From Karl.F.Moschner@urlus.sprint.com Fri Sep 29 00:35:42 1995 Received: from merit-mx1.telemail.net for Karl.F.Moschner@urlus.sprint.com by www.ccl.net (8.6.10/950822.1) id AAA09360; Fri, 29 Sep 1995 00:34:07 -0400 From: X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Thu, 28 Sep 1995 14:43:00 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Thu, 28 Sep 1995 14:43:00 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Thu, 28 Sep 1995 14:43:00 -0400 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Thu, 28 Sep 1995 14:43:00 -0400 Date: Thu, 28 Sep 1995 14:43:00 -0400 X400-Originator: Karl.F.Moschner@urlus.sprint.com X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/;Thu Sep 28 14:43:50 199501] X400-Content-Type: P2-1984 (2) Content-Identifier: Re: CCL:G92 B3LY Message-ID: <"Thu Sep 28 14:43:50 199501*/I=F/G=Karl/S=Moschner/OU=4267EDUR/O=TMUS.URL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> To: chemistry@www.ccl.net Subject: Re: CCL:G92 B3LYP calculations for iodine with ECP MIME-version: 1.0 Content-type: multipart/mixed; boundary="TqCIyCFAWrrbdP9XHGoapXd74fIW23gW" --TqCIyCFAWrrbdP9XHGoapXd74fIW23gW Content-type: text/plain; charset="us-ascii" > I'm performing G92 B3LYP calculations for iodine with ECP and get the > following messages: > > "No unpruned grid is available for this atom. > No unpruned grid is available for this atom. > No unpruned grid is available for this atom. > No unpruned grid is available for this atom. > No unpruned grid is available for this atom. > No unpruned grid is available for this atom. > No unpruned grid is available for this atom." > > I do get the job completed, but I'd really appriciate it if someone would > explain to me what this message means and what the consequences are. > > -Sergei I was hoping someone more qualified would offer an explanation. But since they haven't, I'll risk getting flamed.... I beleive the DFT contribution (numerical integartiuon) to the potential and correlation energy is computed on a grid of points which, in the case of G94/G94, is assembled from grids defined for each element. Redundant points and nonsense locations, such as those "inside" other atoms, are necessarily discarded/ignored. The process can be sped up by using "pruned grids", judiciously optimized reduced sets of grid points for each element. Pruned grids can impact the energy calculation but those supplied with well known codes should cause small or insignificant differences (=<+/-0.001 hartree), apperently worth the trad-off with what I've heard is a 10-20% speedup in the computation of the DFT contribution to the energy. In short, don't worry about the message. They simply prompt users to bug developers about it so they don't forget to implement the pruned grids as and when they become available to speedup the calculations. Hope thsi helps. I appologise in advance for errors or misrepresentations. Karl _______________________________________________________________________ / \ | Comments are those of the author and not Unilever Research U. S. | | | | Karl F. Moschner, Ph. D. | | | | Unilever Research U. S. e-mail: Karl.F.Moschner@urlus.sprint.com | | 45 River Road Phone: (201) 943-7100 x2629 | | Edgewater, NJ 07020 FAX: (201) 943-5653 | \_______________________________________________________________________/ --TqCIyCFAWrrbdP9XHGoapXd74fIW23gW Content-type: text/plain; charset="us-ascii" --TqCIyCFAWrrbdP9XHGoapXd74fIW23gW-- From Jeffrey.Gosper@brunel.ac.uk Fri Sep 29 04:05:46 1995 Received: from monge.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.6.10/950822.1) id EAA11256; Fri, 29 Sep 1995 04:03:11 -0400 Received: from chem-pc-18.brunel.ac.uk by monge.brunel.ac.uk with SMTP (PP) id <07613-0@monge.brunel.ac.uk>; Fri, 29 Sep 1995 09:02:24 +0100 Date: Fri, 29 Sep 1995 09:02:16 BST From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: Re: CCL:Wanted - Bond Order Algorithms To: Pat Walters cc: chemistry@www.ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII On Thu, 28 Sep 1995 17:27:05 -0400 (EDT) Pat Walters wrote: > From: Pat Walters > Date: Thu, 28 Sep 1995 17:27:05 -0400 (EDT) > Subject: CCL:Wanted - Bond Order Algorithms > To: chemistry@www.ccl.net > > > Dear Netters, > > I'm looking for references to methods for assigning bond orders to a > chemical structure. I'd like to be able to read in a molecular > representation containing hybridized atom types, and output an accurate > Kekule structure. > > Any algorithms, code, or folklore would be appreciated. > > Thanks in advance, > > Pat > ------------------------------------------------------------------ > W. Patrick Walters, Ph.D. > Scientist, Computational Chemistry and Molecular Modeling > Vertex Pharmaceuticals, Inc., 40 Allston St., Cambridge, MA 02139 > Voice: (617)576-3111 FAX: (617)576-2109 > Dear Pat, we also require this, so please summary or forward any responses. Thanks /\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\ Dr. Jeff Gosper Dept. of Chemistry BRUNEL University Uxbridge Middx UB8 3PH, UK voice: 01895 274000 x2187 facsim: 01895 256844 internet/email/work: Jeffrey.Gosper@brunel.ac.uk internet/WWW: http://http2.brunel.ac.uk:8080/~castjjg \/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/ From galvao@ifi.unicamp.br Fri Sep 29 11:50:52 1995 Received: from obelix.unicamp.br for galvao@ifi.unicamp.br by www.ccl.net (8.6.10/950822.1) id LAA17330; Fri, 29 Sep 1995 11:41:25 -0400 Received: from ifi.unicamp.br by obelix.unicamp.br (5.0/SMI-SVR4-DNI-8.0) id AA05265; Fri, 29 Sep 1995 12:41:03 -0300 Received: from polimero.ifi.unicamp.br by ifi.unicamp.br (4.1/SMI-4.1) id AA18754; Fri, 29 Sep 95 12:40:51 BSC Received: (from galvao@localhost) by polimero.ifi.unicamp.br (8.6.9/8.6.9) id MAA00475 for chemistry@www.ccl.net; Fri, 29 Sep 1995 12:40:42 -0300 Date: Fri, 29 Sep 1995 12:40:42 -0300 From: Douglas Soares Galvao - prof Message-Id: <199509291540.MAA00475@polimero.ifi.unicamp.br> To: chemistry@www.ccl.net Subject: dipivaloylcubane references content-length: 416 Dear Netters In an article in C&EN(1994) there was mentioned that dipivaloylcubane has been used as a potential anti-HIV drug. I have tried to locate references to this compound but in the databases in our library I could not find them. Could someone, please, help me with this matter ? Thanks in advance for your help. Douglas Galvao D.S. Galvao DFA-IFGW-UNICAMP Campinas - SP - BRAZIL galvao@ifi.unicamp.br From huang@mazda.wavefun.com Fri Sep 29 12:07:13 1995 Received: from volvo.wavefun.com for huang@mazda.wavefun.com by www.ccl.net (8.6.10/950822.1) id LAA17293; Fri, 29 Sep 1995 11:38:59 -0400 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA03416; Fri, 29 Sep 95 08:38:54 -0700 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma003414; Fri Sep 29 08:38:27 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@www.ccl.net id AA07537; Fri, 29 Sep 95 08:38:22 -0700 From: "Wayne Huang" Message-Id: <9509290838.ZM7535@mazda.wavefun.com> Date: Fri, 29 Sep 1995 08:38:21 -0700 In-Reply-To: Pat Walters "CCL:Wanted - Bond Order Algorithms" (Sep 28, 5:27pm) References: Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: Pat Walters Subject: Re: CCL:Wanted - Bond Order Algorithms Cc: chemistry@www.ccl.net Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Sep 28, 5:27pm, Pat Walters wrote: > Subject: CCL:Wanted - Bond Order Algorithms > I'm looking for references to methods for assigning bond orders to a > chemical structure. I'd like to be able to read in a molecular > representation containing hybridized atom types, and output an accurate > Kekule structure. Here only are sample of references on Bond Order: (1) Mayer, I. Chem. Phys. Lett., 97, 270 (1983) & 110, 440 (1984). (2) A number of papers by R.F.W. Bader ... (3) Classic papers by R.S. Mulliken and P.O. Lowdin ... (4) Cioslowski, J. & Mixon, S.T. JACS, 113, 4142 (1991). Hope this helps! --Wayne -- +---------------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemist | Irvine, California 92715 | | Wavefunction, Inc. | (714)955-2120 Fax: (714)955-2118 | | huang@wavefun.com | World Wide Web: http://wavefun.com | +---------------------------------------------------------------------+ From elewars@alchemy.chem.utoronto.ca Fri Sep 29 13:20:53 1995 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.10/950822.1) id NAA19046; Fri, 29 Sep 1995 13:09:21 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.10/8.6.10) id NAA10570 for chemistry@www.ccl.net; Fri, 29 Sep 1995 13:09:21 -0400 Date: Fri, 29 Sep 1995 13:09:21 -0400 From: "E. Lewars" Message-Id: <199509291709.NAA10570@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: BOND ORDERS Re the question about algorithms for bond orders: Dr Istvan Mayer (Central Research Institute, Hungarian Acad. of Sciences) argues that only his algorithm really gives correct (sensible?) bond orders. Thus the Mayer bond order of H2+ is 0.5 (a 1-electron bond), but (all?) other approaches give 0.25. Contact him at mayer@cric.chemres.hu or H1376May@ella.hu Errol Lewars ===== From hcj@mazda.wavefun.com Fri Sep 29 14:50:54 1995 Received: from volvo.wavefun.com for hcj@mazda.wavefun.com by www.ccl.net (8.6.10/950822.1) id OAA20996; Fri, 29 Sep 1995 14:43:27 -0400 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA03839; Fri, 29 Sep 95 11:43:14 -0700 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma003837; Fri Sep 29 11:43:03 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@www.ccl.net id AA08579; Fri, 29 Sep 95 11:42:58 -0700 Date: Fri, 29 Sep 95 11:42:58 -0700 From: hcj@mazda.wavefun.com (Harry C. Johnson) Message-Id: <9509291842.AA08579@mazda.wavefun.com> To: CTARG@Levels.UniSA.Edu.Au Cc: chemistry@www.ccl.net In-Reply-To: <01HVRI9GWKHUKZEBGA@Levels.UniSA.Edu.Au> (CTARG@Levels.UniSA.Edu.Au) Subject: Re: CCL:parameters for NiO and CoO Reply-To: hcj@wavefun.com >>>>> "Andy" == CTARG writes: Andy> Two pleas for help Andy> - single crystals? Andy> - parameters for Ni or Co, these can be force field, Andy> semi-empirical, or ab-initio - I don't mind. Spartan's PM3(tm) formalism has parameters for both Ni and Co, as well as 13 other transition metals. If you would like more information, please feel free to contact me. -Harry +-----------------------+------------------+-------------------------+ |Harry C. Johnson IV | ______________ | E-Mail: hcj@wavefun.com | |Computational Chemist | \ _________ / | Phone: (714)955-2120 | |Wavefunction Inc. | \ \\\\\\\\/ | Fax: (714)955-2118 | |18401 Von Karman | \ \\\\\/ | | |Suite 370 | \ \\/ | "Seems to me its all | |Irvine, CA 92715 | \/ | just chemistry" - RUSH | +-----------------------+------------------+-------------------------+ From system@alchemy.chem.utoronto.ca Fri Sep 29 15:05:54 1995 Received: from alchemy.chem.utoronto.ca for system@alchemy.chem.utoronto.ca by www.ccl.net (8.6.10/950822.1) id OAA21121; Fri, 29 Sep 1995 14:50:56 -0400 Received: (from system@localhost) by alchemy.chem.utoronto.ca (8.6.10/8.6.10) id OAA28935 for CHEMISTRY@www.ccl.net; Fri, 29 Sep 1995 14:50:46 -0400 Date: Fri, 29 Sep 1995 14:50:46 -0400 From: Mike Peterson (System Admin) Message-Id: <199509291850.OAA28935@alchemy.chem.utoronto.ca> To: CHEMISTRY@www.ccl.net Subject: BOND ORDERS Errol Lewars wrote: >Re the question about algorithms for bond orders: Dr Istvan Mayer (Central >Research Institute, Hungarian Acad. of Sciences) argues that only his >algorithm really gives correct (sensible?) bond orders. Thus the >Mayer bond order of H2+ is 0.5 (a 1-electron bond), but (all?) other >approaches give 0.25. Although there is a theoretical basis for the Mayer method given in the papers, and it gives very sensible bond orders for a wide range of molecules and basis sets, including the * basis sets, it can be made to fail. For example, using 3-21+G, you will get C-C "bond order" results like: Molecule Mulliken Mayer --------------- -------- ----- Ethane -0.328 0.566 Benzene -5.008 2.179 Ethylene 1.169 2.480 Acetylene -0.109 4.496 I suspect almost any basis set containing diffuse functions will cause the Mayer method to fail similarly, though it at least still produces ascending numbers. Note that the Mayer scheme can not produce negative bond orders due to its formulation. For 3-21G, you get almost exactly 1.0, 1.5, 2.0 and 3.0 respectively with the Mayer method, and pretty close to that for 6-31G* as I recall. Mike. -- When the chips are down, switch to pretzels. | Mike Peterson, SysAdmin | U/Toronto Chemistry E-mail: system@alchemy.chem.utoronto.ca Tel: (416)978-7094 WWW: http://www.chem.utoronto.ca/ Fax: (416)978-8775 From shemetn@ddi11.cadd.aa.wl.com Fri Sep 29 16:05:55 1995 Received: from envoy.wl.com for shemetn@ddi11.cadd.aa.wl.com by www.ccl.net (8.6.10/950822.1) id PAA22250; Fri, 29 Sep 1995 15:56:30 -0400 Received: by envoy.wl.com (5.65/allen-042593); id AA19742; Fri, 29 Sep 1995 15:56:27 -0400 Received: by ddi11.cadd.aa.wl.com (940816.SGI.8.6.9/940406.SGI) id TAA15120; Fri, 29 Sep 1995 19:56:24 GMT Date: Fri, 29 Sep 1995 15:56:24 -0400 (EDT) From: Norah Shemetulskis Subject: CCL:unsubscribe To: CHEMISTRY@www.ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII please unsubscribe Norah E. Shemetulskis Biomolecular Structure and Drug Design Parke-Davis Pharmaceutical Research Division Warner Lambert Company (313)998-3360 shemetn@aa.wl.com