From chemistry-request@server.ccl.net Thu Jan 27 16:00:12 2000 Received: from mim.mandic.com.br (mim.mandic.com.br [200.246.227.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA00378 for ; Thu, 27 Jan 2000 16:00:10 -0500 Received: from hermes.mandic.com.br. (hermes2 [200.246.227.50]) by mim.mandic.com.br (8.9.3/8.9.3) with ESMTP id RAA26134; Thu, 27 Jan 2000 17:45:22 -0200 (EDT) Received: from LINUX (b19192.dial-rjo.impsat.com.br [200.196.82.192]) by hermes.mandic.com.br. (8.9.3/8.9.3) with SMTP id RAA02022; Thu, 27 Jan 2000 17:45:09 -0200 (EDT) Message-ID: <002e01bf6902$2c3e6180$c052c4c8@LINUX.mandic.com.br> From: "Victor Rodrigues" To: "Computational Chemistry List" , "OrgList" Subject: GC-MS Date: Thu, 27 Jan 2000 18:07:06 -0200 Does anyone know any free program capable of reading GC-MS = files with extension .MS?? Please answer to my personal e-mail: vicerj@mandic.com.br From chemistry-request@server.ccl.net Thu Jan 27 20:02:13 2000 Received: from shiva.hunter.cuny.edu (shiva.hunter.cuny.edu [146.95.128.96]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA01421 for ; Thu, 27 Jan 2000 20:02:08 -0500 Received: from bigfoot.com (mol06.ch.hunter.cuny.edu [146.95.18.106]) by shiva.hunter.cuny.edu (8.9.3/8.9.3) with ESMTP id TAA06979; Thu, 27 Jan 2000 19:01:10 -0500 (EST) Message-ID: <3890EC72.D3ABFD0A@bigfoot.com> Date: Thu, 27 Jan 2000 20:10:10 -0500 From: AM X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en,ru MIME-Version: 1.0 To: uccatvm CC: chemistry@ccl.net, Tanja van Mourik , Dominik.Horinek@chemie.uni-regensburg.de, uccatvm@ucl.ac.uk Subject: Re: bsse and second derivatives in G98 References: <9099.200001271447@socrates-a.ucl.ac.uk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Tanja, Dominik, and all, There is no phisical law forbidding frequency calculations on Ar atom. And Hessian (as opposed to frequencies) makes sence at any point on potencial surface, not only at the crytical points. In fact, this is how Opt=CalcFC works in Gaussian. If you are interested in Hessian, there is a workarownd: use keyword FORCE instead of FREQ. Try HF first. We found that in some cases FORCE on single atom won't work with MP2. If you try GAMESS-UK, you may get Hessian in more readable format :) Artem > What you are trying to do here is to calulate the frequency of the Ar > atom (albeit with some basis functions on the formic acid ghost atoms). > This is not possible. > > Similarly, you cannot calculate the frequencies of formic acid in the > presence of ghost functions like this (i.e. by replacing the last 5 lines > by "6 Nuc 0.0"). To calculate a hessian, your molecule has to be in the minimum > (for the given method/basis), and this is not the case (I assume the geometry > above comes from an optimization on the cluster). > > I am afraid that there is not an easy way to calculate counterpoise-corrected > frequencies automatically. You would need a potential energy surface and > calculate the frequencies on it numerically, but this is not practical on any > higher level of theory. > > Best regards, > > Tanja > > > to do the calculation with ghost atoms for the organic molecule and > > electrons only at the argon atom. Unfortunately, with G98 this type of > > calculation fails: 'Molecule is non-linear but NTrRo=3'. Who knows how > > to fix this problem, or is there another convenient way to obtain the > > second derivatives without this problem. I used the following input: > > From chemistry-request@server.ccl.net Thu Jan 27 17:05:19 2000 Received: from aorta.physiome.com (mail.physiome.com [204.142.61.124]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA00737 for ; Thu, 27 Jan 2000 17:05:19 -0500 Received: from COMPCHEM ([192.168.1.67]) by aorta.physiome.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2448.0) id ZJKLY4SK; Thu, 27 Jan 2000 15:58:14 -0500 Message-ID: <000d01bf690a$7a972b20$4301a8c0@physiome.com> From: "Roberta Susnow" To: Subject: QSAR review Date: Thu, 27 Jan 2000 16:07:11 -0500 Hi: I would like a list of some good reviews on QSAR. This would include review articles and some relevant books. I am particularly interested=20 in some of the details such as the choice of descriptors, how to design a training set etc. Thank you for your assistance. Roberta Susnow Physiome Sciences Roberta G. Susnow Physiome Sciences Scientist TEL;WORK;VOICE:609-987-1199 x243 TEL;WORK;FAX:609-987-9393 ADR;WORK:;;307 College Road East;Princeton;New Jersey;08540 307 College Road East Princeton, New Jersey 08540 rsusnow@physiome.com From chemistry-request@server.ccl.net Fri Jan 28 07:11:35 2000 Received: from fujitsu.co.uk (phoenix.fujitsu.co.uk [194.33.32.250]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA05105 for ; Fri, 28 Jan 2000 07:11:34 -0500 Received: (from smap@localhost) by fujitsu.co.uk (8.9.1/8.9.1) id LAA05936; Fri, 28 Jan 2000 11:10:20 GMT X-Authentication-Warning: phoenix.fujitsu.co.uk: smap set sender to using -f Received: from (pandora.fujitsu.co.uk [194.33.32.1]) by phoenix.fujitsu.co.uk via smap (V2.0) id xma005899; Fri, 28 Jan 00 11:09:59 GMT Received: from fecit.co.uk ([192.168.101.116]) by pandora.fujitsu.co.uk (8.8.8/8.8.8) with ESMTP id LAA20138; Fri, 28 Jan 2000 11:07:20 GMT Message-ID: <389177B6.8A2C8E5F@fecit.co.uk> Date: Fri, 28 Jan 2000 11:04:22 +0000 From: Herbert Fruchtl Organization: Fujitsu European Centre for Information Technology X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: AM CC: chemistry@ccl.net Subject: Re: bsse and second derivatives in G98 References: <9099.200001271447@socrates-a.ucl.ac.uk> <3890EC72.D3ABFD0A@bigfoot.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > There is no phisical law forbidding frequency calculations on Ar atom. Am I missing something completely? All methods mentioned are based on the Born-Oppenheimer approximation. The Argon can't feel a force, because in this approximation forces only exist between nuclei. The Hessian is the derivative of the force, which is also zero. Everything else is spurious. To the original poster: as I understand Counterpoise, it can only be used to calculate wavefunction properties (e.g. the energy, but not the Hessian). Then you can calculate other properties (gradients, the Hessian, etc.) from the potential energy surface. I don't think you can apply the counterpoise method directly to the Hessian. Even if your program happens to give you non-zero numbers. You will of course get different energies when you move ghost atoms around (and therefore a numerical gradient/Hessian will be non-zero), but that has nothing to do with a physical frequency. Herbert From chemistry-request@server.ccl.net Fri Jan 28 08:26:45 2000 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA05407 for ; Fri, 28 Jan 2000 08:26:44 -0500 Received: (from jochen@localhost) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) id NAA15099; Fri, 28 Jan 2000 13:19:57 +0100 From: "Jochen Küpper" MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14481.35180.855909.312340@bacchus.pc1.uni-duesseldorf.de> Date: Fri, 28 Jan 2000 13:19:56 +0100 (CET) To: Herbert Fruchtl Cc: AM , chemistry@ccl.net Subject: CCL:bsse and second derivatives in G98 In-Reply-To: <389177B6.8A2C8E5F@fecit.co.uk> References: <9099.200001271447@socrates-a.ucl.ac.uk> <3890EC72.D3ABFD0A@bigfoot.com> <389177B6.8A2C8E5F@fecit.co.uk> X-Mailer: VM 6.72 under 21.1 (patch 8) "Bryce Canyon" XEmacs Lucid Herbert Fruchtl writes: > > There is no phisical law forbidding frequency calculations on Ar atom. > > Am I missing something completely? All methods mentioned are based on > the Born-Oppenheimer approximation. But then BOA isn't a physical law :-O > The Argon can't feel a force, > because in this approximation forces only exist between nuclei. The > Hessian is the derivative of the force, which is also zero. Well, the derivative of nothing isn't actually zero - but nothing. In the BOA it simply doesn't make sense to talk about _that_ Hessian. > You will of course get different energies when you move ghost atoms > around (and therefore a numerical gradient/Hessian will be non-zero), > but that has nothing to do with a physical frequency. It actually means leaving BOA behind. You should then probably try to do that from the beginning - if you really want :-) Jochen From chemistry-request@server.ccl.net Fri Jan 28 10:09:26 2000 Received: from hermes.iupui.edu (hermes.iupui.edu [134.68.220.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA05896 for ; Fri, 28 Jan 2000 10:09:26 -0500 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by hermes.iupui.edu (8.9.3/8.9.3/1.2IUPUIPO) with SMTP id JAA15547 for ; Fri, 28 Jan 2000 09:02:40 -0500 (EST) Message-ID: Date: 28 Jan 2000 09:14:00 -0500 From: "Boyd" Subject: re: QSAR review To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Hi Roberta, >I would like a list of some good reviews on QSAR. This would include >review articles and some relevant books. >Roberta Susnow >Physiome Sciences You will find the following chapters from Reviews in Computational Chemistry helpful: E. L. Plummer, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1990, Vol. 1, pp. 119-168. L. H. Hall and L. B. Kier, RCC, 1991, Vol. 2, pp. 367-422. I. B. Bersuker and A. S. Dimoglo, RCC, 1991, Vol. 2, pp. 423-460. L. M. Balbes, S. W. Mascarella, and D. B. Boyd, RCC, 1994, Vol. 5, pp. 337-379. G. A. Arteca, RCC, 1996, Vol. 9, pp. 191-253. E. J. Martin, D. C. Spellmeyer, R. E. Critchlow Jr., and J. M. Blaney, RCC, 1997, Vol. 10, pp. 75-100. T. I. Oprea and C. L. Waller, RCC, Wiley, 1997, Vol. 11, pp. 127-182. P.-A. Carrupt, B. Testa, and P. Gaillard, RCC, Wiley, 1997, Vol. 11, pp. 241-315. Good luck, Don Donald B. Boyd, Ph.D. Editor, Reviews in Computational Chemistry http://chem.iupui.edu/rcc/rcc.html Editor, Journal of Molecular Graphics and Modelling (publication of the ACS COMP division and MGMS) http://chem.iupui.edu/~boyd/jmgm.html Department of Chemistry Indiana University-Purdue University at Indianapolis 402 North Blackford Street Indianapolis, Indiana 46202-3274, U.S.A. Telephone 317-274-6891, FAX 317-274-4701 E-mail boyd@chem.iupui.edu From chemistry-request@server.ccl.net Fri Jan 28 04:57:06 2000 Received: from macke.imb-jena.de (macke.imb-jena.de [193.174.235.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA03757 for ; Fri, 28 Jan 2000 04:57:05 -0500 Received: (from csc@localhost) by macke.imb-jena.de (980427.SGI.8.8.8/8.8.8) id JAA15680 for chemistry@ccl.net; Fri, 28 Jan 2000 09:50:23 +0100 (MET) From: Christoph Schneider Message-Id: <200001280850.JAA15680@macke.imb-jena.de> Subject: Re: CCL:Base Pairing To: chemistry@ccl.net Date: Fri, 28 Jan 2000 09:50:21 +0100 (MET) X-Mailer: ELM [version 2.5 PL1] MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Bernd Engels wrote: > hy, > I am interested in Base Pairing and expecially which method > is able to handle such things. I know that MP2 using a smaller > basis set gives reasonable results, but perhaps somebody > can point to a review or other paper. > Thanks, I will summarize > Bernd Engels > Organische Chemie > Universität Würzburg Hi Bernd, Jiri Sponer and Pavel Hobza contributed extensive studies in recent years. For a review you might use @ARTICLE{hobza99, author={Hobza, P. and Sponer, J.}, title={{Structure, Energetics, and Dynamics of the Nucleic Acids Base Pairs: Nonempirical Ab Initio Calculations}}, journal={Chem Rev}, volume={99}, pages={3247-3276}, year={1999 }}. Greetings C. -- ----------------------------------------------------------------- Christoph Schneider csc@imb-jena.de Institute for Molecular Biotechnology Beutenbergstrasse 11, -Biocomputing- Tel.: +49-3641-65-6205 P.O. Box 100 813, D-07708 Jena, Germany Fax: +49-3641-65-6210 http://www.imb-jena.de/~csc/ ----------------------------------------------------------------- Never say, "I tried it once and it did not work." - Lord Ernest Rutherford, 1877-1957 From chemistry-request@server.ccl.net Fri Jan 28 08:56:32 2000 Received: from mailcity.com (fes-qout.whowhere.com [209.1.236.7]) by server.ccl.net (8.8.7/8.8.7) with SMTP id IAA05556 for ; Fri, 28 Jan 2000 08:56:32 -0500 Received: from Unknown/Local ([?.?.?.?]) by mailcity.com; Fri Jan 28 02:01:51 2000 To: CHEMISTRY@ccl.net Date: Fri, 28 Jan 2000 15:31:51 +0530 From: "Manoj Pal" Message-ID: Reply-To: pal_m@mailcity.com Subject: C/C++ source for dihedral angle Organization: MailCity (http://www.mailcity.lycos.com:80) Hi! Can anybody help me obtain C/C++ source code for finding the dihedral angles of protein resediues from ***.pdb files. It will be of great help to me. manoj LYCOShop. Thousands of products! One location! http://shop.lycos.com/ From chemistry-request@server.ccl.net Fri Jan 28 11:14:06 2000 Received: from ccshst04.cs.uoguelph.ca (ccshst04.cs.uoguelph.ca [131.104.96.17]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA06341 for ; Fri, 28 Jan 2000 11:14:06 -0500 Received: from ccshst01 (ccshst01.cs.uoguelph.ca [131.104.96.81]) by ccshst04.cs.uoguelph.ca (8.9.3/8.9.3) with SMTP id KAA06966 for ; Fri, 28 Jan 2000 10:07:19 -0500 (EST) Date: Fri, 28 Jan 2000 10:07:17 -0500 (EST) From: WeiQuan Tian X-Sender: wtian@ccshst01 To: chemistry@ccl.net Subject: Sad News about Dr. Zerner in Florida Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The founder of ZINDO, Dr. Zerner suffers from cancer. ....... After 8 years fight against cancer Dr. Zerner is rapidly failing since late last semester, he has not been able to come to work this year. He is now in North Florida Hospice. He is unable to communicate, eat, and is in and out of conscience. His life is coming to an end very soon. Dr. Zerner is always optimistic, and always kept a dignity and privacy in his fight against cancer, that first formed in his collon, then spread to his liver and bones, and now is taking his life. ..... Best Wishes to Dr. Zerner and his family and Best Regards to our quantum and computational chemistry community! Wei Quan Tian University of Guelph From chemistry-request@server.ccl.net Fri Jan 28 11:01:42 2000 Received: from server.nybc.org (server.nybc.org [192.94.249.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA06294 for ; Fri, 28 Jan 2000 11:01:36 -0500 Received: from iris.nybc.org ([192.94.249.42]) by server.nybc.org (Netscape Mail Server v2.0) with ESMTP id AAA8701; Fri, 3 Dec 1999 09:57:18 -0400 Received: from nybc.org by iris.nybc.org via ESMTP (980427.SGI.8.8.8/940406.SGI.AUTO) id JAA12370; Fri, 28 Jan 2000 09:49:47 -0500 (EST) Sender: debnath@nybc.org Message-ID: <3891AC8B.1444B863@nybc.org> Date: Fri, 28 Jan 2000 09:49:47 -0500 From: Asim Kumar Debnath Organization: New York Blood Center X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Roberta Susnow CC: chemistry@ccl.net Subject: Re: CCL:QSAR review References: <000d01bf690a$7a972b20$4301a8c0@physiome.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Roberta: The following few references (and the references cited therein) will provide you with detail descriptions on QSAR (both methods and applications). 1. "Exploring QSAR" Vol 1 and 2, Hansch, C. et al., 1995. ACS publication. 2. "Comprehensive Medicinal Chemistry", Vol 4 (Rational Drug Design), Hansch et. (Des)., 1990, Pergamon Press. 3. "Classical and Three-Dimensional QSAR in Agrochemistry", Hansch, C. and Fujita, T. (Des), 1995, ACS Symposium Series. 4. "Medicinal Chemistry Vol. 19 (Quantitative Structure-Activity Relationships of Drugs)", Topliss, J.G. (ed), 1983, Academic Press. 5. "Quantitative Drug Design. A critical introduction", Martin, Y.C., 1978, Marcel Dekker. 6. "Strategy of Drug Design. A Molecular Guide to Biological Activity" Purcell, W. P., et al. , 1973, Wiley. 7. "3D QSAR in Drug Design, Theory, Methods and Application." Kubinyi, H. (Ed)., 1993, ESCOM Science Publishers. 8. "Perspectives in Drug Discovery and Design, Vols. 9/10/11 (3D QSAR in Drug Design: Ligand-Protein Interactions and Molecular Similarity", Kubinyi, H. et al. (Des), 1998, Kluwer/ESCOM. 9. "Perspectives in Drug Discovery and Design, Vols. 12/13/14 (3D QSAR in Drug Design: Recent Advances", Kubinyi, H. et al. (Des), 1998, Kluwer/ ESCOM. I just wrote a chapter on QSAR in a book and if you are interested I will send you a reprint when the book comes out later this year. Hope this helps. Asim Debnath Roberta Susnow wrote: > Hi: > > I would like a list of some good reviews on QSAR. This would include > review articles and some relevant books. I am particularly interested=20 > in some of the details such as the choice of descriptors, how to design > a training set etc. > From chemistry-request@server.ccl.net Fri Jan 28 12:29:37 2000 Received: from hugh.chem.uic.edu (hugh.chem.uic.edu [131.193.195.93]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA06776 for ; Fri, 28 Jan 2000 12:29:37 -0500 Received: by hugh.chem.uic.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id MAA11189; Fri, 28 Jan 2000 12:25:56 -0600 Date: Fri, 28 Jan 2000 12:25:43 +36000 From: Richard Wood cc: OSC CCL Subject: Re: CCL:QSAR review In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII As well as any papers by the research group I'm in, Hopfinger et al. Richard On 28 Jan 2000, Boyd wrote: > Hi Roberta, > > >I would like a list of some good reviews on QSAR. This would include > >review articles and some relevant books. > >Roberta Susnow > >Physiome Sciences > > You will find the following chapters from Reviews in Computational > Chemistry helpful: > > E. L. Plummer, in Reviews in Computational Chemistry, K. B. Lipkowitz > and D. B. Boyd, Eds., VCH Publishers, New York, 1990, Vol. 1, pp. 119-168. > > L. H. Hall and L. B. Kier, RCC, 1991, Vol. 2, pp. 367-422. > > I. B. Bersuker and A. S. Dimoglo, RCC, 1991, Vol. 2, pp. 423-460. > > L. M. Balbes, S. W. Mascarella, and D. B. Boyd, RCC, 1994, Vol. 5, pp. > 337-379. > > G. A. Arteca, RCC, 1996, Vol. 9, pp. 191-253. > > E. J. Martin, D. C. Spellmeyer, R. E. Critchlow Jr., and J. M. Blaney, > RCC, 1997, Vol. 10, pp. 75-100. > > T. I. Oprea and C. L. Waller, RCC, Wiley, 1997, Vol. 11, pp. 127-182. > > P.-A. Carrupt, B. Testa, and P. Gaillard, RCC, Wiley, 1997, Vol. 11, pp. > 241-315. > > Good luck, Don > > Donald B. Boyd, Ph.D. > Editor, Reviews in Computational Chemistry > http://chem.iupui.edu/rcc/rcc.html > Editor, Journal of Molecular Graphics and Modelling > (publication of the ACS COMP division and MGMS) > http://chem.iupui.edu/~boyd/jmgm.html > Department of Chemistry > Indiana University-Purdue University at Indianapolis > 402 North Blackford Street > Indianapolis, Indiana 46202-3274, U.S.A. > Telephone 317-274-6891, FAX 317-274-4701 > E-mail boyd@chem.iupui.edu > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Fri Jan 28 13:43:59 2000 Received: from gate-sl1.mdli.com (ns2.mdli.com [208.200.221.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA07146 for ; Fri, 28 Jan 2000 13:43:59 -0500 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id JAA13042; Fri, 28 Jan 2000 09:35:55 -0800 (PST) Received: from puffin.mdli.com(191.254.19.10) by gate-sl1.mdli.com via smap (V2.1) id xma013040; Fri, 28 Jan 00 09:35:54 -0800 Received: from shepherd.mdli.com by puffin.mdli.com (8.8.5/BCH1.0) id JAA11714; Fri, 28 Jan 2000 09:35:54 -0800 (PST) Received: from mdli.com (lchen-95h.mdli.com [191.254.19.100]) by shepherd.mdli.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2650.21) id DTN6PY2Z; Fri, 28 Jan 2000 09:35:53 -0800 Message-ID: <3891D18B.BBE6B1CF@mdli.com> Date: Fri, 28 Jan 2000 09:27:39 -0800 From: Lingran Chen X-Mailer: Mozilla 4.5 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: Roberta Susnow CC: chemistry@ccl.net, LChen@mdli.com Subject: Re: CCL:QSAR review References: <000d01bf690a$7a972b20$4301a8c0@physiome.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Robert: The following chapters in "The Encyclopedia of Computational Chemistry" (Paul Schleyer et al. Eds. John Wiley & Sons: Chichester, 1998, ISBN: 0-471-96588-X) covers QSAR: Environmental Chemistry: QSAR Qnatitative Structure-Activity Relationships in Drug Design Qnatitative Structure-Property Relationships (QSPR) Structure-Activity Relationships in Modeling Nucleic Acid Ligand Interactions -Lingran ********************************************************** Lingran Chen, Ph.D. Senior Scientific Programmer MDL Information Systems, Inc. Phone: (510) 895-1313, Ext. 1305 FAX: (510) 614-3616 Email: LCHEN@MDLI.COM ********************************************************** Roberta Susnow wrote: > Hi: > > I would like a list of some good reviews on QSAR. This would include > review articles and some relevant books. I am particularly interested=20 > in some of the details such as the choice of descriptors, how to design > a training set etc. > > Thank you for your assistance. > > Roberta Susnow > Physiome Sciences > > Roberta G. Susnow > Physiome Sciences > Scientist > TEL;WORK;VOICE:609-987-1199 x243 > TEL;WORK;FAX:609-987-9393 > ADR;WORK:;;307 College Road East;Princeton;New Jersey;08540 > 307 College Road East > Princeton, New Jersey 08540 > rsusnow@physiome.com > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Fri Jan 28 14:52:34 2000 Received: from mail2.panix.com (mail2.panix.com [166.84.0.213]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA07597 for ; Fri, 28 Jan 2000 14:52:34 -0500 From: kynn@panix.com Received: from panix3.panix.com (panix3.panix.com [166.84.0.228]) by mail2.panix.com (Postfix) with ESMTP id 47DF2155B9; Fri, 28 Jan 2000 13:45:33 -0500 (EST) Received: (from kynn@localhost) by panix3.panix.com (8.8.8/8.7.1/PanixN1.0) id NAA14361; Fri, 28 Jan 2000 13:45:33 -0500 (EST) Date: Fri, 28 Jan 2000 13:45:33 -0500 (EST) Message-Id: <200001281845.NAA14361@panix3.panix.com> X-Authentication-Warning: panix3.panix.com: kynn set sender to kynn@panix.com using -f To: CHEMISTRY@ccl.net Subject: Re: CCL:Why WHAM? References: <200001280735.CAA03160@server.ccl.net> Date: Thu, 27 Jan 2000 17:35:55 +0100 From: hinsen@dirac.cnrs-orleans.fr Subject: Re: CCL:Why WHAM? The theory behind WHAM may be more involved, but it's no less transparent. There are a couple of items in WHAM that are less than transparent, I think. One is the assumption that the single integrated correlation time that one can compute from the simulation's energy data is a good enough approximation for the integrated correlation time for the occupancy of each bin (which, in principle, depends on the bin's coordinates); it is the latter that we need to estimate the error that we want to minimize. Given that the minimization of this error is the crux of the method, it seems that the published applications of WHAM are extremely cavalier about determining this error. Also, I've not seen a justification for assuming that the bin occupancy has a Poisson distribution, or at any rate, that its variance equals its mean (this assumption is implicit in the formula Kumar gives for \tau). None of these concerns arise with the more naive approach to combining the histograms, because this method does not depend crucially on a good estimate of the error in the histogram. Thanks for the reference by Roux, and for the Python code. KJ From chemistry-request@server.ccl.net Fri Jan 28 11:44:12 2000 Received: from terra.ifi.unicamp.br (terra.ifi.unicamp.br [143.106.6.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA06497 for ; Fri, 28 Jan 2000 11:44:11 -0500 Received: from ifi.unicamp.br (lua [143.106.6.13]) by terra.ifi.unicamp.br (8.9.3/8.9.3) with ESMTP id NAA23099 for ; Fri, 28 Jan 2000 13:35:22 -0200 (BDB) Received: (from daemon@localhost) by ifi.unicamp.br (8.9.3/8.9.3) id NAA10815 for ; Fri, 28 Jan 2000 13:35:19 -0200 (BDB) Received: from cation.ifi.unicamp.br(143.106.39.135), claiming to be "cation" via SMTP by lua.ifi.unicamp.br, id smtpdAAAa002cx; Fri Jan 28 13:35:16 2000 Message-Id: <4.1.20000128133734.00a60600@lua.ifi.unicamp.br> X-Sender: dasf@lua.ifi.unicamp.br X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Fri, 28 Jan 2000 13:43:48 -0200 To: CHEMISTRY@ccl.net From: Demetrio Antonio da Silva Filho Subject: Excited States Methods In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id LAA06498 Dear CCLers, I will write a small chapter in my PhD thesis about the methods used to calculate excited state properties and geometries. I would like a list of articles and books where I can find some description of those methods. I will summarize. Thanks in advance, Demétrio Filho _____________________________________ Demetrio A. da Silva Filho UNICAMP - IFGW Prédio D - Sala 17 CEP 13083-970 C.Postal 6165 Campinas - SP - Brasil _____________________________________ "Se não houver frutos, valeu a beleza das flores. Se não houver flores, valeu a sombra das folhas. Se não houver folhas, valeu a intenção da semente." Henfil From chemistry-request@server.ccl.net Fri Jan 28 12:27:43 2000 Received: from hugh.chem.uic.edu (hugh.chem.uic.edu [131.193.195.93]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA06763 for ; Fri, 28 Jan 2000 12:27:42 -0500 Received: by hugh.chem.uic.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id MAA11048; Fri, 28 Jan 2000 12:23:55 -0600 Date: Fri, 28 Jan 2000 12:23:48 +36000 From: Richard Wood To: Jochen Küpper cc: Herbert Fruchtl , AM , chemistry@ccl.net Subject: Re: CCL:bsse and second derivatives in G98 In-Reply-To: <14481.35180.855909.312340@bacchus.pc1.uni-duesseldorf.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id MAA06764 On Fri, 28 Jan 2000, Jochen Küpper wrote: > Herbert Fruchtl writes: > Well, the derivative of nothing isn't actually zero - but nothing. > In the BOA it simply doesn't make sense to talk about _that_ Hessian. Isn't zero a constant, and so the derivative of a constant is zero? Richard From chemistry-request@server.ccl.net Fri Jan 28 12:52:12 2000 Received: from fujitsu.co.uk (phoenix.fujitsu.co.uk [194.33.32.250]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA06922 for ; Fri, 28 Jan 2000 12:52:12 -0500 Received: (from smap@localhost) by fujitsu.co.uk (8.9.1/8.9.1) id QAA14799 for ; Fri, 28 Jan 2000 16:51:01 GMT X-Authentication-Warning: phoenix.fujitsu.co.uk: smap set sender to using -f Received: from (pandora.fujitsu.co.uk [194.33.32.1]) by phoenix.fujitsu.co.uk via smap (V2.0) id xma014797; Fri, 28 Jan 00 16:50:44 GMT Received: from fecit.co.uk ([192.168.101.116]) by pandora.fujitsu.co.uk (8.8.8/8.8.8) with ESMTP id QAA28709 for ; Fri, 28 Jan 2000 16:48:06 GMT Message-ID: <3891C793.CAE6CEF6@fecit.co.uk> Date: Fri, 28 Jan 2000 16:45:07 +0000 From: Herbert Fruchtl Organization: Fujitsu European Centre for Information Technology X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:bsse and second derivatives in G98 References: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Richard Wood wrote: > > On Fri, 28 Jan 2000, Jochen Küpper wrote: > > > Herbert Fruchtl writes: > > Well, the derivative of nothing isn't actually zero - but nothing. > > In the BOA it simply doesn't make sense to talk about _that_ Hessian. > > Isn't zero a constant, and so the derivative of a constant is zero? > Of course you're right. Just the quote that you generously attribute to me isn't mine. Herbert From chemistry-request@server.ccl.net Fri Jan 28 12:38:56 2000 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA06852 for ; Fri, 28 Jan 2000 12:38:55 -0500 Received: (from jochen@localhost) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) id RAA15528; Fri, 28 Jan 2000 17:32:04 +0100 From: "Jochen Küpper" MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Message-ID: <14481.50307.818739.97759@bacchus.pc1.uni-duesseldorf.de> Date: Fri, 28 Jan 2000 17:32:03 +0100 (CET) To: Richard Wood Cc: chemistry@ccl.net Subject: Re: CCL:bsse and second derivatives in G98 In-Reply-To: References: <14481.35180.855909.312340@bacchus.pc1.uni-duesseldorf.de> X-Mailer: VM 6.72 under 21.1 (patch 8) "Bryce Canyon" XEmacs Lucid Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id MAA06853 Richard Wood writes: > On Fri, 28 Jan 2000, Jochen Küpper wrote: > > Well, the derivative of nothing isn't actually zero - but nothing. > > Isn't zero a constant, and so the derivative of a constant is zero? Your statement as such ios correct. But if you read the earlier messages (e.g the one you cited), you will see that he was calcualting the derivative outside the definition range of the function. Consider t: ]-1,+1[ ---> R x |--> tan( x ) What's the derivative of dt/dx at x = 5 ? Jochen From chemistry-request@server.ccl.net Fri Jan 28 15:01:48 2000 Received: from lrz.uni-muenchen.de (lsanca1-ar99-078-106.biz.dsl.gtei.net [4.3.78.106]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA07675 for ; Fri, 28 Jan 2000 15:01:47 -0500 Received: (from eugene.leitl@localhost) by lrz.uni-muenchen.de (8.8.8/8.8.8) id KAA07443 for ; Fri, 28 Jan 2000 10:55:32 -0800 Resent-From: Eugene Leitl Resent-Message-ID: <14481.58916.201588.614095@lrz.uni-muenchen.de> Resent-Date: Fri, 28 Jan 2000 10:55:32 -0800 (PST) Resent-To: Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Precedence: bulk From: To: The Beowulf Mailing List Subject: Beowulf Article Date: Fri, 28 Jan 2000 07:03:31 -0500 (EST) From: Douglas Eadline There was a a very well written article on Beowulf and Chemistry in the January 10 "Chemical and Engineering News" (C&EN). It is one of the most accurate write ups I have seen. Unfortunately, you can not get it on-line unless you are a member of the ACS (American Chemical Society). (I haven't payed my dues for quite a while) In any case, if you know a chemist chances are he or she will have a copy as it is a weekly publication sent to all members of the ACS (or they could get it on line for you). For those interested the web site is pubs.acs.org.cen It is a shame that such a good article is not publicly accessible :( Doug ------------------------------------------------------------------- Paralogic, Inc. | PEAK | Voice:+610.861.6960 115 Research Drive | PARALLEL | Fax:+610.861.8247 Bethlehem, PA 18017 USA | PERFORMANCE | http://www.plogic.com ------------------------------------------------------------------- ------------------------------------------------------------------- To unsubscribe send a message body containing "unsubscribe" to beowulf-request@beowulf.org From chemistry-request@server.ccl.net Fri Jan 28 16:32:39 2000 Received: from hugh.chem.uic.edu (hugh.chem.uic.edu [131.193.195.93]) by server.ccl.net (8.8.7/8.8.7) with SMTP id QAA08034 for ; Fri, 28 Jan 2000 16:32:39 -0500 Received: by hugh.chem.uic.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id QAA11588; Fri, 28 Jan 2000 16:29:08 -0600 Date: Fri, 28 Jan 2000 16:29:01 +36000 From: Richard Wood To: Jochen Küpper cc: chemistry@ccl.net Subject: Re: CCL:bsse and second derivatives in G98 In-Reply-To: <14481.50307.818739.97759@bacchus.pc1.uni-duesseldorf.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id QAA08035 But i WAS responding to what was written, namely the derivative of 0 not being zero. What does 0 have to do with dt/dx anyway? Look at it this way, if dt/dx=0, doesn't d2t/dx2=0 also? Richard On Fri, 28 Jan 2000, Jochen Küpper wrote: > Richard Wood writes: > > On Fri, 28 Jan 2000, Jochen Küpper wrote: > > > Well, the derivative of nothing isn't actually zero - but nothing. > > > > Isn't zero a constant, and so the derivative of a constant is zero? > > Your statement as such ios correct. > But if you read the earlier messages (e.g the one you cited), you will > see that he was calcualting the derivative outside the definition > range of the function. > > Consider > t: ]-1,+1[ ---> R > x |--> tan( x ) > > What's the derivative of dt/dx at x = 5 ? > > Jochen > From chemistry-request@server.ccl.net Fri Jan 28 17:14:00 2000 Received: from hotmail.com (f134.law4.hotmail.com [216.33.149.134]) by server.ccl.net (8.8.7/8.8.7) with SMTP id RAA08163 for ; Fri, 28 Jan 2000 17:13:59 -0500 Received: (qmail 14236 invoked by uid 0); 28 Jan 2000 21:05:08 -0000 Message-ID: <20000128210508.14235.qmail@hotmail.com> Received: from 146.95.18.108 by www.hotmail.com with HTTP; Fri, 28 Jan 2000 13:05:08 PST X-Originating-IP: [146.95.18.108] From: "Artem Masunov" To: chemistry@ccl.net Subject: Re: bsse and second derivatives in G98 Date: Fri, 28 Jan 2000 13:05:08 PST Mime-Version: 1.0 Content-Type: text/plain; format=flowed >Herbert Fruchtl writes: >Well, the derivative of nothing isn't actually zero - but nothing. >In the BOA it simply doesn't make sense to talk about _that_ Hessian. This discussion is getting a bit metaphysical.. >The Argon can't feel a force, >because in this approximation forces only exist between nuclei. The First note that MO LCAO approximation is not a part of BOA. In the perfect world with complete basis sets (or numerical wavefunctions) you would be right. But we have to deal with atom centered basis functions, which don't even satisfy Hellman-Feinman theorem.. And we (OK, some of us) are just trying to make the results a little better. Now, when you move your basis function and leave the atomic nuclei in place, does the energy change? Yes. Can we look at the derivatives with respect to this displacement? Sure. Does it have something to do with physical frequency? As a term in correction formula. Is it part of Counterpoise correction? If it's not, we'll just have to adjust the definitions. >as I understand Counterpoise, it can only be used to calculate wavefunction >properties (e.g. the energy, but not the Hessian). OK, a derivative of a sum equals the sum of the derivative, doesn't it? So to get Hessian of the corrected energy you'll need Hessians of all the corrections... And if not all the corrections have physical meaning, blame your bais for that. Artem ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From chemistry-request@server.ccl.net Fri Jan 28 21:22:31 2000 Received: from canter-n-siegel.schrodinger.com (canter-n-siegel.schrodinger.com [192.156.98.248]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id VAA09769 for ; Fri, 28 Jan 2000 21:22:30 -0500 Received: (from info@localhost) by canter-n-siegel.schrodinger.com (8.8.5/8.8.5) id RAA30542 for chemistry@ccl.net; Fri, 28 Jan 2000 17:23:41 -0800 From: Schrodinger Info account Message-Id: <200001290123.RAA30542@canter-n-siegel.schrodinger.com> Subject: ANNC: MOPAC Users Group (MUG) Meeting To: chemistry@ccl.net Date: Fri, 28 Jan 2000 17:23:41 -0800 (PST) X-Mailer: ELM [version 2.5 PL0b2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit MOPAC USER GROUP (MUG) MEETING In reponse to demand from many users worldwide, the first MOPAC user group meeting has been arranged for the Spring 2000 ACS meeting in San Francisco. All users of any version of MOPAC or any other semiempirical quantum mechanics package are welcome to attend. Dr. James J. P. Stewart, the author of MOPAC, will host a general MOPAC Q & A session, and he will also review some of the recent enhancements to the program. All MOPAC users are also invited to present their applications at the MUG (submission details at www.schrodinger.com). DATE: Saturday, March 25, 2000, 2 - 5 PM. VENUE: San Francisco ACS Meeting Argent Hotel - 50 Third Street, San Francisco ITINERARY: Invited and submitted papers (to be announced) This MUG meeting will be jointly sponsored by Compaq, Fujitsu, and Schrodinger and attendance is free but registration is required to ensure adequate space is available. Register on-line at www.schrodinger.com. Direct any questions or comments to Dr. Shi-Yi Liu at syl@schrodinger.com or +1 503 299-1150. MOPAC Related Talks at ACS: Please let us know if you will be giving a presentation or poster at the San Francisco ACS which includes applications of MOPAC. We will distribute a complete list at the MUG Meeting, as well as post the list on the Schrodinger web site. Send complete information including the name of the presenter, the title, date, time and location using the online template provided at http://www.schrodinger.com/Forms/present_acs.html.