From hughc@extro.ucc.su.oz.au Fri Oct 7 01:17:53 1994 Received: from extra.ucc.su.OZ.AU for hughc@extro.ucc.su.oz.au by www.ccl.net (8.6.9/930601.1506) id AAA22554; Fri, 7 Oct 1994 00:23:40 -0400 Received: from hugh (hugh.pharmacol.su.OZ.AU [129.78.41.50]) by extra.ucc.su.OZ.AU (8.6.8.1/8.6.9) with SMTP id OAA10503 for ; Fri, 7 Oct 1994 14:23:25 +1000 Message-Id: <199410070423.OAA10503@extra.ucc.su.OZ.AU> X-Sender: hughc@postbox.su.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 07 Oct 1994 14:23:12 +1100 To: chemistry@ccl.net From: hughc@extro.ucc.su.OZ.AU (Hugh Capper) Subject: MOPAC 6.0 or 93 for NT X-Mailer: Dear CCLers, Does somebody know where I could obtain a Windows NT or Win32s compiled version either MOPAC 6.0 or 93? Thanks for the help, Hugh Capper From jkl@ccl.net Fri Oct 7 01:21:41 1994 Received: for jkl@ccl.net by www.ccl.net (8.6.9/930601.1506) id AAA22604; Fri, 7 Oct 1994 00:33:39 -0400 Date: Fri, 7 Oct 1994 00:33:39 -0400 From: Jan Labanowski Message-Id: <199410070433.AAA22604@www.ccl.net> To: chemistry@ccl.net Subject: Chemistry related electronic lists Cc: jkl@ccl.net Dear Netters, I am coautoring a chapter in the ACS book: Chemistry on Internet and I need your help. I would like to present an overview of the chemistry related electronic lists. I contacted many people and did my job searching, but I am sure that I missed many active and good lists. When I am done, I will provide/announce the full list in the archives. I ALREADY HAVE information on the following lists (so you do not need to send me info): ANNEAL - simulated annealing; anneal-request@cs.ucla.edu Bucky; bucky@sol1.lrsm.upenn.edu charmm; harmm-bbs-request@emperor.harvard.edu ChE ELECTRONIC NEWSLETTER; sangkim@luther.che.wisc.edu Chemistry Telementoring; chemistrytm-request@dhvx20.csudh.edu CHMINF-L; LISTSERV@IUBVM.INDIANA.EDU CICOURSE; LISTSERV@IUBVM.INDIANA.EDU HyperChem; hyperchem-request@hyper.com Interfacial Phenomena" (INTERF-L); listserv@taunivm.tau.ac.il MMODINFO; DSMITH@uoft02.utoledo.edu Org-Geochem; mailbase@mailbase.ac.uk orgchem parallel molecular dynamics; pmd-request@cumbnd.bioc.columbia.edu Pharmacy Mail Exchange; pharm-request@dmu.ac.uk QUANTA-L, C2-L, XPLOR-L; listproc@msi.com sybyl Water Science Network (WSN); listserv@unc.edu WATOC; listserver@ic.ac.uk wmcic-l (women in Chemistry in Canada list); Listserv@qucdn.queensu.ca If you know about other active lists please send me the: Name of the list Address of the list coordinator/administrator. Jan Labanowski jkl@ccl.net From sanja@indigo.irb.hr Fri Oct 7 05:18:00 1994 Received: from indigo.irb.hr for sanja@indigo.irb.hr by www.ccl.net (8.6.9/930601.1506) id EAA23875; Fri, 7 Oct 1994 04:49:32 -0400 From: Received: by indigo.irb.hr (920330.SGI/920502.SGI) for CHEMISTRY@ccl.net id AA04459; Fri, 7 Oct 94 09:44:00 +0200 Date: Fri, 7 Oct 94 09:44:00 +0200 Message-Id: <9410070744.AA04459@indigo.irb.hr> To: CHEMISTRY@ccl.net Subject: help_on_NBO Hello, I am trying to do NBO (Natural Bond Orbital) analysis within Gaussian92. I used resonance keyword to allow strongly delocalized NBO set. In the middle of calculations following warning appear: Population inversion found on atom C1 Population inversion found on atom C2 Population inversion found on atom H Population inversion found on atom Cl Population inversion found on atom O I am not sure I understand what happend hier. Can somebody give me some hints or comments on that? Thank you for your help in advance Sanja ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Sanja Sekusak Rudjer Boskovic Institute Phone: (385-41) 46 10 89 P.O.B. 1016 Fax: (385-41) 27 26 48 Zagreb, Croatia E-mail: sanja@indigo.irb.hr ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From g112976@iris.ufscar.br Fri Oct 7 11:18:05 1994 Received: from fpsp.fapesp.br for g112976@iris.ufscar.br by www.ccl.net (8.6.9/930601.1506) id KAA27848; Fri, 7 Oct 1994 10:41:47 -0400 Received: from merak.fapesp.br by fpsp.fapesp.br with PMDF#10108; Fri, 7 Oct 1994 11:39 BSC (-0300 C) Received: from power.ufscar.br by merak.fapesp.br with PMDF#10108; Fri, 7 Oct 1994 11:00 BSC (-0300 C) Received: from iris.ufscar.br by power.ufscar.br via SMTP (931110.SGI/911001.SGI) for @fpsp.fapesp.br:CHEMISTRY@oscsunb.ccl.net id AA03786; Fri, 7 Oct 94 11:02:17 -0200 Received: by iris.ufscar.br (920110.SGI/911001.SGI) for @power.ufscar.br:CHEMISTRY@oscsunb.ccl.net id AA07180; Fri, 7 Oct 94 11:04:32 -0200 Date: Fri, 7 Oct 94 11:04:32 -0200 From: g112976@iris.ufscar.br (Augusto C. C. Neto) Subject: Contact V.R. To: CHEMISTRY@oscsunb.ccl.net Message-id: <9410071304.AA07180@iris.ufscar.br> X-Envelope-to: CHEMISTRY@oscsunb.ccl.net Federal University of Sao Carlos, October 4, 1994 Hi netters !! I would like to contact groups wich are using Virtual Reality in Chemistry ... Send answer right to me please ... Thank you .... Augusto Cesar From waller@thor.herl.epa.gov Fri Oct 7 12:18:01 1994 Received: from thor.herl.epa.gov for waller@thor.herl.epa.gov by www.ccl.net (8.6.9/930601.1506) id LAA28320; Fri, 7 Oct 1994 11:23:25 -0400 Received: by thor.herl.epa.gov (931110.SGI/1.34) id AA06544; Fri, 7 Oct 94 08:36:05 -0400 Date: Fri, 7 Oct 1994 08:36:05 -0400 (EDT) From: "Dr. Chris L. Waller" Sender: "Dr. Chris L. Waller" Reply-To: "Dr. Chris L. Waller" Subject: PB-PK Models To: COMP CHEM Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear CCLers: At EPA, in the Environmental Toxicology Division, there is a group dedicated to developing physiologically-based pharmacokinetic-models (PB-PK) - thus the name of the Branch to which I belong. In short, a PB-PK model attempts to model uptake, distribution, and elimintion of chemicals (toxic or pharmacologic) by representing the body as a series of compartments (lung, heart, liver, etc.) connected in parallel. Factors such as blood flow rates and tissue:blood partition coefficients for given chemicals are included as terms in differential equations which are solved simulataneously to model the system. I know, you are asking, what does this have to do with Comp Chem? Well, PB-PK models are typically single chmeical specific (i.e. a model works for chloroform and that's it!). When one wants to develop a model for carbontetrachloride, let's say, one goes to the lab and kills rats or whatever to determine the specific partitioning and metabolic rate constants, etc. for this chemical. Not very efficient. I have been interested in using QSARs/QSPRs to allow the application of a model developed for one chemical to be used for an entire congerneric series of chemcials. So far, clogP can be used to "predict" fat:blood and liver:blood partitioning pretty well. I have some other techniques which predict metabolic rate constants and such. So far, this is going OK. The major bottleneck seems to be with the PB-PK modeling packages themselves. I am spoiled by the admittedly debatable "user friendliness" of most of the commercial molecular modeling packages. PB-PK modeling packages are not quite as friendly (at least the few that I have access to aren't). We have ACSL (which runs on a PC or a VAX) and another package called SimuSol (which runs on a VAX). My questions are (1) do any other molecular modelers have an interest in or know of anyone doing work of the type described above (i.e. using molecular modeling concepts to extend PB-PK models) and (2) what other PB-PK packages are commercially available/in-use in the pharmaceutical company/academic environment? The desired answer to this latter question is of course "Why yes we have a package that runs on an Unix box with an X-windows interface which is extremely friendly named ________ (fill in the blank)." CW ******************************************************************** *Chris L. Waller, Ph.D. PHONE 919-541-7976* *Research Chemist FAX 919-541-5394* *waller@thor.herl.epa.gov * *Pharmacokinetics Branch (MD-74) * *ETD/HERL/USEPA * *Research Triangle Park, NC 27711 * * * *Disclaimer: Mention of trade names or products does not constitute* *endorsement by the United States Environmental Protection Agency. * ******************************************************************** From shenkin@still3.chem.columbia.edu Fri Oct 7 12:19:25 1994 Received: from still3.chem.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.9/930601.1506) id LAA28373; Fri, 7 Oct 1994 11:27:15 -0400 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA18373; Fri, 7 Oct 94 11:26:51 -0400 From: "Peter Shenkin" Message-Id: <9410071125.ZM18371@still3.chem.columbia.edu> Date: Fri, 7 Oct 1994 11:25:51 -0400 In-Reply-To: biosym.com!biosym.com!tony (Tony Schmidt) "CCL:implicit solvation" (Oct 6, 9:58am) References: <9410061358.AA11236@east1.biosym.com> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: tony@biosym.com, chemistry@ccl.net Subject: Re: CCL:implicit solvation Cc: tony@biosym.com, lchiche@cbs.univ-montp1.fr Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Oct 6, 9:58am, Tony Schmidt wrote: > >Conclusion of the summary was: > > >> Finally, when using the "Eisenberg" approach of surface area changes and > >> atomic solvation parameters: > >> > >> 1) It is currently unclear as to what is the most appropriate > >> set of atomic solvation parameters to use for docking > >> or protein folding. > >> > >> 2) Given the potential benefits of such a calculation there > >> seem to be surprisingly few tests of this method. > ... > The paper "A CFF91-based continuum solvation model: solvation free energies > of small molecules and conformations of the alanine dipeptide in solution" > by A.B.Schmidt and R.M.Fine to be published in Molecular Simulation, 1994. > > In particular, we have shown that the Wesson-Eisenberg model used in [7] > provides the differences in the solvation energies of the alanine dipeptide > within the full Ramachandran map not exceeding 4 kcal/mol while the > Poisson-Boltzmann approach exhibits the difference between C7 axial and > alpha L minima of about 9 kcal/mol (not to mention energy maxima). I don't quite follow you. Are you saying that W-E gets things right to +/- 4 kcal/mol whereas P-B gets things right to only +/- 9 kcal/mol? If this isn't what you're saying, what are you saying? I'd have expected P-B to do better than W-E. It is interesting to try to define test cases which will exhibit differences in rank-orderings of free-energy (including solvation) when calculated using: distance-dependent dielectric purely surface-based methods, such as W-E continuum models, such as P-B, or GB/SA explicit solvent. I list this in order of probable "maximum attainable quality", which corresponds to the the order of increasing difficulty of implementation. As an example, here is a situation which a W-E model should get wrong, but a continuum model could get right: -- -- | | | | | | Different sorts | | B---| | of side-chain | |---A (charged external | | packing can | | (charged external sidechain | | happen in here. | | sidechain) | | | | | | | | | ---------------------- | | (funny U-shaped protein) | ---------------------------- The question is: How do the optimal conformations of A and B vary, according to what happens to the sidechains in the cavity? All a surface-based solvation model does is to try to optimize the solvent exposure of A and B with respect to their immediate local environments. But the dielectric shielding between A and B depends importantly on the dielectric constant in the cavity, which, even ignoring fluctuations, depends on how much water is in there. The work of Gilson and Honig points out other situations which share the same feature: the solvation energy (and the optimal conformation) of a charged group can depend upon what happens in a remote location. I believe that more recent work by Anthony Nicholls and Marilyn Gunner shows that this can be important in real proteins as well as in concocted models. -P. -- *********** World music: What bluegrass is to a Bulgarian. ********** *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* * New York, NY 10027; shenkin@columbia.edu; (212) 854-5143 * **** If Sammy the Bull can turn Rat, who can feel safe any more? ***** From WALKERD@sask.usask.ca Fri Oct 7 13:18:02 1994 Received: from skycat.usask.ca for WALKERD@sask.usask.ca by www.ccl.net (8.6.9/930601.1506) id MAA29900; Fri, 7 Oct 1994 12:57:11 -0400 From: Received: from SKYCAT.USask.CA by SKYCAT.USask.CA (PMDF V4.3-11 #5952) id <01HHZQN1KPNK8WWH7G@SKYCAT.USask.CA>; Fri, 07 Oct 1994 10:57:00 -0600 (CST) Date: Fri, 07 Oct 1994 10:56:59 -0600 (CST) Subject: avs on a decalpha To: CHEMISTRY@ccl.net Message-id: <01HHZQN1N4GI8WWH7G@SKYCAT.USask.CA> X-Envelope-to: CHEMISTRY@ccl.net X-VMS-To: IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT Hello, WE are considering buying a DEC alpha system for our computational chemsitry group. I need to know if AVS or another similar visualization package is available for the alpha systems running OSF, if they are available, what the academic pricing is, and finally how is the performace for generation of isosurfaces. I am especially interested in avs with the chemistry viewer added. all information appreciated Duane Walker Mathematical Chemistry Research Unit University of Saskatchewan Saskatoon, Saskatchewan, Canada walkerd@usask.sask.ca From biosym.com!tony@biosym.com Fri Oct 7 14:18:04 1994 Received: from bioc1.biosym.com for biosym.com!tony@biosym.com by www.ccl.net (8.6.9/930601.1506) id NAA00492; Fri, 7 Oct 1994 13:21:31 -0400 Received: from biosym.com by bioc1.biosym.com (5.64/0.0) id AA04574; Fri, 7 Oct 94 10:09:21 -0700 Received: by east1.biosym.com (920330.SGI/920502.SGI) for bioc1!still3.chem.columbia.edu!shenkin id AA15483; Fri, 7 Oct 94 13:01:51 -0400 Date: Fri, 7 Oct 94 13:01:51 -0400 From: biosym.com!tony@biosym.com (Tony Schmidt) Message-Id: <9410071701.AA15483@east1.biosym.com> To: "Peter Shenkin" Subject: Re: CCL:implicit solvation Cc: chemistry@ccl.net Reply-To: biosym.com!tony@biosym.com References: <9410061358.AA11236@east1.biosym.com> Peter Shenkin writes: > The paper "A CFF91-based continuum solvation model: solvation free energies > of small molecules and conformations of the alanine dipeptide in solution" > by A.B.Schmidt and R.M.Fine to be published in Molecular Simulation, 1994. > > In particular, we have shown that the Wesson-Eisenberg model used in [7] > provides the differences in the solvation energies of the alanine dipeptide > within the full Ramachandran map not exceeding 4 kcal/mol while the > Poisson-Boltzmann approach exhibits the difference between C7 axial and > alpha L minima of about 9 kcal/mol (not to mention energy maxima). I don't quite follow you. Are you saying that W-E gets things right to +/- 4 kcal/mol whereas P-B gets things right to only +/- 9 kcal/mol? If this isn't what you're saying, what are you saying? I'd have expected P-B to do better than W-E. ------------------------------------------------------------------------ We certainly believe P-B approach is more accurate than W-E. For the alanine dipeptide, W-E provides rather flat Ramachandran map, i.e.the difference between the maximum and minimum conformational energy is about 4 kcal/mol. P-B yields much more pronounced energetic profile. Tony Schmidt tony@biosym.com From elcana@iqm.unicamp.br Fri Oct 7 17:18:07 1994 Received: from circe.iqm.unicamp.br for elcana@iqm.unicamp.br by www.ccl.net (8.6.9/930601.1506) id QAA04486; Fri, 7 Oct 1994 16:51:30 -0400 Received: (elcana@localhost) by circe.iqm.unicamp.br (8.6.8/8.3) id RAA04350; Fri, 7 Oct 1994 17:42:24 -0300 From: Anselmo Elcana de Oliveira Message-Id: <199410072042.RAA04350@circe.iqm.unicamp.br> Subject: colligative property To: CHEMISTRY@ccl.net Date: Fri, 7 Oct 1994 17:42:23 -0300 (EST) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 278 Hi netters, I'm looking for a computer program for evaluation of colligative property equilibrium data. all information appreciated Thanks, Elcana elcana@iqm.unicamp.br Universidade Estadual de Campinas - Unicamp Departamento de Fisico-Quimica Campinas - SP Brasil From regina@lioness.cm.utexas.edu Fri Oct 7 19:18:05 1994 Received: from lioness.cm.utexas.edu for regina@lioness.cm.utexas.edu by www.ccl.net (8.6.9/930601.1506) id SAA05648; Fri, 7 Oct 1994 18:40:45 -0400 Received: by lioness.cm.utexas.edu (4.1/SMI-4.1) id AA14898; Fri, 7 Oct 94 17:44:08 CDT Date: Fri, 7 Oct 94 17:44:08 CDT From: regina@lioness.cm.utexas.edu (Regina Monaco) Message-Id: <9410072244.AA14898@lioness.cm.utexas.edu> To: CHEMISTRY@ccl.net Subject: A counterion utility for macs Hello Netters! We have written a Mac application, CounterIon 1.0, which will place counterions around a DNA helix (from a pdb file format). This may be useful to users of CHARMm and INSIGHT, as well as any other molecular modellers who may be interested. We are prepared to do bugfixes, please send comments to the email address in the README file. It is in anonymous ftp at: lioness.cm.utexas.edu Regina R. Monaco Tom Loomis From g112976@iris.ufscar.br Fri Oct 7 20:18:06 1994 Received: from fpsp.fapesp.br for g112976@iris.ufscar.br by www.ccl.net (8.6.9/930601.1506) id UAA06231; Fri, 7 Oct 1994 20:08:22 -0400 Received: from power.ufscar.br by fpsp.fapesp.br with PMDF#10108; Fri, 7 Oct 1994 16:08 BSC (-0300 C) Received: from iris.ufscar.br by power.ufscar.br via SMTP (931110.SGI/911001.SGI) for @fpsp.fapesp.br:CHEMISTRY@oscsunb.ccl.net id AA06012; Fri, 7 Oct 94 16:10:08 -0200 Received: by iris.ufscar.br (920110.SGI/911001.SGI) for @power.ufscar.br:CHEMISTRY@oscsunb.ccl.net id AA08573; Fri, 7 Oct 94 16:12:26 -0200 Date: Fri, 7 Oct 94 16:12:26 -0200 From: g112976@iris.ufscar.br (Augusto C. C. Neto) Subject: APOLLO programs To: CHEMISTRY@oscsunb.ccl.net Message-id: <9410071812.AA08573@iris.ufscar.br> X-Envelope-to: CHEMISTRY@oscsunb.ccl.net Federal University at Sao Carlos, october 7, 1994 Dear Netters !!! I'm looking for some softwares to run in HP APOLLO Seria 700, like : CDROM Utilities, RASMOL, Xmol, Xview and a 2D and 3D plotter from XYZ coordinates . I'm having some difficulties to compile this programs, if anyone has these in the right form to compile in APPOLOi, I'll really apreciate. Thank you ... Augusto Cesar From maxv@iserver.pdl.com Fri Oct 7 21:18:07 1994 Received: from iserver.pdl.com for maxv@iserver.pdl.com by www.ccl.net (8.6.9/930601.1506) id UAA06474; Fri, 7 Oct 1994 20:50:54 -0400 Received: from pdlmvci2.pdl.com by iserver.pdl.com (5.67/1.37) id AA18943; Fri, 7 Oct 94 17:50:52 -0700 Date: Fri, 7 Oct 94 17:50:52 -0700 Message-Id: <9410080050.AA18943@iserver.pdl.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: CHEMISTRY@ccl.net From: maxv@iserver.pdl.com (Max Vasquez) Subject: GNU graphics on IRIX 5.2 Hello, I wonder if anyone has any experience with GNU graphics (successor to GNUplot perhaps) on Silicon Graphics running IRIX 5.2 In particular, has anyone being able to build the executables and reproduce the test examples? Best regards ************************************************ Max Vasquez, PhD Protein Design Labs, Inc. 2375 Garcia Ave. Mountain View, CA 94043 (415) 903-3744 (415) 903-3730 (FAX) Internet: maxv@pdl.com *************************************************