From chemistry-request@server.ccl.net Mon Jan 7 04:17:40 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g079HcI21487 for ; Mon, 7 Jan 2002 04:17:39 -0500 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 16NVrN-00081o-00; Mon, 07 Jan 2002 09:14:25 +0000 Date: Mon, 7 Jan 2002 09:14:25 +0000 (GMT) From: Szilveszter Juhos To: Csaba Hetenyi cc: chemistry@ccl.net Subject: Re: CCL:cluster configuration In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII If the application generates lot of network traffic, switches also can be an issue. I saw a cluster where changing from the "usual" 3com to ExtremeNetworks switches improved the speed with about 30% (Dell dual 1G PIII 1550 servers as nodes). Szilva From chemistry-request@server.ccl.net Sun Jan 6 12:03:12 2002 Received: from epimetheus.hosting4u.net ([209.15.2.70]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g06H3BS25902 for ; Sun, 6 Jan 2002 12:03:11 -0500 Received: (qmail 13201 invoked from network); 6 Jan 2002 17:03:08 -0000 Received: from zeus.hosting4u.net (HELO proinformatix.com) (209.15.2.56) by mail-gate.hosting4u.net with SMTP; 6 Jan 2002 17:03:08 -0000 Received: from pyrodictium ([130.67.55.50]) by proinformatix.com ; Sun, 06 Jan 2002 11:03:06 -0600 Reply-To: From: "Sergio Manzetti" To: "Chemistry Discussion G" Subject: Zn ion coordination Date: Sun, 6 Jan 2002 18:06:20 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 X-Rcpt-To: Dear CCLers, a Zn ion gives me headaches since it occurs hexa-coordinated in a molecular simulations, is tricoordinated in the crystal structures, but is cited to be tetra- and penta-coordinated at transition states in metalloenzymes. The neighbours chelating this Zn-ion are: Imidazole ring, Glutamate and a backbone carbonyl oxygen. Can anybody recommend a good review or publication of Zn in metalloenzymes? I have Parkin (2001), but my questions still remains after reading it. Best regards and Happy New year Sergio From chemistry-request@server.ccl.net Mon Jan 7 07:28:46 2002 Received: from mail-nord.nord.univ-mrs.fr ([194.214.97.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g07CSjI23552 for ; Mon, 7 Jan 2002 07:28:45 -0500 Received: from [194.214.91.105] ([194.214.91.105]) by mail-nord.nord.univ-mrs.fr (8.9.3/8.9.3) with ESMTP id NAA20789 for ; Mon, 7 Jan 2002 13:49:39 +0100 X-Sender: sampieri@mail-nord.nord.univ-mrs.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 7 Jan 2002 13:22:54 +0200 To: CHEMISTRY@ccl.net From: Francois Sampieri Subject: Free software for potential energy calculation Dear all, I have to sort a huge number (more than 3000 pdb files) of conformations of the same protein, according to their potential energies (bonded + non-bonded). The first step could be to automatically launch a software capable of achieving energy calculation from each pdb file, then to extract the energy values from the ca. 3000 created files, and sort them into a single file, the all processes being driven by a Perl script running on O2 SGI under Irix 6.5. I got references for some such free softwares, but I found them as source files only and this is a problem for us since we don't have (and don't have skills for coping with) Fortran or C compilers. After unsuccessfully searching on the Web, I'm asking to the CCL community if anyone could point me to such executable programs. All responses will be summarized. Many thanks in advance. Happy new year to you all! Francois ____________________________________________ UMR 6560 CNRS-Universite de la Mediterranee Laboratoire de Biochimie - IFR Jean Roche Faculte de Medecine Nord Bd Pierre Dramard 13916 Marseille Cedex 20 E-mail: sampieri.f@jean-roche.univ-mrs.fr Fax: (33) 4 91 65 75 95 Tel: (33) 4 91 69 88 44 From chemistry-request@server.ccl.net Mon Jan 7 09:10:06 2002 Received: from mail.crs4.it ([156.148.1.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g07EA6I24956 for ; Mon, 7 Jan 2002 09:10:06 -0500 Received: from mercurio.crs4.it (mercurio.crs4.it [156.148.4.11]) by mail.crs4.it (Postfix) with SMTP id 06E6410CC for ; Mon, 7 Jan 2002 15:23:39 +0100 (MET) Sender: ronzitti@crs4.it Message-ID: <3C39AF09.687D@crs4.it> Date: Mon, 07 Jan 2002 15:22:01 +0100 From: Cristina Ronzitti X-Mailer: Mozilla 3.01Gold (X11; I; HP-UX B.10.20 9000/778) MIME-Version: 1.0 To: chemistry@ccl.net Subject: visualizing box axes Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I need to show box axes together with my system molecules : any suggestion ? I usually use, to visualize my system, the software Rasmol wich read pdb format. Thanks in advance, Cristina -- ____________________________________________________________________ Cristina Ronzitti Degree: final-year in chemistry Chemical Processes and Material Modelling Area - Fuel Cells Project CRS4 - VI strada ovest - Z.I. - Macchiareddu - UTA - Cagliari FAX:+39-070-2796216 ____________________________________________________________________ From chemistry-request@server.ccl.net Mon Jan 7 11:19:41 2002 Received: from bute.st-andrews.ac.uk (im17@[138.251.12.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g07GJeI26719 for ; Mon, 7 Jan 2002 11:19:40 -0500 Received: from localhost (im17@localhost) by bute.st-andrews.ac.uk (8.9.1a/8.9.1) with SMTP id QAA14924 for ; Mon, 7 Jan 2002 16:19:36 GMT Date: Mon, 7 Jan 2002 16:19:35 +0000 (GMT) From: Ibrahim Moustafa X-Sender: im17@st-andrews.ac.uk To: chemistry@ccl.net Subject: GROMOS package Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL users, Happy new year to all users. We're thinking to get GROMOS package to do MD for my protein of interest (dimer of about 800 aa ). I'd love to ask about whether GROMOS can do this job on a SGI-O2 machine ( R10000, 270 MH processor and 380 MB RAM ). Also, is GROMOS supported on a PC or not? Another thing to ask about, does GROMOS has parameters for Ca+2 ? appreciated if anyone answer my quwstions. Ibrahim Name :Ibrahim M.Moustafa Mail address :Center for Biomolecular Science, BIOMOLECULAR SCIENCE BUILDING, North Haugh,St-Andrews, Fife,KY16 9ST Scotland,U.K. Tel :+44(0)1334-467257 E-mail :im17@st-andrews.ac.uk From chemistry-request@server.ccl.net Mon Jan 7 16:52:32 2002 Received: from mxout1.cac.washington.edu ([140.142.32.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g07LqWI32114 for ; Mon, 7 Jan 2002 16:52:32 -0500 Received: from mailhost1.u.washington.edu (mailhost1.u.washington.edu [140.142.32.2]) by mxout1.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW01.12) with ESMTP id g07LqS2N009762 for ; Mon, 7 Jan 2002 13:52:28 -0800 Received: from donald ([128.95.128.116]) by mailhost1.u.washington.edu (8.12.1+UW01.12/8.12.1+UW01.12) with SMTP id g07LqSZU027072 for ; Mon, 7 Jan 2002 13:52:28 -0800 From: "Carsten Detering" To: Subject: autodock/solvation parameters for rna Date: Mon, 7 Jan 2002 22:41:58 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Importance: Normal hi ccl'ers, did anybody of you calculate solvation parameters for rna using autodock? and if, how did you do it?? carsten email: detering@u.washington.edu From chemistry-request@server.ccl.net Mon Jan 7 19:24:44 2002 Received: from talisker.emsl.pnl.gov ([198.128.80.38]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g080OhI04259 for ; Mon, 7 Jan 2002 19:24:44 -0500 Received: (from ng570@localhost) by talisker.emsl.pnl.gov (8.8.6 (PHNE_17135)/8.8.6) id QAA07700 for chemistry@ccl.net; Mon, 7 Jan 2002 16:24:34 -0800 (PST) From: Kirk Peterson Message-Id: <200201080024.QAA07700@talisker.emsl.pnl.gov> Subject: Frozen core definition in Gaussian To: chemistry@ccl.net Date: Mon, 7 Jan 2002 16:24:34 -0800 (PST) X-Mailer: ELM [Revision: 213.1] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit All: after stumbling across something today, I thought that it would be of enough interest to bring it to people's attention. Perhaps this is common knowledge, but I'm guessing it's not. When carrying out ab initio calculations on molecules containing 3rd row main group elements, i.e., Ga - Kr, the natural definition of the core electrons for these 3rd row elements (at least in my opinion) includes the following electrons: 1s, 2s, 2p, 3s, 3p, and 3d. (Of course, when doing calculations on Ga- or Ge-containing species, one should at some point be interested in 3d correlation.) Much to my surprise, it appears that the default frozen core in Gaussian does NOT include the 3d electrons (i.e., the 3d electrons are included in the valence shell with the 4s and 4p electrons). Perhaps this was to make the definition consistent with the 3d transition metals where they are obviously valence, but I would be willing to guess that not too many people would guess this choice for an element such as Br. Besides probably doing much more work than desired (correlating 10's of extra electrons usually adds nontrivial amounts of computational expense), most basis sets for these elements do not describe 3d correlation. In particular, the cc-pVnZ basis sets for these elements were developed for valence correlation only, the definition of which did NOT include the 3d electrons of these elements. So in addition to the added computational expense, you might actually do some harm since one may be introducing extra BSSE > from correlating core-like electrons with a valence basis set (never a good idea). Of course, one can change the definition of the frozen core in Gaussian by using the old ReadWindow (RW) option, but the quick FC (i.e., MP2=FC or just MP2) will result in the situation described above. I guess one should note that just mentioning in a publication that the frozen core approximation was used is surprisingly ambiguous... best wishes, Kirk Peterson Washington State University EMSL/Pacific Northwest Nat'l Laboratory From chemistry-request@server.ccl.net Mon Jan 7 21:41:45 2002 Received: from chem_mail.mail.chem.sc.edu ([129.252.75.7]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g082fjI09278 for ; Mon, 7 Jan 2002 21:41:45 -0500 Received: FROM glu.chem.sc.edu BY chem_mail.mail.chem.sc.edu ; Mon Jan 07 21:41:41 2002 -0500 Date: Mon, 7 Jan 2002 21:41:41 -0500 (EST) From: Vitaly Rassolov X-X-Sender: To: Computational Chemistry List Subject: Re: CCL:Frozen core definition in Gaussian In-Reply-To: <200201080024.QAA07700@talisker.emsl.pnl.gov> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A related issue is the definition of core orbitals in molecules such as GaF (where 3d "core" orbitals of Ga are energetically above the valence 2p orbitals of F -> source of many errors). This and the inclusion of Ga 3d orbitals into valence space are discussed in two recent articles. One is Published in Chem. Phys. Lett. last month (vol. 350, 573--576) by Rassolov, Pople, Redfern, and Curtiss; the other one is appearing presently in Theor. Chem. Accounts by G. Petersson and coworkers. The original problem that prompted the inclusion of Ga 3d into valence space was discovered by Radom et al. and Bauschlicher et al. a while ago. It looks like we will be able to return 3d orbitals of Ga back to its core, without much loss of accuracy. On Mon, 7 Jan 2002, Kirk Peterson wrote: > > All: > > after stumbling across something today, I thought that it would > be of enough interest to bring it to people's attention. Perhaps > this is common knowledge, but I'm guessing it's not. When > carrying out ab initio calculations on molecules containing 3rd row > main group elements, i.e., Ga - Kr, the natural definition of the > core electrons for these 3rd row elements (at least in my opinion) > includes the following electrons: 1s, 2s, 2p, 3s, 3p, and 3d. (Of course, > when doing calculations on Ga- or Ge-containing species, one should at > some point be interested in 3d correlation.) Much to my surprise, > it appears that the default frozen core in Gaussian does NOT > include the 3d electrons (i.e., the 3d electrons are included in > the valence shell with the 4s and 4p electrons). Perhaps this was > to make the definition consistent with the 3d transition metals where > they are obviously valence, but I would be willing to guess that not > too many people would guess this choice for an element such as Br. > > Besides probably doing much more work than desired (correlating 10's > of extra electrons usually adds nontrivial amounts of computational > expense), most basis sets for these elements do not describe 3d correlation. > In particular, the cc-pVnZ basis sets for these elements were developed for > valence correlation only, the definition of which did NOT include the 3d > electrons of these elements. So in addition to the added computational expense, > you might actually do some harm since one may be introducing extra BSSE > > from correlating core-like electrons with a valence basis set (never a good idea). > > Of course, one can change the definition of the frozen core in Gaussian > by using the old ReadWindow (RW) option, but the quick FC (i.e., > MP2=FC or just MP2) will result in the situation described above. I guess > one should note that just mentioning in a publication that the frozen core > approximation was used is surprisingly ambiguous... > > best wishes, > > Kirk Peterson > Washington State University > EMSL/Pacific Northwest Nat'l Laboratory > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > -- Vitaly Rassolov Dept. of Chemistry and Biochemistry (803) 777-7811 University of South Carolina fax (803) 777-9521 631 Sumter St Columbia, SC 29208 rassolov@mail.chem.sc.edu