From "PSI%SURFNET.1412007::MOIRA::groot"@caos.caos.kun.nl Thu Jun 24 03:21:14 1993 Date: Thu, 24 Jun 1993 09:16:53 METDST From: "PSI%SURFNET.1412007::MOIRA::groot"@caos.caos.kun.nl Subject: interaction function To: CHEMISTRY@ccl.net Message-Id: <01GZR26QY6N6AATYZP@caos.caos.kun.nl> Dear Netters, I have a series of noncovalently bound enzyme-inhibitor complexes for which the 3D-structures have been determined/modelled. I am trying to find computational methods that will allow me to estimate the binding between the enzyme and these inhibitors. In other words: does somebody know of A VALIDATED (published) INTERACTION FUNCTION ? Are there papers in which experimentally determined binding data are correlated with calculated interaction energies? Since I am interested in both a large number and a wide variety of inhibitor structures I don't think free energy perturbation methods will help me with respect to this. Peter Grootenhuis -------------------------------------------------------------------------------- E-mail address: grootenhuis@akzo.akzo.400net.nl ==> The "reply" or "answer" commands will NOT work for answering this mail. You need to specify the whole e-mail address. Postal address: Organon International bv --- Dr. Peter D.J. Grootenhuis --- CMC group KR1004 P.O. Box 20 --- 5340 BH OSS --- The Netherlands Phone: 31-4120-61920 --- Fax: 31-4120-62539 -------------------------------------------------------------------------------- From chp1aa@surrey.ac.uk Fri Jun 25 08:24:34 1993 From: Mr Andrew D Allen Message-Id: <9306251152.AA12386@central.surrey.ac.uk> Subject: RE:AMSOL 3.5 To: chemistry@ccl.net Date: Fri, 25 Jun 93 12:52:20 BST Dear those interested, AMSOL can do small molecule work but not proteins, I have recently done a preliminary AM1 (AMPAC) calculation on a 69 atom system without the PRECISE keyword and this took about 1hr 40mins on a SG Indigo. I am running the same system through with the PRECISE keyword, and am expected a time increase of at least 10 fold on the SCF convergence. When these studies have completed I look forward to doing the AM1 SM1 method on the same system. Andy. From UDIM018%FRORS31.BITNET@phem3.acs.ohio-state.edu Fri Jun 25 06:19:25 1993 Date: Fri, 25 Jun 1993 10:19:25 -0400 (EDT) From: UDIM018%FRORS31.BITNET@phem3.acs.ohio-state.edu Subject: SAM1 paper To: chemistry@ccl.net Message-Id: <01GZSHNA1OZM9GYZT1@phem3.acs.ohio-state.edu> E. M. EVLETH Dynamique des Interactions Moleculaires Universite Pierre et Marie Curie 4 Place Jussieu, Tour 22, Paris 75005 33-1-44-27-42-08 (work), 33 = France; 1 = Paris 33-1-45-48-67-20 (home) FAX 33-1-44-27-41-17 (lab);44-27-38-66(University) e-mail UDIM018 at FRORS31.BITNET In response to Graham Hurst request for clarification, the recent Dewar et al. paper describing SAM1 does not give sufficient details such that the independent investigator can program the method her/himself. This has already caused considerable private comment and Andy Holder is very aware of the problem of his commercializing the only program capable of doing these calculations. I think he is planning to completely explain the method in the literature when the SAM1 parameterization for second row elements are completed. For most of the user community this is no problem in that very few users of any semiempirical parameterization program the methods themselves. However, two significant portions of the user community which what something more concrete. First, those developping new methods need to know what went into the older ones. Some of us like to know what goes into the pot to make the soup. More importantly, some 3rd world groups can not afford to buy commercial programs. Some can not even have legal access to them! The embargo laws apply to scientific software and apply to countries like Cuba, Iraq, Libya, Haiti, Serbia, Vietnam, North Korea, and Iran. Therefore, there is no legal way, for instance, that a Cuban scientist can obtain a copy of a US based program which is generally used in the open scientific literature. If the calculation in question used SAM1 and the work originated from Cuba, it is proof that the program was illegally acquired. If the paper containing those calculations were submitted to a American based scientific journal, the editors of that journal would be faced with a curious moral and possible legal problem (up to a one million dollar fine). From AHOLDER@VAX1.UMKC.EDU Fri Jun 25 10:05:50 1993 Date: Fri, 25 Jun 1993 15:05:50 -0500 (CDT) From: AHOLDER@VAX1.UMKC.EDU Subject: SAM1 reference and assorted comments following To: CHEMISTRY@ccl.net Message-Id: <01GZSSNQIWX2AOKE3K@VAX1.UMKC.EDU> Netters, In a recent posting, Graham Hurst at Hypercube is "disturbed" at the publication of results without a thorough description of the model being present. I have spoken with Graham on the phone since I received his note and I had a few points I wanted to make: 1. He did not obtain the paper and examine it before making his statement. 2. The paper DOES contain a limited discussion of the method. A more detailed explanation may be found in James Ruiz's dissertation as published at the University of Texas at Austin in 1990, which is clearly referenced in the paper. 3. This paper was submitted, refereed, and accepted by knowledgeable scientists as a preliminary description of work of high interest to the chemical community in a journal that somewhat specializes in that activity. It will be followed up by a more complete paper. The purpose of this paper was to allow users to make independent conclusions about the performance of the new method on classes of compounds of interest to them. This is in keeping with the formats of the MNDO and AM1 papers. 4. It should be noted that, whatever is stated to the contrary, suff- icient detail will be published on SAM1 so that other establishments and individuals will be able to generate reproducible code. Note that none of MJS Dewar's previous methods could have been coded from scratch as many have claimed, (see above) without reference to the code itself, either MOPAC or AMPAC. it is impossible to obtain completely correct results for AM1 and MNDO from the papers alone. Certain special corrections were omitted from publication due to an oversight. (These corrections form the subject of another paper to be released shortly.) So, while Dr. Hurst's point is well-taken and fully subscribed to by me both in my capacity as a university researcher and president of Semichem, there is no intention to "hide" anything. I understand the sensitivity of this issue and I am committed to the pur- suit of science in an open atmosphere. I also realize that other scientists must be able to reproduce our results for them to be considered valid. The development of SAM1 is my primary research activity at UMKC, but Semichem is also spending money to develop this method and will be giving it to the scientific community freely. We withold only our code. We have completed a number of non-d-orbital parameter- izations and these are what is presented in the referenced paper. The d-orbital work is under way, but not to a sufficient stage to be desc- ribed in any detail, as we are not yet sure how it will turn out when the model is finalized. It should be noted, however, that some interests are not scientific, but competitive. This aspect of the situation seems to be of the most concern to Dr. Hurst and Hypercube. This company includes a number of Michael Dewar's previously released methods in their software. Iam committed to keeping AMPAC development and my scientific activities as divided as possible. This is not always as clear as I would like, but I do my best. Please give me the benefit of the doubt whenever possible. I will be more than happy to discuss the details of this with anyone who wishes to pursue the matter further. Andy Holder From d3f012@pellucidar.pnl.gov Fri Jun 25 05:48:09 1993 Date: Fri, 25 Jun 93 12:48:09 -0700 From: d3f012@pellucidar.pnl.gov Subject: SAM1 Reference To: chemistry@ccl.net Message-Id: <9306251948.AA03317@pellucidar.pnl.gov> On the discussion of a possible "official" SAM1 reference: I personally have not seen the stated SAM1 reference, so I will withold my judgment on that specific paper until I read it. My comments below do not refer to any specific scientific work or literature reference. Let me address the more fundamental issue that this topic brings forth. I share Graham Hurst's concerns. One of the basic tenets of good science is that of reproducibility, and independant verification. If the results of a new method are published without sufficiently describing the method to fulfill the above criteria, then I personally could not take the results seriously. Furthermore, I would never have recommended such work for publication. I feel very strongly that when a new method is developed and implemented that it must pass the peer review process to gain legitimacy in the scientific community, regardless of whether most other scientists care to reimplement that method or not. Proprietary methods are fine, as long as it is openly known that they are proprietary. Results of proprietary methods do not belong in the open scientific literature. Of course, these are just my personal opinions. ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Argus available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. Disclaimer: The views expressed in this message are solely my own and do not represent Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients. ************************************************************************** From jstewart@fujitsu.fai.com Fri Jun 25 08:25:52 1993 Date: Fri, 25 Jun 93 15:25:52 PDT From: jstewart@fai.com (Dr. James Stewart) Message-Id: <9306252225.AA02833@fujitsu.fai.com> To: chemistry@ccl.net Subject: MOPAC 93 Manual - how to order MOPAC 93 MANUAL MOPAC 93 is currently being distributed by the QCPE, as manual and source code, etc. Users who want to get extra copies of the manual for MOPAC 93 can get them from: Ms Miyoko Murakami Fujitsu Systems Business of America 5200 Patrick Henry Drive Santa Clara, CA 95054 Tel: (408) 988-8012 x 217 Fax: (408) 492-1982 The cost is $70 plus $2 - $5 for shipping, plus tax. A quantity discount may be available. James J. P. Stewart Tel: (719) 488-9416 FAX: (719) 488-9758 Email: jstewart@fai.com