From haney@netcom.com Wed Nov 16 02:26:56 1994 Received: from netcom4.netcom.com for haney@netcom.com by www.ccl.net (8.6.9/930601.1506) id BAA01724; Wed, 16 Nov 1994 01:51:45 -0500 Received: by netcom4.netcom.com (8.6.9/Netcom) id WAA23098; Tue, 15 Nov 1994 22:42:36 -0800 From: haney@netcom.com (Dr. David N. Haney) Message-Id: <199411160642.WAA23098@netcom4.netcom.com> Subject: CCL:Zn potentials in biomolecular modeling (fwd) To: CHEMISTRY@ccl.net Date: Tue, 15 Nov 1994 22:42:35 -0800 (PST) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 786 tps@iris27.biosym.com (Tom Stockfisch) writes: > > The CFF93 force field released by the Potential Energy Functions Consortium > at Biosym has parameters for Zn, as well as the metal ions > > Ca Cs Cu Fe K Li Mg Na Rb > This is a wonderful step for people who need to do simulations with ions. Could someone let us know how to get this forcefield as it does not appear to be in the $BIOSYM_LIBRARY directory of the 235 (latest?) release. -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * ************** Email - haney@netcom.com *************** From ernst@bkfug.kfunigraz.ac.at Wed Nov 16 06:27:03 1994 Received: from bkfug.kfunigraz.ac.at for ernst@bkfug.kfunigraz.ac.at by www.ccl.net (8.6.9/930601.1506) id FAA03102; Wed, 16 Nov 1994 05:51:42 -0500 Received: by bkfug.kfunigraz.ac.at (MX V4.0-1 AXP) id 26; Wed, 16 Nov 1994 11:51:44 --0100 Date: Wed, 16 Nov 1994 11:51:44 --0100 From: MARGOT To: chemistry@ccl.net CC: ernst@bkfug.kfunigraz.ac.at Message-ID: <009878D0.E473DFBD.26@bkfug.kfunigraz.ac.at> Subject: Thanks/Bader's program (aimpac) Hi again, and many thanks for many helpful replies. As some people indicated interest, I have summarized the replies below. Keywords: AIMPAC, also proaim; charge-density partitioning/analysis the replies I've received follow below. mce --------------------------- Send mail to: bader@mcmail.cis.mcmaster.ca requesting a copy of AIMPAC. ---------- bader@sscvax.cis.mcmaster.ca ------- Try BADER@MCMASTER.CA or bader@babbage.Chemistry.McMaster.CA ---------- ask Sean Howard (HOWARDST@taff.cardiff.ac.uk). He knows Bader's address and developed the Program to analyse experimental electron density from ----------- You are referring to what has been called AIMPAC and is a collection of programs some of which will be integrated into Gaussian 94 I believe. You can inquire about distribution from: Todd Keith m10!keith@uunet.uu.net Todd is a former member of Richard Bader's group. --------------- Two former members of Bader's group are now working as postdoctoral associates in Wiberg's labs, actually. Anyway, they are some of the best people to contact about getting a new copy of proaim. If your copy was old, you might find the new one significantly improved, as an additional benefit. The two people I have discussed are Dr. Jim Cheeseman and Dr. Todd Keith. There electronic mail addresses (internet) are: cheese@lorentzian.com keith@lorentzian.com ----------------------------- From MROZEK@Trurl.ch.uj.edu.pl Wed Nov 16 07:27:01 1994 Received: from if.uj.edu.pl for MROZEK@Trurl.ch.uj.edu.pl by www.ccl.net (8.6.9/930601.1506) id GAA03677; Wed, 16 Nov 1994 06:51:46 -0500 From: Received: from Trurl.ch.uj.edu.pl by if.uj.edu.pl (5.0/SMI-SVR4) id AA24103; Wed, 16 Nov 1994 12:52:00 +0100 Received: from TRURL/MAILQUEUE by Trurl.ch.uj.edu.pl (Mercury 1.13); Wed, 16 Nov 94 12:49:25 GMT+2 Received: from MAILQUEUE by TRURL (Mercury 1.13); Wed, 16 Nov 94 12:49:17 GMT+2 Organization: Faculty of Chemistry, UJ To: chemistry@ccl.net Date: Wed, 16 Nov 1994 12:49:16 MET+2 Subject: Re: CCL:shareware version of Mopac for osf/1 Priority: normal X-Mailer: Pegasus Mail v3.1 (R1a) Message-Id: <1CC9F09776C@Trurl.ch.uj.edu.pl> content-length: 605 We are using our own mofification of MOPAC 6.0 - it has been extensively changed as far as the file use and error diagnostics is concerned (I think it is more convenient to use than the standard version). Both the OSF/1 and OS/2 compiled versions are available on request. Best regards, Janusz Mrozek ==================================================== Janusz Mrozek, Department of Theoretical Chemistry & Department of Computational Methods in Chemistry Faculty of Chemistry, Jagiellonian University 3 R. Ingardena St. 30-060 Cracow, Poland ==================================================== From LONCHARICH_RICHARD_J@Lilly.com Wed Nov 16 10:27:42 1994 Received: from Lilly.com for LONCHARICH_RICHARD_J@Lilly.com by www.ccl.net (8.6.9/930601.1506) id JAA05999; Wed, 16 Nov 1994 09:35:02 -0500 Received: from DECNET-MAIL (RX82788@MCVAX0) by INET.D48.LILLY.COM (PMDF V4.3-10 #6224) id <01HJJJCP68DS0000MP@INET.D48.LILLY.COM>; Wed, 16 Nov 1994 09:34:21 -0500 (EST) Date: Wed, 16 Nov 1994 09:34:21 -0500 (EST) From: Rick Loncharich Subject: CCL:"Stereokit" Twin 35mm 3-D Slide Viewer To: CHEMISTRY@ccl.net Message-id: <01HJJJCPA91U0000MP@INET.D48.LILLY.COM> X-VMS-To: MCDEV1::IN%"CHEMISTRY@ccl.net" MIME-version: 1.0 Content-transfer-encoding: 7BIT SUBJ: "Stereokit" Twin 35mm 3-D Slide Viewer I am inquiring to see if anyone knows of a company that sells a "Stereokit" Twin 35mm 3-D Slide Viewer. This slide viewer is imported from Italy and features a screw interocular adjustment, vertical right side adjustment, and hold-up-to-the-light illumination. This device allows one to view 35mm slide stereo images of molecules. Twin format is also know as 2X2X2 format (inches) or 2X50X50 format (mm). The last place we purchased these viewers from was Reel 3-D Enterprises Inc., Culver City, CA (for about $19.95). This company is no longer in business. Your help is greatly appreciated. Rick Internet: rjl@lilly.com From: LONCHARICH RICHARD J (MCVAX0::RX82788) To: FOREIGN TRANSPORT ADDRESSEE (MCDEV1::IN%"CHEMISTRY@ccl.net") From thacher@iris158.biosym.com Wed Nov 16 12:27:04 1994 Received: from bioc1.biosym.com for thacher@iris158.biosym.com by www.ccl.net (8.6.9/930601.1506) id MAA08726; Wed, 16 Nov 1994 12:26:24 -0500 From: Received: from iris158.biosym.com by bioc1.biosym.com (5.64/0.0) id AA21401; Wed, 16 Nov 94 09:25:53 -0800 Received: by iris158.biosym.com via SMTP (931110.SGI/930416.SGI) for @bioc1.biosym.com:chemistry@ccl.net id AA28166; Wed, 16 Nov 94 09:26:03 -0800 Message-Id: <9411161726.AA28166@iris158.biosym.com> To: chemistry@ccl.net Subject: CCL:Zn potentials in biomolecular modeling Date: Wed, 16 Nov 94 09:26:02 -0800 chelle@picard.niehs.nih.gov (Rachelle J. Bienstock) writes: > I would like to know what people have been using for Zn potentials in > modeling Zn containing proteins. I have noticed that none of the Biosym > forcefields nor AMBER contains potentials for Zn. The ESFF force field recently released by Biosym has parameters for Zn. The force field is a broad rule-based force field which covers the periodic table to Randon (86). From woolft@ERE.UMontreal.CA Wed Nov 16 17:27:07 1994 Received: from condor.CC.UMontreal.CA for woolft@ERE.UMontreal.CA by www.ccl.net (8.6.9/930601.1506) id QAA12311; Wed, 16 Nov 1994 16:34:06 -0500 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA22241 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Wed, 16 Nov 1994 16:32:29 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA04497; Wed, 16 Nov 94 16:32:28 -0500 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA24426; Wed, 16 Nov 94 16:32:27 -0500 Date: Wed, 16 Nov 94 16:32:27 -0500 From: woolft@ERE.UMontreal.CA (Serv. Cyber Usagers Sans Categorie) Message-Id: <9411162132.AA24426@cyclone.ERE.UMontreal.CA> To: chemistry@ccl.net Subject: CCL: optimizing code for SGI Challenge I'm wondering if anyone has experience in optimizing molecular dynamics code to take advantage of the cache space on the new SGI Challenge machines. In principle, the Challenge machine should be capable of a large speed-up over the R440 machines if the code is optimized. Does anyone have experience working on this? I would be happy to summarize to the net if people want to reply directly to me. Thanks! From jle@world.std.com Wed Nov 16 19:27:07 1994 Received: from europe.std.com for jle@world.std.com by www.ccl.net (8.6.9/930601.1506) id SAA14134; Wed, 16 Nov 1994 18:30:20 -0500 Received: from world.std.com by europe.std.com (8.6.8.1/Spike-8-1.0) id SAA12553; Wed, 16 Nov 1994 18:30:18 -0500 Received: by world.std.com (5.65c/Spike-2.0) id AA28326; Wed, 16 Nov 1994 18:30:38 -0500 Date: Wed, 16 Nov 1994 18:30:38 -0500 From: jle@world.std.com (Joe M Leonard) Message-Id: <199411162330.AA28326@world.std.com> To: chemistry@ccl.net Subject: LogP estimation questions Folks, Kantola, Villar and Loew discuss an atom-based method for estimating Log P for molecules containing H, C, N, O, F and Cl. The specific reference is "Atom Based Parameterization for a Conformationally Dependent Hydrophobic Index", A. Kantols, H. O. Villar and G. H. Loew, J. Comp. Chem. 12, 681(1991). I have several questions about this work, and I hope somebody familiar with it is reading... 1) It refers to Van der Waals radii from Gavezzotti, J. Am. Chem. Soc. 105, 5220(1983). Does anybody have these numbers on-line or at hand to post or email them? The article implies that there are differences with these values as compared with "typical" values, and I am curious (havving spent some time collecting VdW radii). 2) Has there been any corrections to this work? If I compare my results against those published in the article, the results for F-containing compounds seem VERY different. 3) Has this work been extended to additional atoms? A later review article (Viswanadhan et al, J. Comp. Chem. 14, 1019(1993)) does not refer to this work. 4) This work refers to the total charge of individual atoms. In order to reproduce the published results, I have to substitute the valence charge (particularly for Cl). This discrepancy, coupled with the fact that MNDO and AM1 are being used, suggests the valence charge was used without explicit reference. Is this correct? I would appreciate any comments from folks interested in log-P estimation, particularly in regards to non-database methods (atom or fragment QSAR models, etc). Thanks in advance, Joe Leonard jle@world.std.com From sunger@crl.com Wed Nov 16 22:27:10 1994 Received: from mail.crl.com for sunger@crl.com by www.ccl.net (8.6.9/930601.1506) id WAA16410; Wed, 16 Nov 1994 22:06:55 -0500 Received: from crl7.crl.com by mail.crl.com with SMTP id AA17300 (5.65c/IDA-1.5 for ); Wed, 16 Nov 1994 19:06:18 -0800 Received: by crl7.crl.com id AA03620 (5.65c/IDA-1.5); Wed, 16 Nov 1994 19:06:25 -0800 Date: Wed, 16 Nov 1994 19:06:25 -0800 (PST) From: Stefan Unger To: Joe M Leonard Cc: chemistry@ccl.net Subject: Re: CCL:LogP estimation questions In-Reply-To: <199411162330.AA28326@world.std.com> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > I would appreciate any comments from folks interested in log-P estimation, > particularly in regards to non-database methods (atom or fragment QSAR > models, etc). If you mean by "atom or fragment QSAR" that you dont want additive substituent models (like CLOGP from Hansch and Leo, or Rekker's method), then there is a commercially available package (which I happen to sell...) called SciLogP (and also SciLogW for solubility estimation) which is an implimentation of Bodor's method. This uses an open regression model, based on a database, but is not "additive" in the same sense as the CLOGP method. Another old-by-now "computational" method was by Hopfinger, for example. And, HyperChem (which I also sell...) has Crippen and Ghose method. I hope this helps. From mrigank@imtech.ernet.in Wed Nov 16 23:27:10 1994 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.9/930601.1506) id XAA16828; Wed, 16 Nov 1994 23:13:14 -0500 Received: (from root@localhost) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with UUCP id JAA04959 for chemistry@ccl.net; Thu, 17 Nov 1994 09:42:57 +0500 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA14660; Wed, 16 Nov 94 00:09:21+050 Message-Id: <9411151909.AA14660@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Tue, 15 Nov 94 22:16:38 +0530 Date: Tue, 15 Nov 94 22:16:38 +0530 From: Mrigank To: chemistry@ccl.net Subject: Protein Structure/COnformational Analysis ? Hi everyone I am looking for the programs/algorithms/references regarding protein structure analysis. I mean the analysis of various conformational features by which we can compare two proteins, Can comment on flexibility/accesibility or get other topological/geometrical feauters. I remember P-Curve long back but do not have a ready reference or address of source to get it. In case of programs I am mainly interested in PD stuff, but will appreciate commercial also and may even go for it if budget permit. Thanks Mrigank ---- Mrigank \/Phone +91 172 49057 Institute of Microbial Technology /\Email: mrigank@imtech.ernet.in Sector 39A, \/FAX: +91 172 40958, +91 172 28032 Chandigarh 160 014 India. /\ ==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+ -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran