable. NPhi = Number of equally spaced phi values for numerical surface integration, or total number of points in a Special grid. Number is per origin. Default is Special 302. Legitimate Special grids are currently: 110 146 194 302 434 590 770 and 974. NTheta = Number of Gauss-Legendre theta values for numerical surface integration, or 1 to use a Special grid, which is the default. If using Gauss-Legendre, this number should be about half of NPhi. ISurf = Whether to do surface integrals numerically using a single center (2) - the center of nuclear charge - or piecewise, using a multi-center method (3). 3 is, in principle, more generally applicable than 2 and is the default, but (2) is much faster and more accurate when applicable, which is often. (2) is applicable when, for every point on the cavity surface, the projection of the surface normal vector onto the corresponding unit vector from the single center is greater than zero. The SCI-PCM solute geometry optimizations require reasonably accurate surface integrals to work well. The accuracy of the SCI-PCM surface integrations can be monitored by the calculated total flux of the nuclear electric field thru the cavity surface, which should equal 4*Pi*Qnuc, where Qnuc is the total nuclear charge within the cavity. Another measure of accuracy is the total surface polarization charge, Qpol, as compared to the net charge of the cavity, Qcav, which is (1/(4*Pi)) times the net flux of the solute electric field through the cavity surface. If things are done correctly then: Qpol=-(1-1/Epsilon)*Qcav. I would strongly recommend using the single center integration procedure by default. As implied above, the G94 SCI-PCM implementation calculates useful independent measures of the accuracy of the SCI-PCM surface integrals. Unfortunately, the values of these quantities (along with other useful info like the cavity volume and surface area) are not printed out by default, but can only be seen (for every SCF iteration particularly the final one) by requesting #P and IOp(5/33=2), which also causes the A LOT of other printing in the .log file (Fock matrices, density matrices, etc.). Specifying #P alone will cause the interesting quantities to be printed out for the first SCF iteration, which may be adequate to determine whether the surface integrals are sufficiently accurate to proceed. So, if one uses the single center procedure, the main question is how many integration points to use. Here is a rough! guide of molecular size versus total number of points to use: 1 to 6 atoms --> 434 points (Special grid: NPhi = 434, NTheta = 1) 7 to 11 atoms --> 590 points (Special grid: NPhi = 590, NTheta = 1) 12 to 15 atoms --> 770 points (Special grid: NPhi = 770, NTheta = 1) 16 to 20 atoms --> 974 points (Special grid: NPhi = 974, NTheta = 1) > 20 atoms --> use equally spaced Phi, Gauss-Legendre theta with the total number of points being at least NAtoms*100 (e.g., for 1800 total points use NPhi = 60 and NTheta = 30). Of course, the actual shape of the solute molecule might dictate the need for more or less points, or possibly, for very large or very complex solutes the complete failure of the single center method. Here is an example input file for a HF/6-31G* SCI-PCM geometry optimization of N,N-dimethyl acetamide in acetonitrile (Epsilon = 35.9): #P HF/6-31+G* Opt SCRF=SCIPCM N,N dma HF/6-31+G* opt SCI-PCM e=35.9, Cont=0.0004, 770 pts, single cent 0 1 Z-Matrix, molecule specification 35.9 0.0004 770 1 2 Note that the use of the default multi-center procedure in the above case would require many more integration points (like 1500) and would thus be relatively slow and the optimization may not converge due to relatively inaccurate surface integrals. Good Luck. T. A. Keith keith@kbw350.chem.yale.edu >From MAILER-DAEMON@www.ccl.net Tue Jul 16 02:39 EDT 1996 Received: from irene for MAILER-DAEMON@www.ccl.net by www.ccl.net (8.7.5/950822.1) id CAA07999; Tue, 16 Jul 1996 02:39:47 -0400 (EDT) Received: by irene (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id BAA14162; Tue, 16 Jul 1996 01:39:48 -0500 Date: Tue, 16 Jul 1996 01:39:48 -0500 From: christin@irene (Christine Byrd) Message-Id: <199607160639.BAA14162@irene> To: chemistry@www.ccl.net Subject: MOPAC output files Content-Type: text Content-Length: 1136 Status: RO I have a few questions regarding Mopac .out and .syb files. My observation: I've noticed that .syb files are created after running a MOPAC, despite failure of a compound to pass one of the gradient tests (Herbert's or Peter's). On the other hand, .syb files are not generated when MOPAC "abandons" a calculation for a specific compound. I was hoping if perhaps someone would explain: (1) The criteria according to which MOPAC chooses to submit a compound to either "Peter's Test" or "Herbert's Test." (2) Which consequences not passing one of the gradient tests has on the resulting MOPAC calculation. I need to run MOPAC calculations on a rather large database and would like to run them using SPL Macros, for the sake of time and accuracy. Should the failure to pass one of the tests mentioned above have consequences on the MOPAC calculation and thus on the .syb file, is there a clever way to check for compliance with the tests utilizing a Macro? I would appreciate any advice. Cheers, Christine Byrd Christine Byr e-mail: christin@irene.uams.edu From steve@bellatrix.pcl.ox.ac.uk Fri Jul 12 09:13:34 1996 Received: from oxmail3.ox.ac.uk for steve@bellatrix.pcl.ox.ac.uk by www.ccl.net (8.7.5/950822.1) id IAA17483; Fri, 12 Jul 1996 08:49:59 -0400 (EDT) Received: from joule.pcl.ox.ac.uk by oxmail3 with SMTP (PP) with ESMTP; Fri, 12 Jul 1996 10:35:08 +0100 Received: from bellatrix (bellatrix.pcl.ox.ac.uk [163.1.21.231]) by joule.pcl.ox.ac.uk (8.6.10/8.6.5) with ESMTP id KAA13032 for <@joule.pcl:chemistry@www.ccl.net>; Fri, 12 Jul 1996 10:34:44 +0100 Received: by bellatrix (940816.SGI.8.6.9/940406.SGI.AUTO) id KAA27057; Fri, 12 Jul 1996 10:33:06 GMT Date: Fri, 12 Jul 1996 10:33:05 +0000 (GMT) From: Steve Doughty To: chemistry@www.ccl.net Subject: MGMS EC-1 Announcement Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII FIRST ELECTRONIC MOLECULAR GRAPHICS AND MODELLING SOCIETY CONFERENCE ******************************************************************** The First Electronic Molecular Graphics and Modelling Society Conference (MGMS EC-1) will be held on the Internet (the Net) and World Wide Web (the Web) from Oct 7-18, 1996. The conference is sponsored by Elsevier and the Molecular Graphics and Modelling Society and will be co-organized by Graham Richards, Art Olson, Rod Hubbard and Barry Hardy. MGMS EC-1 will be a fully international event open to all members of the scientific community and will cover a broad range of disciplines related to molecular modelling, graphics and simulation methods and applications. Conference subject areas are: Protein Structure; Membranes and Membrane Proteins; Bioinformatics; Computational Nanotechnology; Protein Folding; Modelling of In Vivo Activity; Knowledge-based Library Design; Surface Science; Host-guest interactions; Carbohydrates; Enzyme Mechanisms; Conformational Analysis; Nucleic Acids; Quantum Chemistry; Car-Parrinello Methods and Applications; Structure-based Design; Visualization; and Perspectives. Each subject area has a section convener who will screen abstracts sent by authors for suitability. Authors can opt to submit a non-permanent presentation like a normal conference poster or a presentation which will be refereed and considered for publication in the Journal of Molecular Graphics. Referees will be appointed by the section conveners. Presentations must be prepared in Hypertext Markup Language (HTML), graphics (GIF,JPEG) and other web-compatible formats (VRML,Java,PDF) so that participants can view the papers via the World Wide Web. Aid and consultation will be provided to participants in the weeks prior to the event to help them with their presentation (Email:mgmsorg@bellatrix.pcl.ox.ac.uk). Further details will be given in the authors' guide accessible via the URL: http://bellatrix.pcl.ox.ac.uk/mgms/ During the conference discussions will take place via the Internet in real-time using a virtual conference centre based on a MOO (multiple-user domain, object oriented) and via Internet-accessible electronic mailing lists. Trial sessions for those not familiar with MOOs will be held before the conference. Before the conference, a timetable for MOO discussion sessions of each section will be posted. Since these realtime discussions are an integral part of the conference, authors will be expected to attend one for their subject; the right is reserved not to referee submissions by authors who do not attend one of these sessions. The Conference will feature a Virtual Trade Center where commercial vendors, software and hardware developers, consultants, and contractors will be able to display their goods and services and provide software demonstrations in return for exhibition fees to support conference activities. Any potential exhibitors should contact Barry Hardy at barry@bellatrix.pcl.ox.ac.uk ******************* DEADLINES AND DATES 1) DO NOW - The MGMS mailing list Conference-related news and announcements will be posted regularly to the MGMS mailing list (http://bellatrix.pcl.ox.ac.uk/hypermail/mgms/). If you wish to subscribe to the MGMS list send the following one line message to majordomo@bellatrix.pcl.ox.ac.uk: subscribe mgms@bellatrix.pcl.ox.ac.uk your_email@address your_name 2) DO NOW - Registration The deadline for registration is Sept 15th 1996. Early registration is strongly encouraged to aid the efficient operation of the conference including the establishment of timely access to the conference. If you intend to participate in MGMS EC-1 please use the registration form accessible via http://bellatrix.pcl.ox.ac.uk/mgms/ which is available for electronic registration. The registration will be used to construct a registrant database for the conference which will generate the conference mailing list and handle assignment of userids and passwords. In addition it is necessary to pay for registration via ordinary means: The conference fee will be 35 pounds sterling (50 US dollars) with a special rate for students of 20 pounds sterling (30 US dollars). A copy of a suitable student identification or a letter from the supervisor will be required to be charged at the lower rate. Registration payments can be accepted by credit card, direct bank transfer, cheque or bank draft. Regardless of method of payment we ask you to supply accompanying correspondence with your complete name, address, fax and phone number, and email address which should be mailed directly to: Dr. Barry Hardy, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK Payment Instructions: a) Credit Card We can currently accept Visa, Mastercard, Switch or JCB. We cannot yet accept American Express as our application with them has still to be processed. Please send your credit card type, number and expiration date via regular mail to: Dr. Barry Hardy, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK b) Bank Transfer Your payment can be made in sterling by direct bank transfer into the folowing account: Account Number: 20-6518 50772712 Account Name: Greenlea Communications Bank: Barclays Bank, Oxford City Centre Branch, P.O. Box 333, Oxford, OX1 3HS, UK --Please ensure your full name is listed with the transfer details. --You are responsible for any bank charges associated with the transfer from your bank. --Please notify us directly of your transfer payment. 3) Cheque/Bank Draft Cheques or bank orders (in pounds or dollars) should be made out to Greenlea Communications and mailed to: Dr. Barry Hardy, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK Acknowledgement of Registration and Payment: When you first register at the conference site you should receive an acknowledgement email with a password and userid. After receipt of your registration fee you will receive a further acknowledgement and your userid and password will be validated to allow access to the conference site (when it opens). (Note: Registration payments received during the period July 23- August 14 will not be immediately processed and acknowledged. They will be processed as soon after August 14 as possible.) Academic registrants from economically-disadvantaged countries can write to Barry Hardy requesting an exemption to the registration fee. Exemptions will be made on a discretionary basis taking into account the reasons given for the request and will be dependent on suitable funds being available. We will consider economically disadvantaged countries to include those of Eastern Europe, Africa, Central and South America, Indian sub-continent, etc. 3) DEADLINE for receipt of ABSTRACT. The deadline for receipt of presentation abstracts is August 1. Email your abstract directly to the appropriate section convener listed below. Fuller details of the scope of each section will be given in the authors' guide accessible via http://bellatrix.pcl.ox.ac.uk/mgms/ Your abstract should be no longer than 300 words. And remember to state which category of presentation (non-permanent poster or refereed paper) you wish. If you are unsure as to which section your abstract is suitable for, please email a possible section convener or Barry Hardy (barry@bellatrix.pcl.ox.ac.uk). Section conveners do have the discretion to reject abstracts, ask for revisions to an abstract or to send the abstract to the convener of a more suitable section. 4) DEADLINE for receipt of PRESENTATION The deadline for receipt of papers and posters is Sept 15th. You must deposit your text and graphics files at the conference ftp site for presentation at the conference. Ftp instructions will be provided at the conference site. Hard copies of final refereed papers following the format of the Journal of Molecular Graphics should be sent by Dec 1 to: Graham Richards, Journal of Molecular Graphics, Physical & Theoretical Chemistry Lab, Sth Parks Rd, University of Oxford, Oxford, OX1 3QZ, UK. Journal guidelines are posted at http://bellatrix.pcl.ox.ac.uk/mgms/ Although there is no limit to the graphics authors choose to display in their conference presentation, the editor reserves the right to limit the number of free colour figures in each printed journal article. 5) Refereeing Period The refereeing period will commence upon completion of the conference. If you have a presentation at MGMS EC-1 you may be requested to contribute a refereeing evaluation on another conference presentation. Referee reports will be due November 15. ******************* SECTIONS AND SECTION CONVENERS (Please email section conveners with questions related to your particular section and presentation. Details on the sections are accessible via http://bellatrix.pcl.ox.ac.uk/mgms/) Any general emails (such as registration queries, maillist queries, HTML queries, password queries, timetable queries, general technical advice on browsers and graphics, MOO queries, etc.) should be sent to: mgmsorg@bellatrix.pcl.ox.ac.uk 1. Protein Structure Rod Hubbard University of York, UK Email:rod@yorvic.york.ac.uk 2. Nucleic Acids David Beveridge and Dennis Sprous Wesleyan University, USA Email:bever@rose.chem.wesleyan.edu,dsprous@rose.chem.wesleyan.edu 3. Membranes and Membrane Proteins Alan Robinson University of Oxford, UK Email:alan@bellatrix.pcl.ox.ac.uk and Terry Stouch Bristol-Myers Squibb, USA Email:stouch@dino.bms.com 4. Bioinformatics Steve Gardner Oxford Molecular, UK Email:sgardner@oxmol.co.uk 5. Computational Nanotechnology Al Globus NASA-Ames, USA Email:globus@nas.nasa.gov 6. Protein Folding Jeffrey Skolnick Scripps Institute, USA Email:skolnick@scripps.edu 7. Modelling of In Vivo Activity Edward Hodgkin Wyeth-Ayerst Research, USA Email:hodgkie@war.wyeth.com 8. Knowledge-based Library Design Mike Hann GlaxoWellcome, UK Email:mmh1203@ggr.co.uk 9. Surface Science Donald Brenner North Carolina State, USA Email:dwb@ripley.mte.ncsu.edu 10. Host-Guest interactions Jon Essex Southampton University, UK Email:J.W.Essex@soton.ac.uk 11. Carbohydrates and Protein-Carbohydrate Interactions Anne Imberty CNRS, France Email:imberty@nantes.inra.fr 12. Enzyme Mechanisms Guy Grant University College Dublin, Ireland Email:ggrant@macollamh.ucd.ie 13. Stochastic Methods for Conformational Sampling Robert Topper The Cooper Union, USA Email:topper@cooper.edu 14. Quantum Chemistry Tim Clark University of Erlangen, Germany Email:clark@organik.uni-erlangen.de 15. Structure-based Design David Winkler CSIRO, Australia Email:D.Winkler@chem.csiro.au 16. Car-Parrinello Methods and Applications Michele Parrinello Max-Planck Institute, Germany Email:prr@prr.mpi-stuttgart.mpg.de 17. Visualization Art Olson Scripps Institute, USA Email:olson@scripps.edu 18. Perspectives in Molecular Modelling Graham Richards University of Oxford, UK Email:gr@vax.ox.ac.uk ------------------------------------------------------------------ // || \\ // Stephen Doughty || "The best and most \\ // Physical & Theoretical Chemistry Lab.||beautiful things in \\ // Oxford University, ||this world cannot be \\ // South Parks Road, OXFORD, OX1 3QZ, UK||seen or even touched.\\ // ||They must be felt \\ // Tel: +44 1865 275475 ||with the heart." \\ //--------------------------------------------------------------\\ // Email : steve@bellatrix.pcl.ox.ac.uk \\ // WWW : http://bellatrix.pcl.ox.ac.uk/people/steve/ \\ ------------------------------------------------------------------ >From gwaltney@qtp.ufl.edu Fri Jul 5 12:44 EDT 1996 Received: from qtp.ufl.edu for gwaltney@qtp.ufl.edu by www.ccl.net (8.7.5/950822.1) id MAA19290; Fri, 5 Jul 1996 12:44:41 -0400 (EDT) Received: from red5.qtp.ufl.edu by qtp.ufl.edu (SMI-8.6/4.11) id LAA24020; Fri, 5 Jul 1996 11:44:31 -0500 Received: by red5.qtp.ufl.edu (SMI-8.6/4.11) id LAA20439; Fri, 5 Jul 1996 11:43:44 -0500 From: "Steve Gwaltney" Date: Fri, 5 Jul 1996 11:43:44 -0500 Message-Id: <199607051643.LAA20439@red5.qtp.ufl.edu> To: chemistry@www.ccl.net Subject: Re: CCL:MCSCF freq. + scaling factors Cc: muguet@poly.polytechnique.fr Mime-Version: 1.0 Content-Transfer-Encoding: 7bit Content-MD5: jkxo4rPvdNWiF4B5b5LYew== Content-Type: text/plain; charset=us-ascii Content-Length: 2949 Status: RO > Dear CCL Netters CHEMISTRY@www.ccl.net > > Ref: CAS vs HF frequencies, vibration scaling factors, > > I would like to add my grain of salt to these 2 threads. > > 1/ I would tend to think that MCSCF ( and then CAS ) frequencie are > much better than HF and ALSO MP2. > In the case, where static correlation is important, no doubt MCSCF > is better. It has been argued (in the CCL discussion) > than MP2 might be better to describe dynamic correlation, why ? > In fact, I begun to be suspicious of MP2 schemes, when I realized > that most MP2 energy is coming from the highest virtual MOs, which > feature extremely bizarre contours ( plot them !) and also > very large MO coefficients. > > 2/ For frequencies computed within the harmonic approximation, > scaling factors might correct both for > lack of proper correlation treatment,and > lack of anharmonicity. > > It is safer, whenever possible, to try to separate these 2 issues. > In fact MP2 frequencies, often seem better than MCSCF frequencies > but this might come from a compensation of error with anharmonicity. > Most of the MP2 energy does not come from the highest virtual MO's. The MP2 energy formula is 2 (2) 1 || E = _ sum(ijab) ___________ 4 e +e -e -e i j a b where e and e are the energies of the occupied (spin) orbitals, i j and e and e are the energies of the virtual orbitals. What this a b shows is that when you are exciting out of very low lying occupied orbitals or you are exciting into very high lying virutal orbitals, the denominator is large, and therefore that term contributes very little to the total energy correction. The large energy corrections come when you are exciting from high lying occupied orbitals into low lying virtual orbitals. As to the quality of MP2 vibrational frequencies: in R.J. Bartlett and J.F. Stanton, _Reviews_in_Computational_Chemistry_ Vol. 5, K.B. Lipkowitz and D.B. Boyd, eds. (VCH, New York) 1994, the authors give the following figures. For eight small molecules for which experimental harmonic vibrational frequencies are known, here are the average percent errors for various methods using a DZP basis: SCF 8.7 CISD 3.7 MBPT(2) (also known as MP2) 3.2 SDQ-MBPT(4) 2.5 CCSD 2.2 MBPT(4) 3.1 CCSD(T) 2.4 By the time we get to CCSD(T), the basis set error is probably larger than the method error. No MCSCF values were given, so it is not possible to directly compare the quality of MP2 and MCSCF frequencies. However, it is clear that the quality of MP2 frequencies does not come from a cancellation of method and anharmonicity errors. Steve Steven Gwaltney gwaltney@qtp.ufl.edu Quantum Theory Project University of Florida >From owner-chemistry@ccl.net Sat Jul 13 05:29 EDT 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.5/950822.1) id FAA22413; Sat, 13 Jul 1996 05:29:10 -0400 (EDT) Received: from po8.andrew.cmu.edu for ar1z+@andrew.cmu.edu by bedrock.ccl.net (8.7.5/950822.1) id FAA23424; Sat, 13 Jul 1996 05:29:10 -0400 (EDT) Received: (from postman@localhost) by po8.andrew.cmu.edu (8.7.5/8.7.3) id FAA17792; Sat, 13 Jul 1996 05:29:01 -0400 Received: via switchmail; Sat, 13 Jul 1996 05:29:00 -0400 (EDT) Received: from po6.andrew.cmu.edu via qmail ID ; Sat, 13 Jul 1996 05:28:17 -0400 (EDT) Received: from unix14.andrew.cmu.edu via qmail ID ; Fri, 12 Jul 1996 13:45:46 -0400 (EDT) Received: from mms.4.60.Jun.27.1996.03.02.53.sun4.51.EzMail.2.0.CUILIB.3.45.SNAP.NOT.LINKED.unix14.andrew.cmu.edu.sun4m.54 via MS.5.6.unix14.andrew.cmu.edu.sun4_51; Fri, 12 Jul 1996 13:45:46 -0400 (EDT) Message-ID: <8ltcx_K00YUq0EM1E0@andrew.cmu.edu> Date: Fri, 12 Jul 1996 13:45:46 -0400 (EDT) From: Alexander J Ropelewski To: chemistry@www.ccl.net Subject: CCL:biomedical workshop announcement BIOMEDICAL WORKSHOPS PITTSBURGH SUPERCOMPUTING CENTER August 25-28, 1996 The Pittsburgh Supercomputing Center is offering an "ADVANCED NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS" workshop. The workshop is open to researchers who have previously attended one of the PSC's annual "Nucleic Acid and Protein Sequence Analysis" workshops or who have previous experience with computerized sequence analysis. The workshop will build on previous experience to teach techniques for what is commonly referred to as "homology modeling", specifically the methods known as threading techniques. This involves fitting the sequences of proteins whose structure is not known to the known three-dimensional structure of another protein. The workshop will feature the threading techniques developed by Dr. Stephen H. Bryant of the Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine. Dr. Bryant's work focuses on empirical energy functions that measure the complementarity of sequence and folding motif and on algorithms for rapid threading. His group is also developing computer programs for automatically creating homology models derived from core structural motifs identified by other sequence analysis techniques. Instructors are: Dr. Stephen H. Bryant, National Center for Biotechnology Information, National Library of Medicine Dr. Michael Gribskov, San Diego Supercomputer Center and Dr. Hugh B. Nicholas Jr., Pittsburgh Supercomputing Center. APPLICATION DEADLINE: July 17, 1996. For additional information, please refer to http://www.psc.edu/biomed/workshops.html CONTACT INFORMATION: Nancy Blankenstein, Biomedical Program Assistant, (412)268-4960, blankens@psc.edu ********** PITTSBURGH SUPERCOMPUTING CENTER ADVANCED SEQUENCE ANALYSIS WORKSHOP APPLICATION Name: ________________________________________________________________ Affiliation: ________________________________________________________________ Address: ________________________________________________________________ (Business) ________________________________________________________________ ________________________________________________________________ (Home) ________________________________________________________________ Telephone: ____________________________ ______________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:___________________ Electronic Mail Address:_______________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) Please indicate specifically any special housing, transportation or dietary arrangements you will need: __________________________________________ How did you learn about this workshop:_________________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, the sequence analysis problems encountered in your research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vitae. Graduate students must have a letter of recommendation from a faculty member. Please return all application materials to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue, Suite 230C Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, blankens@psc.edu or 412/268-4960. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. >From milet@quantix.u-strasbg.fr Thu Jul 11 06:30 EDT 1996 Received: from quantix.u-strasbg.fr for milet@quantix.u-strasbg.fr by www.ccl.net (8.7.5/950822.1) id GAA08404; Thu, 11 Jul 1996 06:30:16 -0400 (EDT) Received: by quantix.u-strasbg.fr (AIX 3.2/UCB 5.64/4.03) id AA38252; Thu, 11 Jul 1996 12:30:28 +0200 From: Date: Thu, 11 Jul 1996 12:30:28 +0200 Message-Id: <9607111030.AA38252@quantix.u-strasbg.fr> To: chemistry@www.ccl.net Subject: CCL: random stops in G94 Content-Type: text Content-Length: 1042 Status: RO Dear All, We have a strange and random problem : we are running Gaussian 94 on a IBM 43P (Power PC) under AIX4.1.4 with 128 Meg of memory and 284 Meg of pagingspace. Gaussian 94 was compiled with IBM Fortran 3.2. We run Gaussian with : nohup 'script-in-csh' and it stops mysteriously with no error message (nor in the output file nor in the errlog), no core dump...just stops (the scratch files are not removed by Gaussian). Sometimes after a re-start of the script it goes to the end and sometimes it stops again after one or more optimisation steps. It happens after writing the energy on the output file. There is enough temporary scratch space available. Does anyone have had the same problem ? or have an idea what it could be and/or what to do ? Thanks in advance Anne Milet =========================================================== Anne Milet Laboratoire de Chimie quantique UPR 139 4, rue Blaise Pascal 67000 Strasbourg e-mail : milet@quantix.u-strasbg.fr =========================================================== >From csilmt12@area.BA.CNR.IT Wed Jul 10 05:40 EDT 1996 Received: from icnucevx.cnuce.cnr.it for csilmt12@area.BA.CNR.IT by www.ccl.net (8.7.5/950822.1) id FAA00975; Wed, 10 Jul 1996 05:40:07 -0400 (EDT) Received: from area.ba.cnr.it by mailsrv.cnuce.cnr.it (PMDF V5.0-6 #9955) id <01I6WN70C15CAC2VQH@mailsrv.cnuce.cnr.it> for CHEMISTRY@www.ccl.net; Wed, 10 Jul 1996 11:38:58 +0100 (MET) Received: by area.ba.cnr.it; (5.65/1.1.8.2/27Mar96-1138AM) id AA25733; Wed, 10 Jul 1996 11:38:52 +0200 Date: Wed, 10 Jul 1996 11:38:52 +0200 (MET DST) From: Massimo Trotta Subject: basic fluorescence information To: CHEMISTRY@www.ccl.net Message-id: <9607100938.AA25733@area.ba.cnr.it> MIME-version: 1.0 X-Mailer: ELM [version 2.4 PL24 PGP3 *ALPHA*] Content-transfer-encoding: 7bit Content-Type: text/plain; charset=US-ASCII Content-Length: 929 Status: RO Dear All, this is probably not exactly a question for a computational chemistry list, but it is possible that some of you have experience in basic fluorescence spectroscopy: I am looking for literature or any suggestion regarding the fluorescenze of substituted benzoquinones: Should they fluoresce or not? Also indication on Electronic Lists on fluorescence related topics. thank you in advances massimo trotta -- !==============================================================! ! Massimo Trotta ! ! Centro Studi Chimico Fisici sull'Interazione Luce Materia ! ! c/o Dept. of Chemistry ! ! V. Orabona, 4 I-70126 Italy ! ! e-mail: csilmt12@area.ba.cnr.it ! ! http://www.ba.cnr.it/~csilmt12 !==============================================================! >From ipcakc@Postoffice.ncst.ernet.in Mon Jul 15 23:44 EDT 1996 Received: from sangam.ncst.ernet.in for ipcakc@Postoffice.ncst.ernet.in by www.ccl.net (8.7.5/950822.1) id XAA07479; Mon, 15 Jul 1996 23:44:20 -0400 (EDT) Received: from postoffice.iisc.ernet.in (twisha.ece.iisc.ernet.in [144.16.64.4]) by sangam.ncst.ernet.in (8.6.12/8.6.6) with ESMTP id JAA19048 for ; Tue, 16 Jul 1996 09:13:10 +0530 Received: by postoffice.iisc.ernet.in (SMI-8.6/SMI-SVR4) id JAA08392; Tue, 16 Jul 1996 09:00:03 -0500 Date: Tue, 16 Jul 1996 09:00:03 -0500 From: ipcakc@Postoffice.ncst.ernet.in (Dr.A.K.Chandra) Message-Id: <199607161400.JAA08392@postoffice.iisc.ernet.in> To: CHEMISTRY@www.ccl.net Subject: Norrish Content-Type: text Content-Length: 511 Status: RO Dear netters, Does anybody have an idea of NORRISH TYPE II (Intramolecular gamma-Hydrogen abstraction processes) in ORGANO-THIO (C=S) compounds in ground or excited states? If so, please send me a reference/s. Thanks in advance, V.SREEDHARA RAO **************************************** V. SREEDHARA RAO Department of Inorganic and Physical Chemistry Indian Institute of Science (I.I.Sc) BANGALORE - 560 012. India. E-mail : ipcakc@postoffice.iisc.ernet.in (or) akc@hamsadvani.serc.iisc.ernet.in >From rino@ibc.wustl.edu Wed Jul 10 10:26 EDT 1996 Received: from wugate.wustl.edu for rino@ibc.wustl.edu by www.ccl.net (8.7.5/950822.1) id KAA02918; Wed, 10 Jul 1996 10:26:39 -0400 (EDT) Received: from ibc.wustl.edu by wugate.wustl.edu (8.7.5/8.6.11) with SMTP id JAA15455 for ; Wed, 10 Jul 1996 09:26:41 -0500 Received: by ibc.wustl.edu (SMI-8.6/SMI-SVR4) id JAA25619; Wed, 10 Jul 1996 09:26:36 -0500 Date: Wed, 10 Jul 1996 09:26:36 -0500 (CDT) From: Rino Ragno To: chemistry@www.ccl.net Subject: Conf. space & RBs Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 1326 Status: RO Dear Netters, any of you out there knows if there is any program/routine that is able to compute both the number of rotatable bonds and the number of geometrically possible number of conformers of a given molecules? Thank in advance to every one is going to answer. Rino Ragno ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ || || || Dr. Rino Ragno E-mail: rino@wucmd.wustl.edu || || Institute for Biomedical Computing or: rino@ibc.wustl.edu || || Center for Molecular Design Phone : 314-362-2273 || || Box 8036, Washington University FAX : 314-362-0234 || || 700 South Euclid Avenue || || St. Louis, Missouri 63110 || || U. S. A. || || || ++---------------------------------------------------------------------------++ ++---------------------------------------------------------------------------++ >From kallies@serv.chem.uni-potsdam.de Thu Jul 4 14:15 EDT 1996 Received: from mail-buffer.sbu.ac.uk for kallies@serv.chem.uni-potsdam.de by www.ccl.net (8.7.5/950822.1) id OAA13950; Thu, 4 Jul 1996 14:15:38 -0400 (EDT) Received: from psb.sbu.ac.uk (psb.sbu.ac.uk [136.148.1.5]) by mail-buffer.sbu.ac.uk (8.7.4/8.7.3) with SMTP id TAA14255; Thu, 4 Jul 1996 19:08:41 +0100 (BST) Received: by vax.sbu.ac.uk (MX V4.2 VAX) with SITE; Thu, 04 Jul 1996 19:15:26 BST Received: from www.ccl.net by psb.sbu.ac.uk (MX V4.2 VAX) with SMTP; Tue, 28 May 1996 12:09:31 BST Received: for chemistry-request@www.ccl.net by www.ccl.net (8.7.5/950822.1) id GAA15261; Tue, 28 May 1996 06:47:50 -0400 (EDT) Received: from hp.rz.uni-potsdam.de for kallies@serv.chem.uni-potsdam.de by www.ccl.net (8.7.5/950822.1) id GAA15248; Tue, 28 May 1996 06:47:11 -0400 (EDT) Received: from serv.chem.uni-potsdam.de by hp.rz.uni-potsdam.de with SMTP (1.37.109.10G/16.2) id AA147940342; Tue, 28 May 1996 09:59:02 +0200 Received: from pch10.chem.uni-potsdam.de by serv.chem.uni-potsdam.de (AIX 3.2/UCB 5.64/4.03) id AA19368; Tue, 28 May 1996 10:00:24 +0100 Date: Tue, 28 May 1996 10:00:24 +0100 Message-ID: <9605280900.AA19368@serv.chem.uni-potsdam.de> To: csilmt12@area.ba.cnr.it From: "B. Kallies" Subject: CCL:autoprotolysis constant of alcohols CC: chemistry@www.ccl.net Content-Type: text Content-Length: 1381 Status: RO Dear Dr. Trotta, Christian Reichardt collected some pK(auto) for amphiprotic solvents in "Solvents and Solvent Effects in Organic Chemistry" 2nd. ed., VCH 1990, p. 431 ff. There will be found for 2 ROH =3D R(OH)2(+) + RO(-) Solvent R pK(auto) at 25=B0C ----------------------------------------- Methanol CH3 17.20 Ethanol C2H5 18.88 1-Propanol C3H7 19.43 1-Butanol C4H9 21.56 1-Pentanol C5H11 20.65 and some others. Original references and some other original literature citations are given, too. Yours sincerely B. Kallies --------------------------------------------------- DC Bernd Kallies Institut fuer Physikalische und Theoretische Chemie Universitaet Potsdam Am Neuen Palais 10 14469 Potsdam GERMANY e-mail: kallies@serv.chem.uni-potsdam.de Fax: ++49 / 0331 977 1315 --------------------------------------------------- -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: kallies@serv.chem.uni-potsdam.de -- Original Sender From: Address: kallies@serv.chem.uni-potsdam.de CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html From MCDI3CMW@fs1.ch.umist.ac.uk Thu Jul 18 05:14:53 1996 Received: from ursa.cns.umist.ac.uk for MCDI3CMW@fs1.ch.umist.ac.uk by www.ccl.net (8.7.5/950822.1) id EAA23448; Thu, 18 Jul 1996 04:52:22 -0400 (EDT) Received: from fs1.ch.umist.ac.uk by ursa.cns.umist.ac.uk with SMTP (PP); Thu, 18 Jul 1996 09:51:34 +0100 Received: from UK-AC-UMIST-CH-FS1/SpoolDir by fs1.ch.umist.ac.uk (Mercury 1.21); 18 Jul 96 09:51:34 BST Received: from SpoolDir by UK-AC-UMIST-CH-FS1 (Mercury 1.21); 18 Jul 96 09:51:02 BST From: "C.M.Windsor" Organization: UMIST To: CHEMISTRY@www.ccl.net Date: Thu, 18 Jul 1996 09:51:01 BST Subject: OPT=TS....FREQ....IRC Return-receipt-to: "C.M.Windsor" Priority: normal X-mailer: Pegasus Mail v3.31 Message-ID: <1D8DC342F4A@fs1.ch.umist.ac.uk> I am reposting this due to an error sending a previous version (sorry for wasted bandwith) I am using G94 to perform TS calculations using the methods employed by Kendall Houk et al (Modelling of Diels-Alder TS) where by LST was used for the initial guess, OPT=TS for the optimisation to TS, FREQ to confirm it is a real TS and then an IRQ search around the reaction trajectory. I would like to know the purpose of the FREQ calculation other than to calculate the ZPE and check for presence of single -ve eigenvalue (already shown in OPT=TS calculation). Am I missing something that I should be checking? Thanks in advance. Carl -------------------------------------------------------------- Brought to you by the letters Q & S and the number 7 -------------------------------------------------------------- From Carl Mark Windsor University of Manchester Institute of Science and Technology. (U.M.I.S.T.) Chemistry Department. -------------------------------------------------------------- From D.van.der.Spoel@chem.rug.nl Thu Jul 18 06:14:55 1996 Received: from mailhost.rug.nl for D.van.der.Spoel@chem.rug.nl by www.ccl.net (8.7.5/950822.1) id FAA23630; Thu, 18 Jul 1996 05:36:46 -0400 (EDT) Received: from rugch4.chem.rug.nl by mailhost.rug.nl with SMTP (PP); Thu, 18 Jul 1996 11:36:29 +0200 Received: from rugmd0.chem.rug.nl by rugch4.chem.rug.nl (LAA10418); Thu, 18 Jul 1996 11:36:23 +0200 Received: from rugmd17.chem.rug.nl by rugmd0.chem.rug.nl (5.x/SMI-SVR4) id AA22078; Thu, 18 Jul 1996 11:36:21 +0200 Received: by rugmd17.chem.rug.nl (5.x/SMI-SVR4) id AA19562; Thu, 18 Jul 1996 11:36:20 +0200 From: D.van.der.Spoel@chem.rug.nl (David van der Spoel) Message-Id: <9607180936.AA19562@rugmd17.chem.rug.nl> Subject: Diffusion of Phosphate in Water To: chemistry@www.ccl.net Date: Thu, 18 Jul 1996 11:36:19 +0200 (MET DST) Reply-To: D.van.der.Spoel@chem.rug.nl X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi. Does anyone know where I can find diffusion constants for phosphate ions in water ? I've calculated them using the Einstein relation from MD simulations, and found 0.7 * 10e-5 cm^2/s, which seems to be reasonable, but I would like to see experimental numbers. David van der Spoel --------------------------------------------------------- EMAIL: spoel@chem.rug.nl WWW: http://rugmd0.chem.rug.nl/~spoel PHONE: 31-50-3634327 FAX: 31-50-3634800 MAIL: Nijenborgh 4, 9747 AG Groningen, The Netherlands. --------------------------------------------------------- From peter@indi.biochem.dote.hu Thu Jul 18 06:19:44 1996 Received: from indi.biochem.dote.hu for peter@indi.biochem.dote.hu by www.ccl.net (8.7.5/950822.1) id FAA23653; Thu, 18 Jul 1996 05:52:52 -0400 (EDT) Received: by indi.biochem.dote.hu (920330.SGI/920502.SGI.AUTO) for chemistry@www.ccl.net id AA25683; Thu, 18 Jul 96 11:52:40 +0200 Date: Thu, 18 Jul 1996 11:52:30 +0200 (MDT) From: Peter Bagossi Subject: UFF To: chemistry@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I'm looking for any information about the Universal Force Field (UFF). I have the original paper (JACS,1992,114,10024-10035) and the two accompanied papers (JACS,1992,114,10035-10046; JACS,1992,114,10046-10053), but I cannot find any recent application in our limited searching possibilities. Any information or reprint are greatly appreciated. Thanks, Peter ************************************************************* * Peter Bagossi * * Department of Biochemistry, University Medical School * * Debrecen, Nagyerdei krt. 98., P.O.Box 6., H-4012, HUNGARY * * Phone and Fax: (36-52) 416-432 * ************************************************************* From uscqorrv@cesga.es Thu Jul 18 11:14:54 1996 Received: from ds for uscqorrv@cesga.es by www.ccl.net (8.7.5/950822.1) id KAA25254; Thu, 18 Jul 1996 10:43:17 -0400 (EDT) Received: by ds (4.1/1.34) id AA16604; Thu, 18 Jul 96 16:43:01 +0200 Date: Thu, 18 Jul 1996 16:43:00 +0200 (MET DST) From: Latypov Shamil To: "Chemistry, List Computational" Subject: Discovery, cff91 and pcff91 comparison Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, We carried out conformational analysis of Aryl-MAA esters of variety of prime alcohols (ca. 20) by DNMR and theory (AM1 and MM). In MM calculations different force fields were used to consider scopes and limitations of these ff to describe conformational preference of these esters. I found that cff91 and pcff91 gives essentially same prediction for most of the compounds but in several cases remarkable different results were obtained (esters of alpha-amino alcoholes). In manual there is nothing about pcff91. So, the question is What is the difference between cff91 and pcff91 and if there are some references dealing with pcff91. Thank you, Sincerely yours, Shamil Latypov, ******************************************************************************** Temporal * Permanent uscqorrv@ds.cesga.es (to contact) * lshamil@glass.ksu.ras.ru qoshamil@correo.usc.es * slatypov@ksu.ru ******************************************************************************** Depart. of Organic Chemistry, * Institute of Organic&Physical Chemistry, Chemical Faculty, University of * Russian Academy of Sciences, 420083, Santiago de Compostela, 15706, * Kazan, Tatarstan, Russian Federation Spain, Fax: 34-81-595012 * ******************************************************************************** From pcm@usmps550.psrc.usm.edu Thu Jul 18 13:14:56 1996 Received: from usmps550.psrc.usm.edu for pcm@usmps550.psrc.usm.edu by www.ccl.net (8.7.5/950822.1) id MAA26179; Thu, 18 Jul 1996 12:41:10 -0400 (EDT) Received: by usmps550.psrc.usm.edu (AIX 4.1/UCB 5.64/4.03) id AA14160; Thu, 18 Jul 1996 11:38:37 -0500 From: pcm@usmps550.psrc.usm.edu (Phillipe Camelio) Message-Id: <9607181638.AA14160@usmps550.psrc.usm.edu> Subject: Re: CCL pcff91, cff91 ... To: CHEMISTRY@www.ccl.net Date: Thu, 18 Jul 1996 11:38:37 +22324924 (CDT) X-Mailer: ELM [version 2.4 PL5] Content-Type: text Hey, PCFF91 is an extension of CFF91, ie it is normal that you find the same results using both :) The only reference I have for PCFF is the Biosym manual itself :( but I have some references on CFF91/93. @String{jcc = "J. Comp. Chem."} @String{macro = "Macromolecules"} @String{jacs = "J. Am. Chem. Soc."} @String{jpc = "J. Phys. Chem."} @article{PCFF1, author = {J.A. Maple and M.J. Hwang and T.P. Stockfisch and U. Dinur and M . Waldman C.S. Ewig and A.T. Hagler}, journal = jcc, year = {1994}, volume = {15}, pages = {162} } @article{PCFF2, author = {M.J. Hwang and T.P. Stockfisch and A.T. Hagler}, title = {Derivation of Class II Force Fields. 2. Derivation and Character ization of a Class II Force Field, CFF93, for the Alkyl Functional Group and Alkane Molecules}, journal = jacs, year = {1994}, volume = {116}, pages = {2515--2525}, annote = {Classeur A, Champ de Force} } @article{PCFF3, author = {H. Sun and S.J. Mumby and J.R. Maple and A.T. Hagler}, title = {An ab Initio CFF93 All-Atom force Field for Polycarbonates}, journal = jacs, year = {1994}, volume = {116}, pages = {2978--2987}, annote = {Classeur A, Champ de Force} } @article{PCFF4, author = {H. Sun}, journal = jcc, year = {1994}, volume = {15}, pages = {7} } @article{PCFF5, author = {H. Sun}, journal = macro, year = {1995}, volume = {28}, pages = {701} } @article{PCFF6, author = {J.-R. Hill and J. Sauer}, title = {Molecular Mechanics Potential for Silica and Zeolite Catalysts Based on ab Initio Calculations. 1. Dense and Microporous Silica}, journal = jpc, year = {1994}, volume = {98}, pages = {1238}, annote = {Classeur B, Champ de Force} } I hope this will be helpful, Cordially Philippe Camelio Lab. de Stereochimie, Marseille, France E-mail: sophie@ms5342u02.u-3mrs.fr WWW: http://www.u-3mrs.fr/people/PCamelio From sals@midway.uchicago.edu Thu Jul 18 15:14:56 1996 Received: from haven.uchicago.edu for sals@midway.uchicago.edu by www.ccl.net (8.7.5/950822.1) id OAA26976; Thu, 18 Jul 1996 14:29:13 -0400 (EDT) Received: from kimbark.uchicago.edu (sals@kimbark.uchicago.edu [128.135.12.52]) by haven.uchicago.edu (8.7.5/8.7.3) with ESMTP id NAA19786 for ; Thu, 18 Jul 1996 13:28:12 -0500 (CDT) Received: (from sals@localhost) by kimbark.uchicago.edu (8.7.1/8.7.2) id NAA18767 for chemistry@www.ccl.net; Thu, 18 Jul 1996 13:28:11 -0500 (CDT) Date: Thu, 18 Jul 96 13:28:11 CDT From: Fred Salsbury To: chemistry@www.ccl.net Subject: Rare gas densities Message-ID: Hello, I'm doing work with Robert Harris at UC Berkeley on developing new methods of calculating chemical shifts and magnetic suscetibilties from ground state electron densities. Right now I'm trying to test some functionals on the noble gases, so what I'm looking for are analytic fits to the Hartree-Fock electron densities of Ar, Ne, Kr, and Xe. I'm sure someone must have done this sort of calculation already, but I haven't found any references. So if anyone knows of any references to such calculations could you email me. thanks Fred Salsbury sals@dirac.cchem.berkeley.edu