From fares@host11.lctn.u-nancy.fr Wed Dec 1 03:52:05 1993 Received: from arcturus.ciril.fr for fares@host11.lctn.u-nancy.fr by www.ccl.net (8.6.4/930601.1506) id DAA04214; Wed, 1 Dec 1993 03:00:32 -0500 Received: from host11.lctn.u-nancy.fr by arcturus.ciril.fr with SMTP (1.37.109.4/16.2) id AA05684; Wed, 1 Dec 93 09:00:37 +0100 Received: by host11.lctn.u-nancy.fr (AIX 3.2/UCB 5.64/4.03) id AA18662; Wed, 1 Dec 1993 08:47:50 +0100 Date: Wed, 1 Dec 1993 08:47:50 +0100 From: fares@host11.lctn.u-nancy.fr (Mohamed Fares) Message-Id: <9312010747.AA18662@host11.lctn.u-nancy.fr> To: chemistry@ccl.net, diz@qtp.ufl.edu Subject: Re: STO integral packages? Dear A. Diz, try to get this packages from CPC library: * ABZK1 and ABZK2 ref. Comp. Phys. Commun. 72 (1992) 304 Calculation of two-center one-electron molecular integrals with STOs. J. Fernandez Rico, R. Lopez, M. Paniagua, G. Ramirez. * ACJU ref. Comp. Phys. Commun. 72 (1992) 269 Programs for the evaluation of overlap integrals with B functions. H.H.H. Homeier, E.J. Weniger, E.O. Steinborn. Subroutine required: AARL 25(1982)149. * ACNV ref. Comp. Phys. Commun. 77(1993) 135 Programs for the evaluation of nuclear attraction integrals with B functions H.H.H. Homeier and E.O. Steinborn Subroutine required: ACJU 72(1992)269 ( if you can get this subroutine(ie. ACNV) please send it to me) * ALCHEMY package for linear molecules written by: D McLean and M. Yoshimine, IBM Laboratory, San Jose CA USA. regards, M. Fares, From DSMITH@uoft02.utoledo.edu Wed Dec 1 08:52:09 1993 Received: from uoft02.utoledo.edu for DSMITH@uoft02.utoledo.edu by www.ccl.net (8.6.4/930601.1506) id IAA06098; Wed, 1 Dec 1993 08:46:47 -0500 Received: from UOFT02.UTOLEDO.EDU by UOFT02.UTOLEDO.EDU (PMDF V4.2-10 #3438) id <01H5YJN3DW740032O0@UOFT02.UTOLEDO.EDU>; Wed, 1 Dec 1993 08:46:40 EST Date: Wed, 01 Dec 1993 08:46:40 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: new address for MMODINFO anonymous ftp To: mmodinfo@uoft02.utoledo.edu, chemistry@ccl.net, hyperchem@autodesk.com, neomig@charles.polymer.uakron.edu Message-id: <01H5YJN3EP4Y0032O0@UOFT02.UTOLEDO.EDU> X-Envelope-to: chemistry@ccl.net X-VMS-To: MMODINFO, CHEMISTRY, HYPERCHEM, NEOMIG MIME-version: 1.0 Content-transfer-encoding: 7BIT The address of the anonymous ftp site for the MMODINFO mailing list has been changed from 131.183.1.1 to 131.183.1.4. The name, ftp.utoledo.edu, remains the same. Sorry for any inconvenience this may have caused. Douglas A. Smith Assistant Professor Department of Chemistry and member, Center for Drug Design and Development The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From hongma@mcnc.org Wed Dec 1 09:05:38 1993 Received: from robin.mcnc.org for hongma@mcnc.org by www.ccl.net (8.6.4/930601.1506) id IAA06076; Wed, 1 Dec 1993 08:38:34 -0500 Received: by robin.mcnc.org (5.59/MCNC/8-10-92) id AA24234; Wed, 1 Dec 93 08:38:33 -0500 for chemistry@ccl.net Date: Wed, 1 Dec 93 08:38:33 -0500 From: Hong Ma Message-Id: <9312011338.AA24234@robin.mcnc.org> To: chemistry@ccl.net Subject: Molecular Modeling Workshop MOLECULAR MODELING WORKSHOP Presented by MCNC's North Carolina Supercomputing Program and Molecular Simulations, Inc. Monday, January 24, 1994 MCNC and Molecular Simulations, Inc. (MSI) are pleased to announce a workshop on molecular modeling. The workshop will involve hands-on training for QUANTA/CHARMm molecular modeling software. Techniques to be demonstrated include: - Conformational Searching - Homology Modeling - Molecular Dynamics - Development of QSAR Models QUANTA/CHARMm is an integrated program combining molecular graphics, construction and simulations, and simulated structural behavior of small and large molecular systems. QUANTA includes protein modeling and polymer dynamics packages as part of its core functionality and is fully integrated with the CHARMm computational program for molecular mechanics and dynamics. The workshop will be held Monday, January 24, 1994, from 8:45 a.m. to 5:00 p.m. Seminar attendance is limited to 15 due to the number of workstations available in the MCNC training lab. Cancellations must be made at least two weeks prior to the seminar to receive a refund. Lunch will be provided. Registration is based upon receipt of payment and a completed registration form. To register for the course, complete the registration form attached and return it with a check or money order for $20.00 payable to MCNC to: QUANTA/CHARMm Seminar Attn. Linda Melville North Carolina Supercomputing Program P.O. Box 12889 Research Triangle Park, NC 27709-2889 For technical information concerning this presentation contact Hong Ma via e-mail (hongma@mcnc.org) or phone (919/248-1176). For registration information contact Linda Melville via e-mail (linda@mcnc.org) or phone (919/248-1133). QUANTA and CHARMm are registered trademarks of Molecular Simulations Inc. REGISTRATION FORM Name: Organization: Street: City: State: Zip: Telephone: FAX: E-mail: Payment Method: _____ Check or money order (make payable to MCNC) _____ Purchase Order (please attach) QUANTA and CHARMm are registered trademarks of Molecular Simulations Inc. From SATYAM@vms.cis.pitt.edu Wed Dec 1 09:52:12 1993 Received: from VM2.CIS.PITT.EDU for SATYAM@vms.cis.pitt.edu by www.ccl.net (8.6.4/930601.1506) id JAA06736; Wed, 1 Dec 1993 09:49:32 -0500 From: Received: from vms.cis.pitt.edu by vms.cis.pitt.edu (PMDF #12376) id <01H5YLLQ5TS0AIE5GQ@vms.cis.pitt.edu>; Wed, 1 Dec 1993 09:39 EST Date: Wed, 1 Dec 1993 09:39 EST Subject: Where can one find X-ray Structures of DNA's// To: chemistry@ccl.net Message-id: <01H5YLLQ5TS0AIE5GQ@vms.cis.pitt.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" Hello Netters, Can anyone suggest us if there is some DATA BANK similar to protein data bank..for crystal structures of DNA and its complexes , which have been reported so far. Thanks in Advance satyam (satyam@vms.cis.pitt.edu) From cletner@remcure.bmb.wright.edu Wed Dec 1 09:53:16 1993 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.4/930601.1506) id JAA06564; Wed, 1 Dec 1993 09:24:29 -0500 Received: by remcure.bmb.wright.edu (920330.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA06776; Wed, 1 Dec 93 09:22:56 -0800 Date: Wed, 1 Dec 1993 09:09:44 -0800 (PST) From: Charles Letner Subject: Protein force fields To: Computational Chemistry List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, I've been reading about M/M force fields for proteins. My inital impression was that the kollman-all-atom force field was a good choice. However, I have just finished two papers that indicate differently. The first presents data that suggest that the kollman united force field gives reslults closer to crystal structures. The authors state this and then waffle on the point by saying more study is needed. The second paper actually goes as far as to state that the united force field is the desired force field based on their study. Ok, enough background... I'm wondering what some of you think about the various protein force fields? This is becoming a point of concern because I'm getting ready to start a project that will involve M/M and dynamics of proteins. Thanks Chuck e-mail: cletner@remcure.bmb.wright.edu From bharatam@titan1.chem.uab.edu Wed Dec 1 10:52:29 1993 Received: from Heath.DPO.UAB.EDU for bharatam@titan1.chem.uab.edu by www.ccl.net (8.6.4/930601.1506) id KAA07667; Wed, 1 Dec 1993 10:45:30 -0500 Received: from titan1.chem.uab.edu by Heath.DPO.UAB.EDU (4.0/SMI-4.0) id AA09082; Wed, 1 Dec 93 09:30:17 CST Received: by titan1.chem.uab.edu (5.51/5.17) id AA02319; Wed, 1 Dec 93 09:55:49 CST Date: Wed, 1 Dec 93 09:55:49 CST From: bharatam@titan1.chem.uab.edu (Prasad Bharatam) Message-Id: <9312011556.AA02319@titan1.chem.uab.edu> To: chemistry@ccl.net Subject: : Free quantum chemistry software Dear Netters, I am planning to set up a quantum chemistry laboratory in an upcoming university in India. The funding situation is very poor there and I will not be able to buy any software. I need some help (information) in obtaining the free quantum chemistry (semi-empirical, ab initio, DFT ) software. Please supply me the list of all the free packages and the addresses or ftp sites from where I can obtain these packages. Thanking you, Bharatam From zrfl0128@awshp.rus.uni-stuttgart.de Wed Dec 1 10:53:52 1993 Received: from noc.BelWue.DE for zrfl0128@awshp.rus.uni-stuttgart.de by www.ccl.net (8.6.4/930601.1506) id KAA07518; Wed, 1 Dec 1993 10:28:35 -0500 Received: from awshp.rus.uni-stuttgart.de by noc.BelWue.DE with SMTP id AA15991 (5.65c8/BelWue-M2.04 for ); Wed, 1 Dec 1993 16:28:31 +0100 Received: by awshp.rus.uni-stuttgart.de (920330.SGI/BelWue-1.0SG(subsidiary)) (for CHEMISTRY@ccl.net) id AA05426; Wed, 1 Dec 93 16:28:30 +0100 From: zrfl0128@awshp.rus.uni-stuttgart.de (Dr. Heinz Poehlmann) Message-Id: <9312011528.AA05426@awshp.rus.uni-stuttgart.de> Subject: Electrolytic Processes To: CHEMISTRY@ccl.net Date: Wed, 1 Dec 93 16:28:29 MEZ X-Mailer: ELM [version 2.3 PL11] Hello all, does anybody know of simulation programs dealing with electrolytic processes, maybe including also diffusion effects and fluid flow components ? Any comments/help welcome. Heinz .-------------------------------------------------------------------------. | Dr. Heinz W. Poehlmann Regionales Rechenzentrum | | Computational Chemistry & Visualization der Universitaet Stuttgart | | e-mail: poehlmann@rus.uni-stuttgart.de Allmandring 30 | | phone: (49)-711-685-5992 D-70550 Stuttgart | | fax: (49)-711-6787626 Germany | '-------------------------------------------------------------------------' From nauss@ucmodl.che.uc.EDU Wed Dec 1 10:54:30 1993 Received: from ROCK.SAN.UC.EDU for nauss@ucmodl.che.uc.EDU by www.ccl.net (8.6.4/930601.1506) id KAA07381; Wed, 1 Dec 1993 10:19:25 -0500 Received: from ucmodl.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V4.2-14 #4918) id <01H5YN275FI89OEQUN@UCBEH.SAN.UC.EDU>; Wed, 1 Dec 1993 10:21:32 EST Received: by ucmodl.che.uc.edu (920330.SGI/920502.SGI.AUTO) for @uc.edu:SATYAM@vms.cis.pitt.edu id AA05284; Wed, 1 Dec 93 10:25:45 -0500 Date: Wed, 01 Dec 1993 10:25:45 -0500 From: nauss@ucmodl.che.uc.EDU (Jeffrey L. Nauss) Subject: Re: Where can one find X-ray Structures of DNA's// To: SATYAM@vms.cis.pitt.EDU Cc: CHEMISTRY@ccl.net Message-id: <9312011525.AA05284@ucmodl.che.uc.edu> Content-transfer-encoding: 7BIT Yes, there is. It is the Nucleic Acid Database at Rutgers University. On March 15 the database had 166 DNA, RNA, and tRNA structures. To obtain general information about the Nucleic Acid Database send the following mail message: to: ndblib@ndbserver.rutgers.edu Subject: send access from newsletter Jeff Nauss ************************************************************************ * Dr. Jeffrey L. Nauss * Telephone: 513-556-0148 * * Department of Chemistry * Fax: 513-556-9239 * * University of Cincinnati * e-mail: nauss@ucmodl.che.uc.edu * * Cincinnati, OH 45221-0172 * * ************************************************************************ From shaoweng@helix.nih.gov Wed Dec 1 11:52:24 1993 Received: from helix.nih.gov for shaoweng@helix.nih.gov by www.ccl.net (8.6.4/930601.1506) id LAA08097; Wed, 1 Dec 1993 11:09:36 -0500 Received: from localhost by helix.nih.gov (8.6.4/1.35(helix-1.0)) id LAA05785; Wed, 1 Dec 1993 11:09:32 -0500 Date: Wed, 1 Dec 1993 11:09:32 -0500 From: shaoweng@helix.nih.gov (Shaomeng Wang) Message-Id: <199312011609.LAA05785@helix.nih.gov> To: SATYAM@vms.cis.pitt.edu, chemistry@ccl.net Subject: Re: Where can one find X-ray Structures of DNA's// the Protein Data Bank does provide you the X-rays structures of not only the proteins, protein-ligand complexes, but also the DNAs and DNA complexes. Hope this will be helpful. -Shaomeng From SHAUN%JASON.DECNET@relay.the.net Wed Dec 1 11:55:10 1993 Received: from NIC.THE.NET for SHAUN%JASON.DECNET@relay.the.net by www.ccl.net (8.6.4/930601.1506) id LAA08206; Wed, 1 Dec 1993 11:28:14 -0500 Received: from decnet-mail (SHAUN@JASON) by nic.the.net (PMDF #3222 ) id <01H5YN3MMIJK000RZR@nic.the.net>; Wed, 1 Dec 1993 10:27:53 CST Date: 01 Dec 1993 10:27:53 -0600 (CST) From: "Shaun D. Black" Subject: Re: Where can one find X-ray Structures or DNA's// To: chemistry@ccl.net Message-id: <01H5YN3MMS6Q000RZR@nic.the.net> X-Envelope-to: chemistry@ccl.net X-VMS-To: THENIC::IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT The PDB, though named 'Protein Data Bank', carries coordinates for all classes of biological macromolecules. That is, protein, DNA, RNA, and polysaccharide x-ray coordinates are housed in the database at present. Also, many complexes are represented, including drug-DNA ones. I have a current index to the PDB that contains Code, Structure name, and Structure resolution (angstroms) either in ASCII text or WordPerfect format. I'd be glad to e-mail a copy of this to anyone who is interested. Be sure to indicate the version you would like and indicate your return e-mail address. Best regards to all. -Shaun =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= = Shaun D. Black, PhD | Internet: shaun%jason.decnet@relay.the.net = = Dept. of Biochemistry | Bitnet: shaun%jason.decnet@thenic.bitnet = = UT Health Center, Tyler | Phone: (903)877-2806 FAX: (903)877-7558 = = Tyler, TX 75710-2003 | B-) (Start every day with a smile...) = =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From mmconn@esau.mit.edu Wed Dec 1 13:52:42 1993 Received: from esau.mit.edu for mmconn@esau.mit.edu by www.ccl.net (8.6.4/930601.1506) id NAA09436; Wed, 1 Dec 1993 13:48:34 -0500 Received: by esau.mit.edu (920330.SGI/920502.SGI) for chemistry@ccl.net id AA16414; Wed, 1 Dec 93 13:55:07 -0500 Date: Wed, 1 Dec 93 13:55:07 -0500 From: mmconn@esau.mit.edu (morgan conn) Message-Id: <9312011855.AA16414@esau.mit.edu> To: chemistry@ccl.net Subject: volume calculation Dear netters, We are trying to calculate the volume of a fully enclosed cavity in a shell-like dimeric molecule. Standard molecular modeling packages (i.e. Macromodel) will calculate the volume of a molecule but do not seem to have the capability to calculate the volume that is enclosed by a shell- like molecule. Does anyone know of a way to do this? Any help you can give would be appreciated. mmc ********************************************************* Morgan Conn MIT Chemistry, 18-148, Cambridge, MA 02139; mmconn@esau.mit.edu, 617.253.6438, 617.253.7929 (fax) ********************************************************* From kb7@tower.york.ac.uk Wed Dec 1 13:54:27 1993 Received: from leeman.york.ac.uk for kb7@tower.york.ac.uk by www.ccl.net (8.6.4/930601.1506) id NAA09030; Wed, 1 Dec 1993 13:02:59 -0500 Received: from tower.york.ac.uk by leeman.york.ac.uk with SMTP (PP) id <22482-0@leeman.york.ac.uk>; Wed, 1 Dec 1993 17:50:29 +0000 Received: by tower.york.ac.uk (920330.SGI/920502.SGI) for @leeman.york.ac.uk:CHEMISTRY@ccl.net id AA01592; Wed, 1 Dec 93 18:02:22 GMT Date: Wed, 1 Dec 1993 17:26:46 +0000 (GMT) From: K Bryson Subject: DNA structure analysis software. To: CHEMISTRY@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, A previous message on a database for Nucleic Acid X-ray structures has got me wondering about how much software is out there to analyse nucleic acid structures. I know of R.E. Dickerson's Newhelix93 program for static structure analysis but do not know any other programs for the analysis of features not provided by this program such as Shear and Opening Parameters between base-pairs. For trajectory analysis I know G. Ravishanker has a program called 'Curves, Dials and Windows' and R. Lavery has a program called CURVES 3.0 ( not sure if it's the same program ), but I do not have sources or know the availability of these. I would be grateful to receive information on these types of packages, personal feelings about their use, and sources to obtain them. If the response is fruitful then I will form a summary of programs, their features and ftp sites. Thanks, Kevin. ----------~~~~~~------~~~~~~~~~~---------------~~~~~----------~~~~~-- K.Bryson email: kb7@tower.york.ac.uk Biophysics Group Tel : +44 904 430000 Extn. 2236 Physics Department Fax : +44 904 432214 University of York Heslington "Molecular modelling of DNA and its YORK, UK interaction with small molecules." YO1 5DD -------------------~~~~~-------------~~~~--------~~~~--------~~~~~--- From news@nntp-server.caltech.edu Wed Dec 1 13:55:03 1993 Received: from punisher.caltech.edu for news@nntp-server.caltech.edu by www.ccl.net (8.6.4/930601.1506) id NAA09397; Wed, 1 Dec 1993 13:44:18 -0500 Received: from gap.cco.caltech.edu by punisher.caltech.edu with SMTP (8.6.4/DEI:4.41) id KAA03570; Wed, 1 Dec 1993 10:44:16 -0800 Received: by gap.cco.caltech.edu (4.1/DEI:4.41) id AA27479; Wed, 1 Dec 93 10:44:12 PST To: mlist-chemistry@nntp-server.caltech.edu Path: nntp-server.caltech.edu!rpm From: rpm@bach.wag.caltech.edu (Richard P. Muller) Newsgroups: mlist.chemistry Subject: SUMMARY: Protein Quasiparticle/Bead Force Fields Date: 1 Dec 93 10:44:08 Organization: Materials Simulations Center Lines: 85 Distribution: mlist Message-Id: Nntp-Posting-Host: bach.wag.caltech.edu Here's the final summary of the responses I received to my query on quasiparticle force fields for proteins. Thanks so much to everyone who replied. Rick ---- Summary of Quasiparticle/Bead Force Fields for Proteins References Wolynes PNAS 89:9029 Crippen Bipol 29:1479 JMolBiol 227:876 IntJPepProtRes 25:487 Sippl JCompAidMolDes 7:473 JMolBiol 213:859 224:725 Schneller Weaver Biopol 33:1519 Gerber Biopol 32:1003 Covell Proteins 14:409 Wilson Doniach Proteins 6:193 Skolnick JMolBiol 212:787 215:183 221:499 PNAS 86:1229 AnRevPhysChem 40:207 Maggiora Meth Bioc Anal 35:1 Levitt CurrOpStrBio 1:224 J Mol Biol 104:49 Grest et al CompPhysComm 55:269 Godzik et al JCompAidMolDes 7:397 Miyazawa Jernigan Macromolecules 18:354 Bryant & Lawrence Proteins 16:92 Sun Protein Science 2:762 Head-Gordon Brooks Biopol 31:77 Book: Computer Simulation of Polymers, Roe, ed. Prentiss Hall, 1991 Misc papers by... Eisenberg, Thornton, Sanders Thanks to Drs. Eofsson, Gordon, Garavelli, Black, Case, Godzik, Burkhart, Vasquez, Davis, Stouten, von Kitzing, Hermann, Loh, for the helpful replies. -- ---------+---------+---------+---------+---------+---------+---------+ Richard P. Muller rpm@wag.caltech.edu Beckman Institute 139-74 (818) 395-2722 Office California Institute of Technology (818) 568-9484 Home Pasadena, California 91125 (818) 585-0918 FAX From Peter_Kazmaier.XRCC@xerox.com Wed Dec 1 15:52:13 1993 Received: from alpha.xerox.com for Peter_Kazmaier.XRCC@xerox.com by www.ccl.net (8.6.4/930601.1506) id PAA11409; Wed, 1 Dec 1993 15:45:02 -0500 Received: from XRCC_Mail2.XRCC.XEROX.xns by alpha.xerox.com via XNS id <15223(1)>; Wed, 1 Dec 1993 12:44:10 PST X-NS-Transport-ID: 080037006910CBE72FFD Date: Wed, 1 Dec 1993 12:43:59 PST From: Peter_Kazmaier.XRCC@xerox.com Subject: Mopac Calculations on Benzoyloxy Radical In-Reply-to: <199308241536.AA12245@oscsunb.ccl.net> To: CHEMISTRY@ccl.net cc: Peter_Kazmaier.XRCC@xerox.com Message-ID: <"1-Dec-93 15:44:25".*.Peter_Kazmaier.XRCC@Xerox.com> I am completing a table of calculations on a series of radicals including the benzoyloxy radical C6H5CO2(.) using the default (Dewar`s half-electron) protocol in Mopac6. Although these calculations proceed without incident for most systems, the benzoyloxy system refuses to converge to a minimum stationary state using keywords: AM1 PRECISE EF GNORM=0.01 GRAD (RECALC=1) I have tried all manner of options for finding the minimum: NLLSQ gives a saddle point as the stationary point UHF also does not converge BFGS does not lead to convergence It seems clear that part of the problem is the SCF procedure since SHIFT, PULAY and the Camp-King SCF convergers are invoked. I have extended the systems to thiobenzoyloxy C6H5COS(.) and acetyloxy CH3CO2(.) but these also give me the same problem. Particularly curious to me is the observation that if one uses the PM3 Hamiltonian, the benzoyloxy system does converge to a minimum! However, starting the AM1 calculation using the PM3 minimized geometry again leads to convergence failure. If anyone has any suggestions on how I might proceed. I would be grateful for your input. Thank you for your help, Peter Kazmaier Xerox Research Centre of Canada pkaz.xrcc@xerox.com From DSMITH@uoft02.utoledo.edu Wed Dec 1 16:52:20 1993 Received: from uoft02.utoledo.edu for DSMITH@uoft02.utoledo.edu by www.ccl.net (8.6.4/930601.1506) id QAA11770; Wed, 1 Dec 1993 16:19:44 -0500 Received: from UOFT02.UTOLEDO.EDU by UOFT02.UTOLEDO.EDU (PMDF V4.2-10 #3438) id <01H5YZFT8OWW0032O0@UOFT02.UTOLEDO.EDU>; Wed, 1 Dec 1993 16:19:35 EST Date: Wed, 01 Dec 1993 16:19:35 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: basis set for ZnR2? To: chemistry@ccl.net Message-id: <01H5YZFT9RHU0032O0@UOFT02.UTOLEDO.EDU> X-Envelope-to: chemistry@ccl.net X-VMS-To: CHEMISTRY MIME-version: 1.0 Content-transfer-encoding: 7BIT What is an appropriate basis set and level of theory for the study of dialkyl zinc compounds, ZnR2? Any references would be appreciated. Doug Douglas A. Smith Assistant Professor Department of Chemistry and member, Center for Drug Design and Development The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From srp@ZGI.COM Wed Dec 1 17:52:18 1993 Received: from m5.ZGI.COM for srp@ZGI.COM by www.ccl.net (8.6.4/930601.1506) id RAA12661; Wed, 1 Dec 1993 17:27:52 -0500 Received: from zgi.com (stella.ZGI.COM) by m5.ZGI.COM (4.1/SMI-4.1) id AA29933; Wed, 1 Dec 93 14:27:25 PST Received: from blaster.ZGI.COM by zgi.com (4.1/SMI-4.1) id AA16862; Wed, 1 Dec 93 14:27:18 PST Received: from localhost by blaster.ZGI.COM (8.6.4/920502.SGI) for CHEMISTRY@ccl.net id OAA02494; Wed, 1 Dec 1993 14:27:17 -0800 Date: Wed, 1 Dec 1993 14:27:17 -0800 From: srp@ZGI.COM (Scott Presnell) Message-Id: <199312012227.OAA02494@blaster.ZGI.COM> To: CHEMISTRY@ccl.net Subject: Summary: Inventory/Bioassay Database Construction Hi Folks, I was asked to post a summary of responses on my question about structure database design. Here are the responses I received. As a result of discussions and e-mail suggestions, we are now also taking under consideration the Daylight and Chemical Design products. Thanks. - Scott Presnell (srp@zgi.com) === From states@ibc.wustl.edu Fri Nov 12 09:43:19 1993 Bottom line is that I consider RDBMS systems to be very low level, and they tend to get solidified early on. For most scientific database, you need the ability to evolve rapidly as technology and interests change. Federated systems with defined interface protocols seems like the best solution to me. === From bruc@horta.bms.com Fri Nov 12 14:13:04 1993 Have you taken a look at Daylight Chemical Information Systems (505) 989-1000? They market a high speed chemical information server and a very nice looking toolkit for accessing and manipulating the chemical data. === From BIENSTOCK@NIEHS.NIH.GOV Fri Nov 12 12:03:44 1993 If you would like to use your database for chemical structural searches, and for being able to search molecular properties and setup structure- activity relationships, I would recommend the product, ISIS, sold by MDL (Contact Randy Helmonds 510-895-1313). There is a version available for both the Mac and the PC. There is also a chemical draw program associated with the database for creating your own structures for import. They have a demo disk available which is a real working copy of the program minus the ability to print and save. There is another chemical database available from CHemical Design Inc. (201-529-3323) called ChemX. If you are interested in structurally oriented relational databases, I think these products will be more suited to your application than Oracle (which is not structurally/graphically oriented). === From MARTIN@cmda.abbott.com Sat Nov 13 07:49:08 1993 If you aren't totally committed to your solution, you might consider also using Daylight or Tripos Unity for your problem. Daylight is very flexible. You would keep all the data in one database. Jeff Blaney built a very nice inventory system while he was at DuPont. Old versions run on VMS, new C/toolkit on Unix. === From ucdavis.edu!lith!kestas Sun Nov 14 04:22:14 1993 We used MACCS/Rdb to create an inventory system. One thing to be aware of is that we were unable to create one-to-many relations from MACCS, so we do not have the structural part normalised. Our biodata is on ORACLE. This is due strictly to political considerations. You could also try MDL's ISIS/BASE, but it is about $4000 per user for licenses. === From mdlag.ch!odin.mdlag.ch!stevew Mon Nov 15 03:55:27 1993 Most of our customer's tend to use MACCS together with one of the three major RDBMS systems - Oracle, Ingres or Rdb - linked via the MACCS Database Interface Module. This gives much greater flexibility than trying to place ALL your data in a MACCS database itself, especially in terms of database admin., security and data loading/updating. There is now a trend to move to "open" client-server architectures, a trend which the ISIS product line now addresses. You can build the same sort of system with ISIS, placing your structures and structure-related data in a MACCS database, and your bio data in one of the 3 RDBMS systems, and link these in a mixed computer/networking environment with much greater flexibilty and power than is possible in the MACCS environment. The ISIS end-user interface on the PC/Mac/SGI allows the end-user chemist or biochemist a much richer environment for report generation, data analysis, etc. There is a custom CIMS (Chemical Inventory Management System) application for MACCS (uses the Database Interface Module to Oracle, Ingres or Rdb), which is quite widely used and can readily be modified, and two ISIS chemical inventory systems which have now been built for/by individual customers. === From weber@Kodak.COM Mon Nov 15 15:35:43 1993 I got your note on using MACCS to set up a database system. Have you looked at the software from Daylight? It is MUCH cheaper and more versatile than MACCS- for example it has similarity searching built in, whereas you must buy the power search module from MDL to get that in MACCS. I also runs on various unix workstations such as the SGI we are using. We are in the process of setting up an inventory system based on their software. We already use it to search the ACD database (which we bought from MDL and converted). === End of Summary. From raman@bioc01.uthscsa.edu Wed Dec 1 19:52:15 1993 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by www.ccl.net (8.6.4/930601.1506) id TAA13925; Wed, 1 Dec 1993 19:19:40 -0500 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Wed, 1 Dec 1993 18:20:27 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA09795; Wed, 1 Dec 93 18:20:07 CST From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9312020020.AA09795@bioc01.uthscsa.edu> Subject: Re: Where can one find X-ray Structures of DNA's// To: chemistry@ccl.net Date: Wed, 1 Dec 1993 18:20:07 -0600 (CST) X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1121 > > Hello Netters, > > Can anyone suggest us if there is some DATA BANK similar to > > protein data bank..for crystal structures of DNA and its > > complexes , which have been reported so far. Helen Burman at Rutgers ( I believe in association with Wilma Olson and colleagues) maintains one such database which is by far the complete one I know. Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 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 ******************************************************************************