From jmw@conti.u-strasbg.fr Thu Jul 7 05:51:05 1994 Received: from conti.u-strasbg.fr for jmw@conti.u-strasbg.fr by www.ccl.net (8.6.9/930601.1506) id EAA09736; Thu, 7 Jul 1994 04:57:49 -0400 From: Received: by conti.u-strasbg.fr; id AA02930; Thu, 7 Jul 1994 10:58:19 +0200 Message-Id: <9407070858.AA02930@conti.u-strasbg.fr> To: chemistry@ccl.net Subject: To be member of the Molecular Graphics Society Date: Thu, 07 Jul 94 10:58:18 +0200 X-Mts: smtp I would like to be member of the Molecular Graphics Society, could somebody tell me whom I should contact. Jean-Marie WURTZ Jean-Marie Laboratoire de Biologie Structurale IBMC, CNRS 15, rue Rene Descarte 67084 STRASBOURG Cedex, FRANCE Phone: 88 41 70 21 E-mail: jmw@conti.u-strasbg.fr From cletner@remcure.bmb.wright.edu Thu Jul 7 07:51:57 1994 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.9/930601.1506) id HAA10567; Thu, 7 Jul 1994 07:32:31 -0400 Received: by remcure.bmb.wright.edu (920330.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA17368; Thu, 7 Jul 94 07:22:56 -0700 Date: Thu, 7 Jul 1994 07:20:22 -0700 (PDT) From: Charles Letner Subject: Re: CCL:More on protonation states in proteins To: Computational Chemistry List In-Reply-To: <9407061831.AA25878@ucmod2.che.uc.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 6 Jul 1994, Jeffrey L. Nauss wrote: > >From chemistry-request@ccl.net Wed Jul 6 14:28:42 1994 > > > You might concider taking a > >look at this if your at all interested in protonation of proteins. > >Bashford & Gerwert (1992) L. Mol. Bio., 224, 473-486. > > Just to clarify things... > > Is this journal L. Mol. Bio. or should it be J. Mol. Biol.? > > Jeff Nauss OOP's. That would be J. Mol. Bio.! Though I hear that L. Mol. Bio. is a really up and coming journal. :) Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 e-mail: cletner@remcure.bmb.wright.edu From nauss@ucmod2.che.uc.EDU Thu Jul 7 08:51:15 1994 Received: from ROLL.SAN.UC.EDU for nauss@ucmod2.che.uc.EDU by www.ccl.net (8.6.9/930601.1506) id IAA11109; Thu, 7 Jul 1994 08:38:57 -0400 Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V4.3-8 #4918) id <01HEF30FFMOGQO9F6E@UCBEH.SAN.UC.EDU>; Thu, 07 Jul 1994 08:39:02 -0500 (EST) Received: by ucmod2.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:CHEMISTRY@ccl.net id AA03716; Thu, 7 Jul 94 08:46:49 -0400 Date: Thu, 07 Jul 1994 08:46:49 -0400 From: nauss@ucmod2.che.uc.EDU (Jeffrey L. Nauss) Subject: Re: CCL:To be member of the Molecular Graphics Society To: CHEMISTRY@ccl.net Message-id: <9407071246.AA03716@ucmod2.che.uc.edu> Content-transfer-encoding: 7BIT For information regarding membership in the MGS, try the following: Dr. R. Hubbard Department of Chemistry University of York Heslington, York Y01 5DD UK (I do not have his e-mail address.) Alternatively, try Dr. Nicole Van Opdenbosch Tripos Associates, Inc. Suite 103 St Louis, MO 63144-2913 USA e-mail: nicole@tripos.com Jeff Nauss **************************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: nauss@ucmod2.che.uc.edu * * CCCCCCC * **************************************************************************** From shenkin@still3.chem.columbia.edu Thu Jul 7 09:51:08 1994 Received: from still3.chem.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.9/930601.1506) id JAA12048; Thu, 7 Jul 1994 09:13:53 -0400 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA00036; Thu, 7 Jul 94 09:14:08 -0400 From: "Peter Shenkin" Message-Id: <9407070913.ZM34@still3.chem.columbia.edu> Date: Thu, 7 Jul 1994 09:13:42 -0400 In-Reply-To: BILL WELSH "CCL:Question about Clark Still's Generalized Born Solvation Model" (Jul 6, 6:32pm) References: <01HEE9FY5SYW8ZDVPS@SLVAXA.UMSL.EDU> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: BILL WELSH , chemistry@ccl.net Subject: Re: CCL:Question about Clark Still's Generalized Born Solvation Model Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Jul 6, 6:32pm, BILL WELSH wrote: > Subject: CCL:Question about Clark Still's Generalized Born Solvation Model > Dear Netters, > > Two questions about the GB solvation Model available in Macromodel: > > 1. The procedure uses the SA ("Surface Area") as a parameter in > calculating > the solvation free energy. What algorithm does Macromodel use to calculate > this SA term for a given molecule. Is this procedure published somewhere in > a detailed manner? The better the calculation of surface area, the better the model will work. The model is parameterized based on accurate numerical calculations of surface area for rigid molecules whose solvation free-energies are known experimentally. The MacroModel/BatchMin program can evaluate energies using this method of calculation, but during iterative procedures, such as minimization or dynamics, calculation is done using an approximate analytical method described in Hasel, Hendrickson and Still, Tetrahedron Computer Methodology, vol 1, p 103 (1988). The analytical method, which is based on earlier work by Shoshana Wodak, also gives derivatives. There are newer algorithms out there for the calculation of surface area, and we may change over to one of them. > 2. I seem to remember that Clark Still, et al., published an article > in JACS or in the J. Comput. Chem. which describes the Generalized Born > method. Can someone cite this (these) references for me? Still, Tempczyk, Hawley and Hendrickson, JACS, vol 112, p 6127 (1990). This publication does not cover our latest (analytical) method of computing the effective Born radius. Our current method will be covered in a publication by Frank Hollinger and Clark Still which is still in progress. As with surface area, the analytical method gives derivatives as well as energies. Hope all this helps.... -P. -- ******* After the revolution, everyone will have a home page... ****** *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* *New York, NY 10027; shenkin@columbia.edu; (212) 854-5143 * *** ... but the Internet will be too busy for anyone to access it. *** From raman@bioc01.uthscsa.edu Thu Jul 7 10:51:09 1994 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.9/930601.1506) id KAA13947; Thu, 7 Jul 1994 10:46:19 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Thu, 7 Jul 1994 9:50:08 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA12763; Thu, 7 Jul 94 09:47:35 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9407071447.AA12763@bioc01.uthscsa.edu> Subject: Re: Are coordinates for beta lactogloblin availabNEXTle? To: SHOHAM%CWBIO.DECNET@CWJCC.INS.CWRU.EDU (Menachem Shoham) Date: Thu, 7 Jul 1994 09:47:35 -0500 (CDT) Cc: chemistry@ccl.net In-Reply-To: <9407062055.AA14555@cwjcc.INS.CWRU.Edu> from "Menachem Shoham" at Jul 6, 94 02:04:15 pm X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1134 > Is there a structure out for beta lactoglobulin? It has been > crystallized (Papiz et al., Nature, vol. 324, 383, 1986) but I could > not find any entry in the Protein Data Bank. Any information would be A theoretical model for Apolipoprotein D (which BTW belongs to the same family as b-lactoglobulin in that it binds small hydrophobic ligands) is available at the PDB. See "2apd" if you are interested. Cheers -raman -- C.S.Raman UNIX Programming & Administration SPARC & SGI Systems raman@bioc01.uthscsa.edu - INTERNET Department of Biochemistry raman@mintaka.chpc.utexas.edu - CHPC UTHSCSA c.raman@launchpad.unc.edu 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From aiba@volta.vmsmail.ethz.ch Thu Jul 7 10:58:35 1994 Received: from bernina.ethz.ch for aiba@volta.vmsmail.ethz.ch by www.ccl.net (8.6.9/930601.1506) id JAA12850; Thu, 7 Jul 1994 09:53:01 -0400 Message-Id: <199407071353.JAA12850@www.ccl.net> Received: from VOLTA.vmsmail.ethz.ch by bernina.ethz.ch id <04416-0@bernina.ethz.ch>; Thu, 7 Jul 1994 15:53:44 +0200 X-Vms-To: ethz::"chemistry@ccl.net" To: chemistry@ccl.net From: aiba@volta.vmsmail.ethz.ch (Aiaz Bakassov, Phys. Chem., ETH Zurich) Subject: G92. Add to summary about 2e-integrals. Date: Thu, 7 Jul 1994 15:53:44 +0200 Dear netters, After I posted a summary and described MY failure with extraction of 2e-integrals from G92, one additional mail arrived. After some correspondence, it was decided that the SCF=DIRECT option must be removed. I have removed it and I have got 2e-integrals in a quite readable format! I thank my adviser who wished to keep anonymous. I must stress that the failure is ENTIRELY MINE, and in fact EXACTLY the same advise came originally from Alberto Gobbi who of course couldn't know beforehand that I will be using his advice together with SCF=DIRECT which caused the failure. The net result is this -- to get 2e-integrals, input the following line (no SCF=DIRECT!!!): #RHF 6-31G EXTRALINKS=L316 NORAFF Symm=NOINT The only thing makes me wonder. I thought before of removing SCF=DIRECT (it seemed natural) however in G92 Programmer's Guide (page 41) it is written in front of the option "InCore": "Insists that the SCF be done storing the full integral list in memory. THIS IS DONE AUTOMATICALLY IN A DIRECT SCF CALCULATION IF SUFFICIENT MEMORY IS AVAILABLE". See what it means ? It means that if SCF=DIRECT then integrals AUTOMATICALLY are stored in memory. If they are stored in memory, then they are available for further manipulations, right ? For printing out, for instance. It has really misled me. And I am upset -- it seems that each line of the manual should checked by trial and error for the precise meaning of words. Who has time for that ? Thanks once more, Ayaz Bakasov. From ramon@ce.ifisicam.unam.mx Thu Jul 7 12:51:11 1994 Received: from ce.ifisicam.unam.mx.ifisicam.unam.mx for ramon@ce.ifisicam.unam.mx by www.ccl.net (8.6.9/930601.1506) id MAA15378; Thu, 7 Jul 1994 12:01:41 -0400 Message-Id: <199407071601.MAA15378@www.ccl.net> Received: by ce.ifisicam.unam.mx (16.7/16.2) id AA10233; Thu, 7 Jul 94 10:10:24 -0500 From: Ramon Garduno Subject: MM3. Where can I get it? To: chemistry@ccl.net (POST MSG's) Date: Thu, 7 Jul 94 10:10:24 CDT Mailer: Elm [revision: 70.30] Dear netters: I would like to know if any of you knows where I can get a copy of MM3, either free or with academic costs?. I thank you all in advance. Cheers, -- ____________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics INSTITUTO DE FISICA | EMAIL: ramon@ifisicam.unam.mx UNIVERSIDAD NAL. AUTONOMA DE MEXICO | rgard@redvax1.dgsca.unam.mx Laboratorio de Cuernavaca | VOICE: (73)175388 Apdo. Postal 139-B | (73)111611 62191 Cuernavaca, Morelos | FAX: (73)111603 MEXICO | (73)173077 ___________________________________ EOF _____________________________________ From ferenc@rchsg8.chemie.uni-regensburg.de Thu Jul 7 12:55:18 1994 Received: from comsun.rz.uni-regensburg.de for ferenc@rchsg8.chemie.uni-regensburg.de by www.ccl.net (8.6.9/930601.1506) id LAA15137; Thu, 7 Jul 1994 11:50:51 -0400 Received: from rchsg8.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA12473 (5.65c/IDA-1.4.4 for ); Thu, 7 Jul 1994 17:51:42 +0200 Received: by rchsg8.chemie.uni-regensburg.de (931110.SGI/URRZ-Sub-1.5-irix) (for CHEMISTRY@ccl.net) id AA06707; Thu, 7 Jul 94 17:49:44 +0200 Date: Thu, 7 Jul 94 17:49:44 +0200 From: Ferenc.Molnar@chemie.uni-regensburg.de (Ferenc Molnar) Message-Id: <9407071549.AA06707@rchsg8.chemie.uni-regensburg.de> To: CHEMISTRY@ccl.net Subject: semiemp. QC with d-orbitals Dear Netters: A friend of mine needs information about thermodynamic data of systems containing compounds similar to PF6-. She wants to do some semiempirical calculations. MOPAC is not able to treat this systems because of the missing d-orbitals. Does anybody know about semiempirical quantum chemical programs which can provide these data? Thank you very much in advance. Best regards, Ferenc Ferenc Molnar --------------------------------------------------------------------------- Institut fuer Physikalische und Theoretische Chemie - Lehrstuhl Prof. Dick - Tel.: (+49) 941 943-4466 /-4486 Universitaet Regensburg Fax.: (+49) 941 943-4488 Universitaetsstrasse 31 D-93053 Regensburg Deutschland / Germany --------------------------------------------------------------------------- EMail (SMTP): Ferenc.Molnar@chemie.uni-regensburg.de --------------------------------------------------------------------------- :-) I wish to have no connection with any ship that does not sail fast, for I intend to go in harm's way. -- John Paul Jones, USN 1747-1792 ;-) --------------------------------------------------------------------------- From bbesler@ouchem.chem.oakland.edu Thu Jul 7 13:51:11 1994 Received: from ouchem.chem.oakland.edu for bbesler@ouchem.chem.oakland.edu by www.ccl.net (8.6.9/930601.1506) id NAA16204; Thu, 7 Jul 1994 13:05:58 -0400 Received: by ouchem.chem.oakland.edu (5.57/Ultrix3.0-C) id AA14611; Thu, 7 Jul 94 13:06:59 -0400 From: bbesler@ouchem.chem.oakland.edu (Brent H. Besler) Message-Id: <9407071706.AA14611@ouchem.chem.oakland.edu> Subject: Native Power PC version of CaChe To: chemistry@ccl.net Date: Thu, 7 Jul 94 13:06:58 EDT X-Mailer: ELM [version 2.3 PL11] DOes anyone know if there is going to be a native Power Mac version of the Tektronix CaChe software? I am a bit worried as it requires an FPU, and the 68040 emulator in the Power Mac's doesn't emulate the FPU. From lohrenz@zinc.chem.ucalgary.ca Thu Jul 7 15:51:13 1994 Received: from zinc.chem.ucalgary.ca for lohrenz@zinc.chem.ucalgary.ca by www.ccl.net (8.6.9/930601.1506) id PAA18376; Thu, 7 Jul 1994 15:20:50 -0400 From: Received: by zinc.chem.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA20750; Thu, 7 Jul 1994 12:59:18 -0600 Date: Thu, 7 Jul 1994 12:59:18 -0600 Message-Id: <9407071859.AA20750@zinc.chem.ucalgary.ca> To: chemistry@ccl.net, lohrenz@zinc.chem.ucalgary.ca, nash@bert.chem.wisc.edu Subject: Re: CCL:G92/DFT: spurious integrated density Hi again, when going through the incoming mail I realized that I made a mistake: of course it should be SCF=NoVarAcc. Sorry for this mistake and the bandwidth ... Bye John Lohrenz From pbays@saintmarys.edu Thu Jul 7 15:54:25 1994 Received: from jade.saintmarys.edu for pbays@saintmarys.edu by www.ccl.net (8.6.9/930601.1506) id PAA18757; Thu, 7 Jul 1994 15:36:15 -0400 Received: by jade.saintmarys.edu (1.37.109.8/16.2) id AA11524; Thu, 7 Jul 1994 14:39:47 -0500 Date: Thu, 7 Jul 1994 14:39:47 -0500 (EST) From: Phil Bays Subject: Re: CCL:Native Power PC version of CaChe To: "Brent H. Besler" Cc: chemistry@ccl.net In-Reply-To: <9407071706.AA14611@ouchem.chem.oakland.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Yes. I have just had a price quote on it. It is currently in the beta test stage. Phil Bays pbays@saintmarys.edu Saint Mary's College Notre Dame IN 46556 On Thu, 7 Jul 1994, Brent H. Besler wrote: > DOes anyone know if there is going to be a native Power Mac version of > the Tektronix CaChe software? I am a bit worried as it requires an FPU, > and the 68040 emulator in the Power Mac's doesn't emulate the FPU. > > ---Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator > MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 > Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search > http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV >