From LKHUNDKR@neu.edu Wed Nov 29 10:39:01 1995 Received: from nuhub.dac.neu.edu for LKHUNDKR@neu.edu by www.ccl.net (8.6.10/950822.1) id KAA11128; Wed, 29 Nov 1995 10:26:29 -0500 From: Received: from neu.edu by neu.edu (PMDF V4.3-7 #11963) id <01HY7ND5JLBO9C4RV6@neu.edu>; Wed, 29 Nov 1995 10:29:26 EST Date: Wed, 29 Nov 1995 10:29:26 -0500 (EST) Subject: New Keywords in MOPAC 7 To: chemistry@www.ccl.net Message-id: <01HY7ND5JLBQ9C4RV6@neu.edu> X-Envelope-to: chemistry@www.ccl.net X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Dear CCLers: I recently downloaded MOPAC 7 (DOS version) from the CCL archives. I would appreciate any suggestions for pointers to locations where I might find information about Keywords that have been added to MOPAC 7 (relative to MOPAC 6) Thanks Lutfur Khundkar Northeastern University From uli@smaug.physics.mun.ca Wed Nov 29 10:54:05 1995 Received: from smaug.physics.mun.ca for uli@smaug.physics.mun.ca by www.ccl.net (8.6.10/950822.1) id KAA11508; Wed, 29 Nov 1995 10:51:52 -0500 Received: by smaug.physics.mun.ca (940816.SGI.8.6.9/911001.SGI) id MAA09542; Wed, 29 Nov 1995 12:21:26 -0330 Date: Wed, 29 Nov 1995 12:13:45 -0330 (NST) From: Uli Salzner Subject: summary spurious intergrated densities To: ccl Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII any thnaks to everyone who replied. Your comments helped al lot. Here is a summary of the answers I received: Hi there, I have encountered the same problem a few times, and what you have to do is to alter the grid over which the integrals are calculated. Refer to pages 6 and 9 of the "New Methods and Features in Gaussian 92/DFT" Release Notes for a complete description. Basically one way to correct this is to compute the integrals using a finer grid. Thiscan most easily be accomplished by using the Int=FineGrid keyword. (gives about 7000-9000 points per atom compared with the default of about 3000 points per atom with Int=Normalgrid). If this fails you can define a numnber of even finer grids by following the Grid Control Appendix in the Releas Notes on pg 9. Stephen Decker decker@jcvsparc.chem.ualberta.ca Dept. of Chemistry, Univ. of Alberta, Canada You need to upgrade to G94...these problems have been fixed...of get G92 Rev Level F. Regards.. John -- John M. McKelvey email: mckelvey@Kodak.COM Computational Science Laboratory phone: (716) 477-3335 2nd Floor, Bldg 83, RL Eastman Kodak Company Rochester, NY 14650-2216 bernhard@quant1.chemie.uni-leipzig.de Subject: Re:DFT/spurious integrated densities Hi, few weeks ago i struggle over the same problem. I got the tip to add the keywords SCF=NoVarACC INT=FineGrid which work in ca. 90% of all cases (using B3LYP). The first is not fully known to me (didn't find the keyword in the g92 manual), but i think it enhance the accuracy of the integrals or is related to this point, the second point results in better numerics while integration. Don't take it for good, i'm just a starter... If this doesn't work, then a slight alteration of the geometry helps sometime (nearly in all remaining cases). Bernhard Eck Dr. Salzner, We have seen this problem with G92 and have made a couple of changes which you can use with G92 that improve the situation dramatically. Add the following Int=FINEGRID to your calculations. This may be sufficient as it improves the integration accuracy. If not also add SCF=NOVARACC which turns off using loose integration cutoffs on early SCF iterations. Both of these will increase computation time but have proven successful enough that INT=FINEGRID is standard in G94. We have modified the cutoffs for early iterations and seldom see this problem with G94. Douglas J. Fox Director of Technical Support help@gaussian.com From mmconn@silibone.cchem.berkeley.edu Wed Nov 29 13:39:04 1995 Received: from hydrogen.CChem.Berkeley.EDU for mmconn@silibone.cchem.berkeley.edu by www.ccl.net (8.6.10/950822.1) id NAA15973; Wed, 29 Nov 1995 13:32:52 -0500 Received: from silibone.cchem.berkeley.edu by hydrogen.CChem.Berkeley.EDU (8.6.10/1.41) id KAA12174; Wed, 29 Nov 1995 10:32:52 -0800 Received: by silibone.cchem.berkeley.edu (920330.SGI/920502.SGI.AUTO) for @hydrogen.cchem.berkeley.edu:chemistry@www.ccl.net id AA15628; Wed, 29 Nov 95 10:29:12 -0800 Date: Wed, 29 Nov 95 10:29:12 -0800 From: mmconn@silibone.cchem.berkeley.edu (morgan conn) Message-Id: <9511291829.AA15628@silibone.cchem.berkeley.edu> To: chemistry@www.ccl.net Subject: binding pocket? Hello all; I'm looking for the impossible. If I have an inhibitor and a protein that are known to associate, and a set of mutations that appear to reduce the in vivo effects of this small molecule, is there a way to (reasonably) find a binding pocket for this molecule on the protein surface? The normal substrate for the molecule shows little, if any, structural similarity to the inhibitor, so the the substrate pocket would _not_ seem to be the binding site. Does anyone have experience/knowledge of this sort of thing. -morgan ******************************************************************** Dr. M. Morgan Conn Department of Chemistry (Schultz group), UC Berkeley mmconn@silibone.cchem.berkeley.edu 510.642.9249; 510.643.6890 (fax) ******************************************************************** From owner-chemistry@ccl.net Wed Nov 29 14:54:05 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id OAA17605; Wed, 29 Nov 1995 14:43:43 -0500 Received: from osf1.gmu.edu for eslone@osf1.gmu.edu by bedrock.ccl.net (8.7.1/950822.1) id OAA23031; Wed, 29 Nov 1995 14:43:40 -0500 (EST) Received: by osf1.gmu.edu; (5.65v3.2/1.1.8.2/07Sep94-1001AM/GMUv3) id AA23355; Wed, 29 Nov 1995 14:43:40 -0500 Date: Wed, 29 Nov 1995 14:43:40 -0500 (EST) From: Eric Slone To: CHEMCONF@UMDD.UMD.EDU, chemistry@ccl.net, CHEMED-L%UWF.BITNET@uga.cc.uga.edu Subject: ACD Labs Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII After noting a number of postings and messages regarding this company and their software in these forums, I have decided to post this "warning" regarding this company and their software. We acted as a beta site for the ACD Labs software, and through the representative we dealt with, met all of the requirements they set. We had even demonstrated the software for a number of people for them on one occassion and distributed their literature at a conference. We began having problems reinstalling our copy of the software after replacing a hard disk on one of our computers. Several calls to ACD revealed that this was something of a known issue and that they didn't know why it happened. We were told that a new set of disks would be sent out immediately (by the president of ACD). We never got the disks. After a month of waiting, we called and were told we wouldn't be getting any new disks. In fact, we were told we were such a non-compliant beta site that we wouldn't be getting any support at all. The person we had originally dealt with had left the company, and the new person apparently had a different way of doing things. Requests to speak with someone higher in the company were denied, correspondence went unanswered. Finally we reached someone else in the company who, after some investigation, echoed the earlier response. Our earlier efforts and assistance apparently meant nothing to ACD. I felt it my obligation to members of this list to make this information known. I have never said anything against any software company before, nor have I experienced any problems like this; and I beta test a lot of software. Considerable effort and time was invested with ACD Labs on our part and yet all we got from them was buggy, non-functional software and non-responsiveness. To date this issue has not been resolved. I would only caution you to beware and be careful. Eric ________________________________________________________________________________ J. Eric Slone Internet: eslone@gmu.edu Compuserve: 73757,2776 "True science teaches, above all, to Fax: (703) 751-6639 doubt, and to be ignorant." Pager: (202) 597-2373 Miguel de Unamuno Voice: (703) 461-7078 ________________________________________________________________________________ From deko@calvin.edu Wed Nov 29 15:24:05 1995 Received: from ursa.calvin.edu for deko@calvin.edu by www.ccl.net (8.6.10/950822.1) id PAA18806; Wed, 29 Nov 1995 15:19:52 -0500 Received: from [153.106.13.206] (mcdeko.calvin.edu [153.106.13.206]) by ursa.calvin.edu (8.6.12/8.6.12) with SMTP id PAA19346 for ; Wed, 29 Nov 1995 15:19:46 -0500 Message-Id: <199511292019.PAA19346@ursa.calvin.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 29 Nov 1995 15:21:04 -0500 To: CHEMISTRY@www.ccl.net From: deko@calvin.edu (Roger L. DeKock) Subject: Dreyfus Fellow teaching postdoc position POSITION ANNOUNCEMENT Camille and Henry Dreyfus Postdoctoral Fellowship, Calvin College. The Department of Chemistry seeks applications from recent Ph.D. recipients to fill a Dreyfus Fellow position for 9/1/96 to 8/30/98. We seek candidates who are committed to a career in undergraduate teaching and research. The successful candidate will teach in general chemistry and physical/computational chemistry and work with the Dreyfus Scholar (Roger L. DeKock) on research projects involving computational chemistry. Preference will be given to those with a Ph.D. in inorganic or physical/computational chemistry. Calvin College is a Christian liberal arts college in the Reformed tradition. Teaching effectiveness, a strong interest or training in computational chemistry, and a religious commitment compatible with the mission of a Christian liberal arts institution are essential. Submit transcripts, C.V., three letters of reference, and a 2-3 page research plan. At least one letter of reference should address the candidate's (potential) teaching abilities, and one his/her research abilities. The search committee will begin its work during the first week of January, 1996 and proceed until the position is filled. Initial E-mail enquiries are welcome to deko@calvin.edu. Address: Search Committee, Department of Chemistry, Calvin College, 3201 Burton St. S.E., Grand Rapids, MI 49546-4388 USA. Calvin College is an EO/AA employer and encourages applications from under-represented minorities and women. ------------------------------------------------ Roger L. DeKock, Professor Department of Chemistry Calvin College 3201 Burton St. S.E. Grand Rapids, Michigan 49546-4388 USA Phone: (616) 957-6344 Fax: (616) 957-6501 E-mail: DEKO@CALVIN.EDU http://www.calvin.edu/~deko From hou@agouron.com Wed Nov 29 16:39:09 1995 Received: from agouron.com for hou@agouron.com by www.ccl.net (8.6.10/950822.1) id QAA19906; Wed, 29 Nov 1995 16:29:12 -0500 Received: from horton by agouron.com via ESMTP (950911.SGI.8.6.12.PATCH825/930901.SGI) id NAA12850; Wed, 29 Nov 1995 13:32:51 -0800 Received: by horton (950215.SGI.8.6.10/940406.SGI) id NAA15467; Wed, 29 Nov 1995 13:29:21 -0800 Date: Wed, 29 Nov 1995 13:29:21 -0800 From: hou@agouron.com (Xinjun Hou) Message-Id: <199511292129.NAA15467@horton> To: mmconn@silibone.cchem.berkeley.edu (morgan conn) Subject: Re: CCL:binding pocket? Cc: CHEMISTRY@www.ccl.net >If I have an inhibitor and a protein that are known to associate, and a set >of mutations that appear to reduce the in vivo effects of this small molecule, >is there a way to (reasonably) find a binding pocket for this molecule on the >protein surface? The normal substrate for the molecule shows little, if any, >structural similarity to the inhibitor, so the the substrate pocket would >_not_ seem to be the binding site. > >Does anyone have experience/knowledge of this sort of thing. Try DOCK. You can get more information on DOCK from http://cornelius.ucsf.edu/kuntz/dock.html C Xinjun J. Hou (hou@agouron.com) Agouron Pharmaceuticals, Inc. C10110000110100101101110011010100111010101101110010010000110111101110101 From huang@mazda.wavefun.com Wed Nov 29 19:09:08 1995 Received: from volvo.wavefun.com for huang@mazda.wavefun.com by www.ccl.net (8.6.10/950822.1) id SAA22831; Wed, 29 Nov 1995 18:59:38 -0500 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA22356; Wed, 29 Nov 95 15:43:00 -0800 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma022352; Wed Nov 29 15:42:35 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@www.ccl.net id AA21934; Wed, 29 Nov 95 15:42:01 -0800 From: "Wayne Huang" Message-Id: <9511291542.ZM21932@mazda.wavefun.com> Date: Wed, 29 Nov 1995 15:42:00 -0800 Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: sparlist@wavefun.com, chemistry@www.ccl.net Subject: Spring-96 Computational Chemistry Workshops Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Dear Colleagues, As we are entering the 4th year of offering Computational Chemistry Workshops to the chemical community, we would like to express our gratitude to the people who have supported and participated these workshops the past three years. We will continue to maintain and improve the quality of these short courses and provide practical instruction and hands-on experience to chemists at all levels. The next year workshops have been scheduled (see below). For more information, please contact me at workshop@wavefun.com or check out our workshop web page at http://www.wavefun.com/workshop.html. Happy Computing, Wayne Huang Attachment is the information on the workshop and course materials. The complete brochure can be sent via fax/mail upon request. ====================================================================== ------------------------------------ | COMPUTATIONAL CHEMISTRY WORKSHOP | ------------------------------------ Intensive 3-day workshops focus on application of modern electronic structure methods to chemistry. Lectures will describe underlying theory, assess performance of modern electronic structure methods, outline practical strategies for doing calculations, and illustrate results of applications to diverse chemical problems. Laboratories provide hands-on experience using a wide selection experiments, as well as ample time to explore your own chemistry. Visualization and animation will also be presented for both educational demonstration and research presentation. Here are the summary of workshop information: _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ _/ _/ _/ COMPUTATIONAL CHEMSITRY WORKSHOPS _/ _/ _/ _/ Format: 3-day intensive workshop on electronic structure _/ _/ methods and applications, and hands-on molecular _/ _/ modeling laboratory on individual workstations. _/ _/ It will provide: _/ _/ _/ _/ o Concise summary of modern electronic structure _/ _/ methods _/ _/ o Assessment of range and performance of their _/ _/ applications _/ _/ o Hands-on experience in molecular modeling _/ _/ o Graphical Analysis of results _/ _/ o Visualization and animation of structures and _/ _/ reactions _/ _/ _/ _/ Schedule: January Workshop: Jan., 10-12, 1996 _/ _/ March Workshop: March, 6-8, 1996 _/ _/ June Workshop: June, 12-14, 1996 _/ _/ _/ _/ Instructors: Lecture Section - Dr. Warren Hehre _/ _/ Lab Section - Dr. Wayne Huang _/ _/ _/ _/ Location: Wavefunction, Inc. Irvine, California, USA _/ _/ _/ _/ Fee: $1000 (50% off for academics, $500), which _/ _/ includes course registration, four computational _/ _/ textbooks and one animated CD-ROM, all breakfasts _/ _/ and lunches. _/ _/ _/ _/ Textbooks: o "Chemistry with Computation", Warren Hehre & _/ _/ Wayne Huang, 1995. _/ _/ o "Experiments in Computational Organic Chemistry"_/ _/ Warren Hehre, Lonnie Burke, Alan Shusterman and _/ _/ William Pietro, 1993. _/ _/ o "A Short Course in Modern Electronic Structure _/ _/ Methods", Warren Hehre, 1995. _/ _/ o Educational CD-ROM "SpartanLive - Visualization _/ _/ of Chemical Structures and Reactions", Tom Hehre_/ _/ Lonnie Burke, Wayne Huang & Warren Hehre, 1995. _/ _/ o "Practical Strategies for Electronic Structure _/ _/ Calculations", Warren Hehre, 1995. _/ _/ _/ _/ Information: Workshop WWW: http://www.wavefun.com/workshop.html_/ _/ or contact Wayne Huang for further information _/ _/ including detailed brochure and course curriculum._/ _/ Tel: (714)955-2120 Fax: (714)955-2118 _/ _/ E-mail: workshop@wavefun.com _/ _/ _/ _/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/ This workshop is also available on site upon request, although the format could be varied. Please contact us for more information. (Sorry for the bandwidth) -- +---------------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemist | Irvine, California 92715 | | Wavefunction, Inc. | (714)955-2120 Fax: (714)955-2118 | | huang@wavefun.com | World Wide Web: http://wavefun.com | +---------------------------------------------------------------------+