From hou@agouron.com Tue Mar 28 01:39:16 1995 Received: from agouron.com for hou@agouron.com by www.ccl.net (8.6.10/930601.1506) id BAA02088; Tue, 28 Mar 1995 01:31:46 -0500 Received: from duck by agouron.com via ESMTP (950215.SGI.8.6.10/930901.SGI) for <@tbone.agouron.com:CHEMISTRY@ccl.net> id WAA07494; Mon, 27 Mar 1995 22:31:04 -0800 Received: by duck (950221.405.SGI.8.6.10/931108.SGI.ANONFTP) for CHEMISTRY@ccl.net id WAA23111; Mon, 27 Mar 1995 22:31:41 -0800 Date: Mon, 27 Mar 1995 22:31:41 -0800 From: hou@agouron.com (Xinjun Hou) Message-Id: <199503280631.WAA23111@duck> To: CHEMISTRY@ccl.net Subject: Metal ions on protein structures Hi Netters: Is there any study or analysis of the structural patterns (bond network) of metal ions in protein/enzyme structures, for example on structures in PDB? I would appreciate very much for references on this topic. I will make a summary if there is enough interests. Thank you Xinjun C Xinjun J. Hou hou@agouron.com C Agouron Pharmaceuticals, Inc. San Diego, CA 92121 C10110000110100101101110011010100111010101101110010010000110111101110101 From aiba@ir.phys.chem.ethz.ch Mon Mar 27 16:52:47 1995 Received: from bernina.ethz.ch for aiba@ir.phys.chem.ethz.ch by www.ccl.net (8.6.10/930601.1506) id QAA03552; Mon, 27 Mar 1995 16:52:42 -0500 Received: from volta (actually volta.ethz.ch) by bernina.ethz.ch with SMTP inbound; Mon, 27 Mar 1995 23:52:32 +0200 Date: Mon, 27 Mar 1995 23:51:56 +0200 Message-Id: <95032723515588@ir.phys.chem.ethz.ch> From: aiba@ir.phys.chem.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zurich) To: chemistry@ccl.net, AMFERREIRA@msuvx2.memphis.edu Subject: Re: Complex Valued Hartree-Calculations X-VMS-To: smtp%"chemistry@ccl.net" X-VMS-Cc: AIBA smtp%"AMFERREIRA@msuvx2.memphis.edu" Dear Netters, I think the question posted by Antonio M. Ferreira is a very interesting one. Should I dare to pass this discission on to our list ? Here is his original question and my (perhaps a bit hastily made) reply. Sincerely, Ayaz Bakasov. > Date: 27-MAR-1995 22:22:28.46 > From: ETHZ::""Antonio M. Ferreira" > " > Subj: Complex Valued Hartree-Calculations > To: chem-comp@mailbase.ac.uk > > I am looking for any information concerning > complex-valued HF calculatoins. I understand > that this has been done in the past, however > I have been unable to find the references. > I would appreciate any information out there, > particularly on such calculations using > complex basis functions leading to complex > density matricies. > >To anyone who can help me, I offer my appreciation > and sincere thanks. > >Tony > Dear Antonio M. Ferreira, I believe that the rejection of complex valued SCF in quantum chemistry is a historical mistake -- it will be eventually improved. The physical ground is that as long as the main features of molecular behavour are concerned, the Coulomb interaction is the leading one - it strongly dominates other interactions like spin-orbit or hyperfine. The Coulomb interaction (taken solely) produces a wave function which has a GLOBAL complex phase which can be put equal to zero everywhere in configuration space (at zero external fields). ONLY magnetic interactions lead to the physical necessity to compexify the wave function and to introduce LOCAL complex phase which depends on coordinates. For instance, in NMR it is a routine to use complex wave functions in ab initio calculations though the magnetic fields are EXTERNAL. Take as example the IGLO package. There are internal magnetic fields but the bulk of quantum chemists believe that they are not significant for most of applications. It is a prejudice and chemists have no motivation to give it up yet. And they make the weather in the field -- the orthodox physicists left long time ago for high energy physics, nuclear physics and so forth (to look for "fundamental problems"), so the molecular physics was left to people who were really interested in it - to chemists. :-) So, "no need to use complex SCF" for zero external magnetic fields. No reason to laugh - one has to have more education in physics, and it will require some time to overcome the inertia to use MOSTLY real wave functions. G92 provides with quite strange means (from physical point of view) which allow to complexify wave function -- look up the manual on page 40, option 'Complex'. It has no great meaning, >from a point of view of a physicist. One idea, is however, accepted (under the pressure of Pople's authority): it is that one has to complexify wave function in the crossing region. The reference is this: J.A.Pople, "Electronic States and Wave Functions Associated with Orbital Energy Crossing" Int. J. Quantum Chem, Symposium, No.5, 175-182 (1971). Beware: it is just TECHNICAL way to avoid (or "solve", as you wish) a purely technical problem INHERENT TO MO APPROACH. It, again, has NO physical significance. I contacted MANY distinguished people in computational molecular physics or in "quantum chemistry" (asking them this "silly" question). It is a very firm consensus NOT to use complex wave functions - and no clear reason to that. I wish you to go ahead in this field and to succeed to create a good HF-code, you will find numerous users to it (I will be the first in queue :-) ). I myself regret to say that present constraints don't allow me to spend more time on this though I will be very glad to cooperate on the topic and to put on the table what I already have about it. I didn't abandon the hope yet that one day I will be working on the problem. If there will be enough material for a summary, it would be nice to have it posted, on CCL for instance. Once more, the best wishes. Sincerely, Ayaz Bakasov. From Jonathan.Connor@mailhost.mcc.ac.uk Tue Mar 28 06:09:20 1995 Received: from nessie.mcc.ac.uk for Jonathan.Connor@mailhost.mcc.ac.uk by www.ccl.net (8.6.10/930601.1506) id GAA15961; Tue, 28 Mar 1995 06:00:04 -0500 Message-Id: <199503281100.GAA15961@www.ccl.net> Received: from mailhost.mcc.ac.uk by mailhost.mcc.ac.uk id <13003-0@mailhost.mcc.ac.uk>; Tue, 28 Mar 1995 11:59:29 +0100 Subject: meeting at UMIST To: chemistry@ccl.net Date: Tue, 28 Mar 1995 11:59:24 +0100 (BST) X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1959 From: Jonathan Connor Sender: Jonathan.Connor@mailhost.mcc.ac.uk Forwarded message: Delivery-Date: Tue, 28 Mar 1995 10:04:06 +0100 Date: Tue, 28 Mar 95 09:50:15 BST Message-Id: <340.9503280850@dir.mcc.ac.uk> To: chest-isi@mailbase.ac.uk From: awhit@dir.mcc.ac.uk X-List: chest-isi@mailbase.ac.uk Reply-To: awhit@dir.mcc.ac.uk Sender: chest-isi-request@mailbase.ac.uk Precedence: list Workshop on Chemical Information Retrieval UMIST 4 & 5 April 1995 This 2 day workshop is aimed at chemists and information specialists who wish to be introduced to or brought up-to-date with a broad range of both structure and keyword based chemical information retrieval systems. Emphasis will be on practical sessions (tailored to the needs of individuals), with demonstrations and hands-on access to a number of different databases provided by several hosts. We shall be using state of the art PC and Macintosh machines. Topics to be covered are: Introductions/Overview; Literature Searching - selection and use of databases, access and search methods Chemical Reactions/Transformations - viable synthetic methods and conditions when using databases Structure Searching -building molecules and substructures, and searching for them on several databases including CAS Online Spectroscopy - NMR spectra prediction, searching databases of known spectra Future Developments For details: Dr M P Coward, Chemistry Department, UMIST, PO BOX 88, Manchester M60 1QD. Tel:061 200 4491 Email: m.p.coward@umist.ac.uk Fax:061 228 1250 -- ****************************************************************************** Professor J.N.L. Connor, Phone(direct line): 061-275-4693 (national) Department of Chemistry, :+44-61-275-4693 (international) University of Manchester, Manchester M13 9PL, Phone(secretary): 061-275-4686 or 4600 England. Fax: 061-275-4734 or 4598 ****************************************************************************** From qftjesus@usc.es Tue Mar 28 10:54:24 1995 Received: from uscmail.usc.es for qftjesus@usc.es by www.ccl.net (8.6.10/930601.1506) id KAA03261; Tue, 28 Mar 1995 10:46:30 -0500 Received: by uscmail.usc.es (5.67b/1.34) id AA19007; Tue, 28 Mar 1995 17:49:45 +0200 Date: Tue, 28 Mar 1995 17:49:45 +0200 From: qftjesus@usc.es (Jesus Otero Rodriguez) Message-Id: <199503281549.AA19007@uscmail.usc.es> To: chemistry@ccl.net Subject: Organic reactivity list ? Dear netters: Anybody knows if there is a List specifically devoted to organic activity subjects??? Thanks From polowin@hyper.hyper.com Tue Mar 28 11:54:24 1995 Received: from www.hyper.com for polowin@hyper.hyper.com by www.ccl.net (8.6.10/930601.1506) id LAA07174; Tue, 28 Mar 1995 11:46:07 -0500 Received: from hyper.hyper.com (hyper.hyper.com [204.50.3.217]) by www.hyper.com (8.6.9/8.6.9) with SMTP id LAA05095 for <@www.hyper.com:CHEMISTRY@ccl.net>; Tue, 28 Mar 1995 11:40:47 -0500 Received: by hyper.hyper.com (920330.SGI/920502.SGI) for @www.hyper.com:CHEMISTRY@ccl.net id AA25864; Tue, 28 Mar 95 11:45:30 -0500 Date: Tue, 28 Mar 95 11:45:30 -0500 From: polowin@hyper.hyper.com (Joel Polowin) Message-Id: <9503281645.AA25864@hyper.hyper.com> To: CHEMISTRY@ccl.net Subject: Re: Molecular Modeling Packages for ALPHA systems My predecessor on customer support, Graham Hurst, corrected errors that I made in a recent posting: > At the moment, the software that we have for the DEC Alpha is the back-end > modules, which let the heavy number-crunching be off-loaded from the > PC front end to a network-linked UNIX box. We can work under OSF/AXP 1.2; > under NT or USF but not on a DEC VAX. (The back-end modules are also > available for SGI Irix 4.0 to 4.0.5F and 5.2, and IBM AIX 3.2.5 and 4.0 .) In fact, we have a version of HyperChem for Windows NT on the DEC Alpha; it is the complete software package, functionally the same as the Windows version. We do not have backends that run under NT, though the NT version can run backends on other systems. I apologize for the errors. Regards, Joel ------------ Joel Polowin, Ph.D. Manager, Scientific Support Email to: polowin@hyper.com Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com From tripos!rigel!david@uunet.uu.net Tue Mar 28 12:54:24 1995 Received: from relay3.UU.NET for tripos!rigel!david@uunet.uu.net by www.ccl.net (8.6.10/930601.1506) id MAA11040; Tue, 28 Mar 1995 12:49:30 -0500 Received: from uucp5.UU.NET by relay3.UU.NET with SMTP id QQyjat10576; Tue, 28 Mar 1995 12:49:28 -0500 Received: from tripos.UUCP by uucp5.UU.NET with UUCP/RMAIL ; Tue, 28 Mar 1995 12:49:28 -0500 Received: from rigel.tripos by tripos (4.1/SMI-4.0) id AA01968; Tue, 28 Mar 95 11:22:46 CST Received: by rigel.tripos (940816.SGI.8.6.9/5.6) id RAA23839; Tue, 28 Mar 1995 17:23:18 GMT Date: Tue, 28 Mar 1995 17:23:18 GMT From: tripos!rigel!david@uunet.uu.net (David Mosenkis) Message-Id: <199503281723.RAA23839@rigel.tripos> To: uunet!ccl.net!chemistry@uunet.uu.net Subject: Residue Based Solvent Accessible Area > Can anyone out there tell me where I can get a program for calculating > the solvent accessible area for each individual residue in a given protein? Weifan, The upcoming 6.2 release of Sybyl from Tripos includes a new module called ProTable for the analysis of protein structures. In addition to numerous other quantities, ProTable displays the relative solvent accessibility of each residue in a protein structure. It uses the latest version of SAVOL developed by Bob Pearlman and colleagues at the University of Texas, Austin to compute the solvent accessibile surface areas. Let me know if you'd like more information. David Mosenkis (david@tripos.com) From shenkin@still3.chem.columbia.edu Tue Mar 28 19:54:30 1995 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.10/930601.1506) id TAA14489; Tue, 28 Mar 1995 19:40:55 -0500 Received: from still3.chem.columbia.edu by mailhub.cc.columbia.edu with SMTP id AA14878 (5.65c+CU/IDA-1.4.4/HLK for <@mailhub.cc.columbia.edu:chemistry@ccl.net>); Tue, 28 Mar 1995 19:40:50 -0500 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for @mailhub.cc.columbia.edu:chemistry@ccl.net id AA26623; Tue, 28 Mar 95 18:58:33 -0500 From: "Peter Shenkin" Message-Id: <9503281858.ZM26621@still3.chem.columbia.edu> Date: Tue, 28 Mar 1995 18:58:32 -0500 In-Reply-To: gilson@indigo14.carb.nist.gov (Michael K. Gilson) "CCL:Predicting protein-ligand structures." (Mar 27, 3:39pm) References: <9503272039.AA16041@indigo14.carb.nist.gov> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: gilson@indigo14.carb.nist.gov (Michael K. Gilson), chemistry@ccl.net Subject: Re: CCL:Predicting protein-ligand structures. Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Mar 27, 3:39pm, Michael K. Gilson wrote: > Subject: CCL:Predicting protein-ligand structures. > Given a flexible ligand and a relatively rigid protein whose 3-D > structure in the absence of the ligand is known, is there a way of > reliably generating a several-thousand member (or smaller) set of > protein-ligand complex structures, which is highly likely to include > something close (say 1.5 Angstrom RMSD) to the true structure of the > complex? Hi, Mike, Any molecular mechanics program which can do a conformational search in a multimolecular context (i.e., varying the relative positions/ orientation of the molecules as well as internal degrees of freedom) can generate such an ensemble. The question that arises is: "Which of the several thousands of docking configurations produces are 'important'?" If one is to try to reliably pick the best configurations out of the ensemble, much may hinge on how well solvent effects are handled, and on how well the relative free- energies can be obtained, or can be reliably correlated with the molecular- mechanics energies. In any case, MacroModel/BatchMin can do this type of calculation, using an implicit solvation model based in part on your own work! I'm sure other programs address this problem as well. -P. -- ************************ The secret of life: ************************* *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* * New York, NY 10027; shenkin@columbia.edu; (212) 854-5143 * ************* If you find a loose thread, don't pull it. ************* From leem@indigo.ucdavis.edu Tue Mar 28 16:52:36 1995 Received: from franc.ucdavis.edu for leem@indigo.ucdavis.edu by www.ccl.net (8.6.10/930601.1506) id QAA05787; Tue, 28 Mar 1995 16:52:33 -0500 Received: from indigo.ucdavis.edu by franc.ucdavis.edu (8.6.11/UCD3.4) id NAA03524; Tue, 28 Mar 1995 13:52:01 -0800 Received: by indigo.ucdavis.edu (920330.SGI/920502.SGI.AUTO) for @smtp.ucdavis.edu:chemistry@ccl.net id AA02703; Tue, 28 Mar 95 13:52:28 -0800 Date: Tue, 28 Mar 95 13:52:28 -0800 From: leem@indigo.ucdavis.edu (Mary Lee) Message-Id: <9503282152.AA02703@indigo.ucdavis.edu> To: chemistry@ccl.net Subject: fermi contact analysis Is anyone out there familiar w/ "Fermi Contact analysis?" Thx, Mary Lee leem@indigo.ucdavis.edu