From chemistry-request@server.ccl.net Wed Oct 23 03:54:30 2002 Received: from ns1.tudelft.nl ([130.161.180.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9N7sUS21169 for ; Wed, 23 Oct 2002 03:54:30 -0400 Received: from CONVERSION-DAEMON.mailhost2.tudelft.nl by mailhost2.tudelft.nl (PMDF V6.1-1 #40925) id <0H4F00501CMSDR@mailhost2.tudelft.nl> for chemistry@ccl.net; Wed, 23 Oct 2002 09:54:30 +0200 (MEST) Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost2.tudelft.nl (PMDF V6.1-1 #40925) with ESMTP id <0H4F001B0CMSMC@mailhost2.tudelft.nl> for chemistry@ccl.net; Wed, 23 Oct 2002 09:54:28 +0200 (MEST) Received: from stm-ltc2.dct.tudelft.nl (stm-ltc2.dct.tudelft.nl [130.161.196.198]) by listserv.tudelft.nl (8.12.5/8.12.5) with ESMTP id g9N7sSFx023495 for ; Wed, 23 Oct 2002 09:54:28 +0200 (MEST) Received: from STM-LTC2/SpoolDir by stm-ltc2.dct.tudelft.nl (Mercury 1.47) ; Wed, 23 Oct 2002 09:54:27 +0000 (MET-1MEST) Received: from SpoolDir by STM-LTC2 (Mercury 1.47); Wed, 23 Oct 2002 09:54:19 +0000 (MET-1MEST) Date: Wed, 23 Oct 2002 09:54:17 +0200 From: Stefan Bromley Subject: Van der Waals parameters for Ge? To: chemistry@ccl.net Message-id: <3DB671C6.21876.22A54071@localhost> MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal Dear CCL, does anyone know of any non-bonded VDW parameters for Germanium. Specifically we want a reasonable representation of the Ge---H non-bonding interaction. So far we have used the UFF/Dreiding values and used mixing rules to get a first approximation but which seems to give a much too large Ge-H equilibrium distance (cf empirical H-Si). We have also seen on the web that MM2 may have such parameters but we have been not been able to find them. Any ideas? Thanks, Stefan ________________________________________________________ Dr Stefan T. Bromley Laboratory of Applied Organic Chemistry and Catalysis DelftChemTech, Delft University of Technology Julianalaan 136, 2628 BL Delft The Netherlands Phone : + 31 1527 89418 e-mail : S.T.Bromley@tnw.tudelft.nl ________________________________________________________ From chemistry-request@server.ccl.net Wed Oct 23 10:12:33 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9NECXS30424 for ; Wed, 23 Oct 2002 10:12:33 -0400 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id KAA29174; Wed, 23 Oct 2002 10:12:31 -0400 (EDT) Sender: richard@cornell.edu Message-ID: <3DB6AE4F.BECF1083@cornell.edu> Date: Wed, 23 Oct 2002 10:12:31 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: Xiang Lu CC: angelschnur@hotmail.com, chemistry@ccl.net Subject: Re: CCL:rotate molecules along princliple moments of inertia References: <200210221900.PAA2986593@rutchem.rutgers.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit This same problem pops up when I have an ensemble of identical, but randomly-oriented bodies (proteins) in solution and I wish to transform them all back to - the same - body coordinate system. You get to the body system by diagonalizing the inertial matix, but I suspect the problem is that eigenvalues can be returned by the numerical routine in any order and with any sign. The resulting body coordinate sytems then differ by permutations and sign changes of axes subject to the condition that the handedness must be preserved. I seem to remember this has something to do with permutation groups so that the required sign changes are related to the parity of the permutation (swap axes and you must change a sign to preserve handedness). At any rate, is there a way of putting eigenvectors in some kind of canonical order with appropriate sign so that the diagonalization routines always land you in the same body system? Richard Gillilan MacCHESS From chemistry-request@server.ccl.net Wed Oct 23 07:23:48 2002 Received: from GWIA.HSC.WVU.EDU ([157.182.105.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9NBNlS26467 for ; Wed, 23 Oct 2002 07:23:48 -0400 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Wed, 23 Oct 2002 07:23:44 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Date: Wed, 23 Oct 2002 07:23:26 -0400 From: "Peter Gannett" To: , Subject: Re: CCL:PDB file editing Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline Alice: There are ways to do this but, if you don't have a lot of files, the easiest way is just to edit the pdb file. Usually, water, ions, etc are after the solute molecule so just cut a past the solute into a new pdb file. We have often done this with pdb files and it works fine. Pete >>> Alice NgarKit Ko 10/22/02 09:34PM >>> Hi, I would like to know if there is an easy way to edit a PDB file. I loaded the structure into VMD for viewing. There are a lot of water molecules that have traveled far from where I wanted them. I hope I can use some program where I can just pick and delete the water molecules and then write out the remaining atoms to a new PDB file. If anyone knows how to do this, please let me know. Thank you very much Alice -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Oct 23 10:10:19 2002 Received: from antivirus.unimo.it ([155.185.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9NEAIS30384 for ; Wed, 23 Oct 2002 10:10:18 -0400 Received: from mail.unimo.it (mail.unimo.it [155.185.1.1]) by antivirus.unimo.it (8.12.5/8.12.5) with ESMTP id g9NEAIFi011578 for ; Wed, 23 Oct 2002 16:10:18 +0200 Received: (from nobody@localhost) by mail.unimo.it (2.1.2/8.9.1/Execmail 2.1) id QAA1643854; Wed, 23 Oct 2002 16:10:18 +0200 (CETDST) To: chemistry@ccl.net Subject: renumbering a pdb file Message-ID: <1035382218.3db6adca04dad@mail.unimo.it> Date: Wed, 23 Oct 2002 16:10:18 +0200 (CETDST) From: sarap@mail.unimo.it MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.4 X-Virus-Scanned: by amavisd-milter (http://amavis.org/) Hi everybody, I have a problem related with the use of DOCK5.0. The default output of the docking run is a mol2 file. In order to visualize the output i need to convert this file to a pdb format. I've have tried the conversion with Babel but the molecules in the pdb files have not progressive numbers. Any suggestion? Thank you in advance. Sara Sara Pacchioni PhD student University of Modena e Reggio Emilia Italy e-mail: pacchioni.sara@unimore.it From chemistry-request@server.ccl.net Wed Oct 23 04:43:11 2002 Received: from laplinux.dcfe.unimi.it ([159.149.31.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9N8hBS22812 for ; Wed, 23 Oct 2002 04:43:11 -0400 Received: from laplinux.dcfe.unimi.it (localhost [127.0.0.1]) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/SuSE Linux 0.6) with ESMTP id g9N8gKuR012237; Wed, 23 Oct 2002 10:42:20 +0200 Received: from localhost (acontini@localhost) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/Submit) with ESMTP id g9N8gKd8012234; Wed, 23 Oct 2002 10:42:20 +0200 X-Authentication-Warning: laplinux.dcfe.unimi.it: acontini owned process doing -bs Date: Wed, 23 Oct 2002 10:42:20 +0200 (CEST) From: Alessandro Contini X-X-Sender: acontini@laplinux.dcfe.unimi.it To: Alice NgarKit Ko cc: chemistry@ccl.net Subject: Re: CCL:PDB file editing In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g9N8hBS22814 Hi, a good open source software for your purpose is the "Swiss PDB Viewer" downloadable at url: http://www.expasy.org/spdbv/ Best reguards Alessandro Dott. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Facoltà di Farmacia, Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm On Tue, 22 Oct 2002, Alice NgarKit Ko wrote: > Hi, > I would like to know if there is an easy way to edit a PDB file. I loaded > the structure into VMD for viewing. There are a lot of water molecules > that have traveled far from where I wanted them. I hope I can use some > program where I can just pick and delete the water molecules and then > write out the remaining atoms to a new PDB file. If anyone knows how to > do this, please let me know. Thank you very much > > Alice > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Wed Oct 23 11:15:18 2002 Received: from rutchem.rutgers.edu ([128.6.1.216]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9NFFIS32530 for ; Wed, 23 Oct 2002 11:15:18 -0400 Received: (from xiangjun@localhost) by rutchem.rutgers.edu (8.9.3/8.9.3) id LAA3054606; Wed, 23 Oct 2002 11:15:18 -0400 (EDT) Date: Wed, 23 Oct 2002 11:15:18 -0400 (EDT) Message-Id: <200210231515.LAA3054606@rutchem.rutgers.edu> From: Xiang Lu To: reg8@cornell.edu CC: angelschnur@hotmail.com, chemistry@ccl.net Subject: Re: CCL:rotate molecules along princliple moments of inertia Reply-to: xiangjun@rutchem.rutgers.edu You raised a good point and there are indeed some technical details to go into to get things "right". While I am not so sure about the mathematics and physics involved, the procedures I used seem to work fine for my purpose: [1] Pre-process xyz (n-by-3 matrix) to reset its orientation according to the reference frame of the first nucleic acid base; or as defined by the first 3 non-linear atoms. This will eliminate the ambiguity (e.g., upside-down) associated with arbitrary initial orientation. [2] get the co-variance matrix (real symmetric, 3-by-3). [3] solve the eigensystem (using e.g. jacobi transformation as in Numerical Recipes), sort the eigenvalues, and normalize eigenvectors. [4] check to make sure the third eigenvector is the cross product of the first two, otherwise reverse its sign. There are two more permutations which can be used to get three orthogonal views. Does anyone out there have a more rigorous way? Xiang-Jun -- Dr. Xiang-Jun Lu | Tel: (732) 445 4619 (O) Department of Chemistry | Rutgers University | Fax: (732) 445 5958 610 Taylor Road | Email: xiangjun@rutchem.rutgers.edu Piscataway, NJ 08854-8087 | URL: http://rutchem.rutgers.edu/~xiangjun/ >>>>> "Richard" == Richard Gillilan writes: Richard> This same problem pops up when I have an ensemble of Richard> identical, but randomly-oriented bodies (proteins) Richard> in solution and I wish to transform them all back to Richard> - the same - body coordinate system. You get to the body Richard> system by diagonalizing the inertial matix, but I suspect Richard> the problem is that eigenvalues can be returned by the Richard> numerical routine in any order and with any sign. The Richard> resulting body coordinate sytems then differ by Richard> permutations and sign changes of axes subject to the Richard> condition that the handedness must be preserved. I seem Richard> to remember this has something to do with permutation groups Richard> so that the required sign changes are related to the Richard> parity of the permutation (swap axes and you must change a sign Richard> to preserve handedness). At any rate, is there a way of putting Richard> eigenvectors in some kind of canonical order with appropriate Richard> sign so that the diagonalization routines always land you in the Richard> same body system? Richard> Richard Gillilan Richard> MacCHESS From chemistry-request@server.ccl.net Wed Oct 23 05:50:53 2002 Received: from mail.nii.res.in ([202.54.102.178]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9N9opS24452 for ; Wed, 23 Oct 2002 05:50:51 -0400 Received: from yadavg (helo=localhost) by mail.nii.res.in with local-esmtp (Exim 3.36 #1) id 184I9Z-0007sh-00; Wed, 23 Oct 2002 15:20:17 +0530 Date: Wed, 23 Oct 2002 15:20:17 +0530 (IST) From: To: Alice NgarKit Ko cc: Subject: Re: CCL:PDB file editing In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi alice there are several ways. The simplest is to remove all water molecules from your pdb file by using the 'grep -v " HOH "' command and redirect the output into a new file. Or using any pdb viewer, display off the waters, and save the displayed atoms into a new file in the pdb format. ----------------------------------------------------------------------- On Tue, 22 Oct 2002, Alice NgarKit Ko wrote: > Hi, > I would like to know if there is an easy way to edit a PDB file. I loaded > the structure into VMD for viewing. There are a lot of water molecules > that have traveled far from where I wanted them. I hope I can use some > program where I can just pick and delete the water molecules and then > write out the remaining atoms to a new PDB file. If anyone knows how to > do this, please let me know. Thank you very much > > Alice > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > -- **************************************************************************** \ / | \ / \ / | | GITANJALI YADAV SENIOR RESEARCH FELLOW BIOINFORMATICS UNIT NATIONAL INSTITUTE OF IMMUNOLOGY ARUNA ASAF ALI MARG NEW DELHI-110067 INDIA. PHONE:9111- 6162281/6103008/6183004/6163009-ext 424 ***************************************************************************** From chemistry-request@server.ccl.net Wed Oct 23 12:21:38 2002 Received: from gatekeeper.tripos.com ([192.160.145.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9NGLbS02599 for ; Wed, 23 Oct 2002 12:21:37 -0400 Received: (from uucp@localhost) by gatekeeper.tripos.com (8.11.6+Sun/8.11.6) id g9NGL4C20380 for ; Wed, 23 Oct 2002 11:21:04 -0500 (CDT) Received: from cairo.tripos.com(172.20.176.21) by gatekeeper.tripos.com via csmap (V6.0) id srcAAAhhayZN; Wed, 23 Oct 02 11:21:03 -0500 Received: (from nmalcolm@localhost) by cairo.tripos.com (SGI-8.9.3/8.9.3) id PAA21162; Wed, 23 Oct 2002 15:16:24 -0100 (BST) Date: Wed, 23 Oct 2002 15:16:24 -0100 (BST) Message-Id: <200210231616.PAA21162@cairo.tripos.com> X-Authentication-Warning: cairo.tripos.com: nmalcolm set sender to nmalcolm@tripos.com using -f From: "Nathaniel O.J. Malcolm" To: ako@cse.nd.edu CC: chemistry@ccl.net In-reply-to: (yadavg@nii.res.in) Subject: Re: CCL:PDB file editing Sender: nmalcolm@tripos.com Reply-To: nmalcolm@tripos.com Organization: Tripos UK Ltd. References: Alice, There is also a cool emacs pdb mode available from Charlie Bond at Dundee Uni which is worth playing with (if you like emacs of course...) Noj -- -------------------------------- Dr. N.O.J. Malcolm Software Application Scientist Tripos UK Ltd nmalcolm@tripos.com Tel +44 (0)1908 650020 Fax +44 (0)1908 650001 -------------------------------- Sybyl, Unity and other products are exclusive property of Tripos & are protected trademarks, copyrights, & patents as appropriate The information in this e-mail is confidential and may have associated legal obligations. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender. From chemistry-request@server.ccl.net Wed Oct 23 18:21:31 2002 Received: from rufus.biomed.brown.edu ([128.148.53.178]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9NMLUS09543 for ; Wed, 23 Oct 2002 18:21:30 -0400 Received: from localhost (pc@localhost) by rufus.biomed.brown.edu (SGI-8.9.3/8.9.3) with ESMTP id SAA27810 for ; Wed, 23 Oct 2002 18:21:25 -0400 (EDT) Date: Wed, 23 Oct 2002 18:21:25 -0400 From: Paul Czodrowski To: Subject: Motion of Proteins: Distance Difference Map Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCL, I read something about evaluation of the motion of a protein: they use a so-called "distance difference map", which take one protein strucuture and calculates sequentially the distancse between the first C-alpha atom and all other one. Then it continues with the second C_alpha etc. I know that this should be really fast to program from scratch, but I'm not a Pro. I know about one program from Garry Paul Gippert (GAP - Geometric Analysis of Proteins) - http://www.fkem2.lth.se/~garry/programs/gap.html - but the server is down, so that I can't download it. Cheers, Paul _____________________________________ Paul Czodrowski Department of Molecular Pharmacology Biomedical Center Box G-B4, Brown University Providence, Rhode Island 02912 USA Voice: +1 401 863 9841 http;//bms.brown.edu/mierke _____________________________________ From chemistry-request@server.ccl.net Wed Oct 23 12:34:02 2002 Received: from EPOCH.arqule.com ([64.212.193.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9NGY2S02844 for ; Wed, 23 Oct 2002 12:34:02 -0400 Received: by EPOCH.arqule.com with Internet Mail Service (5.5.2656.59) id ; Wed, 23 Oct 2002 12:34:02 -0400 Message-ID: From: "Czerminski, Ryszard" To: "'Xiang Lu'" , reg8@cornell.edu Cc: angelschnur@hotmail.com, chemistry@ccl.net Subject: RE: rotate molecules along princliple moments of inertia Date: Wed, 23 Oct 2002 12:34:02 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: text/plain; charset="iso-8859-1" It seems that the method described in the Kabsch paper is what you are looking for: C Wolfgang Kabsch "A solution for the best rotation C to relate two sets of vectors" Acta Cryst. (1976) A32, 922 R Ryszard Czerminski phone: (781)994-0479 ArQule, Inc. email:ryszard@arqule.com 19 Presidential Way http://www.arqule.com Woburn, MA 01801 fax: (781)994-0679 -----Original Message----- From: Xiang Lu [mailto:xiangjun@rutchem.rutgers.edu] Sent: Wednesday, October 23, 2002 11:15 AM To: reg8@cornell.edu Cc: angelschnur@hotmail.com; chemistry@ccl.net Subject: CCL:rotate molecules along princliple moments of inertia You raised a good point and there are indeed some technical details to go into to get things "right". While I am not so sure about the mathematics and physics involved, the procedures I used seem to work fine for my purpose: [1] Pre-process xyz (n-by-3 matrix) to reset its orientation according to the reference frame of the first nucleic acid base; or as defined by the first 3 non-linear atoms. This will eliminate the ambiguity (e.g., upside-down) associated with arbitrary initial orientation. [2] get the co-variance matrix (real symmetric, 3-by-3). [3] solve the eigensystem (using e.g. jacobi transformation as in Numerical Recipes), sort the eigenvalues, and normalize eigenvectors. [4] check to make sure the third eigenvector is the cross product of the first two, otherwise reverse its sign. There are two more permutations which can be used to get three orthogonal views. Does anyone out there have a more rigorous way? Xiang-Jun -- Dr. Xiang-Jun Lu | Tel: (732) 445 4619 (O) Department of Chemistry | Rutgers University | Fax: (732) 445 5958 610 Taylor Road | Email: xiangjun@rutchem.rutgers.edu Piscataway, NJ 08854-8087 | URL: http://rutchem.rutgers.edu/~xiangjun/ >>>>> "Richard" == Richard Gillilan writes: Richard> This same problem pops up when I have an ensemble of Richard> identical, but randomly-oriented bodies (proteins) Richard> in solution and I wish to transform them all back to Richard> - the same - body coordinate system. You get to the body Richard> system by diagonalizing the inertial matix, but I suspect Richard> the problem is that eigenvalues can be returned by the Richard> numerical routine in any order and with any sign. The Richard> resulting body coordinate sytems then differ by Richard> permutations and sign changes of axes subject to the Richard> condition that the handedness must be preserved. I seem Richard> to remember this has something to do with permutation groups Richard> so that the required sign changes are related to the Richard> parity of the permutation (swap axes and you must change a sign Richard> to preserve handedness). At any rate, is there a way of putting Richard> eigenvectors in some kind of canonical order with appropriate Richard> sign so that the diagonalization routines always land you in the Richard> same body system? Richard> Richard Gillilan Richard> MacCHESS -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Oct 23 11:57:25 2002 Received: from medusa.bioc.aecom.yu.edu ([129.98.80.187]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9NFvOS01950 for ; Wed, 23 Oct 2002 11:57:24 -0400 Received: from medusa.bioc.aecom.yu.edu (localhost.bioc.aecom.yu.edu [127.0.0.1]) by medusa.bioc.aecom.yu.edu (8.12.5/8.12.5) with ESMTP id g9NFvJOM002240 for ; Wed, 23 Oct 2002 11:57:19 -0400 Received: from localhost (alewand@localhost) by medusa.bioc.aecom.yu.edu (8.12.5/8.12.5/Submit) with ESMTP id g9NFvFVv002235 for ; Wed, 23 Oct 2002 11:57:19 -0400 Date: Wed, 23 Oct 2002 11:57:15 -0400 (EDT) From: Andrzej Lewandowicz To: chemistry@ccl.net Subject: MEP visualization Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear, I have problem with Molecular electrostatic potential visualization by Molekel with cube generated by G98. For one molecule the shadows of the blue color represent positive values and red negative values, for another there is exactly reverse, so there is no way to compare MEPs by consistent color map. Is another program to visualize MEP from Gaussian (beside GaussView ?) or is any way to manage with this problem during visualization by Molekel. The change of Vmin/Vmax didn't help. Andrzej From chemistry-request@server.ccl.net Wed Oct 23 18:06:32 2002 Received: from pragmatix.bangor.ac.uk ([147.143.2.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9NM6VS09359 for ; Wed, 23 Oct 2002 18:06:32 -0400 Received: from scientifix.bangor.ac.uk (scientifix [147.143.2.119]) by pragmatix.bangor.ac.uk (8.12.1/8.12.1) with ESMTP id g9NM6QwY021649 for ; Wed, 23 Oct 2002 23:06:26 +0100 (BST) Received: from belimawr (chem93 [147.143.16.34]) by scientifix.bangor.ac.uk (8.12.2+Sun/8.12.1) with SMTP id g9NM6PSb015231 for ; Wed, 23 Oct 2002 23:06:26 +0100 (BST) Message-ID: <001401c27ae1$1123e2f0$22108f93@belimawr> From: "Helen Howard-Jones" To: Subject: gamess input ERROR Date: Wed, 23 Oct 2002 23:10:58 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0011_01C27AE9.729262C0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 This is a multi-part message in MIME format. ------=_NextPart_000_0011_01C27AE9.729262C0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Many thanks to those of you who replied to my previous request. Only now = I have another one!! My test input is this (in internal coords as I want to modify molecule = later):=20 $control coord=3Dzmt units=3Dangs scftyp=3DROB3LYP runtyp=3Doptimize = chrg=3D0 mult=3D1 $basis=3D31 ngauss=3D4 $zmat $END $DATA optimisation benzene:rob3lyp cnv 6 x c6 x 1.40304 c1 c6 d1 x a2 c2 c1 d2 c6 120. x 0. 0 c3 c2 d3 c1 120. x 0. 0 c4 c3 d4 c2 120. x 0. 0 c5 c4 d5 c3 120. x 0. 0 x1 c2 1.5 c3 90. c4 -90. 0 x2 c3 1.5 c4 90. c5 -90. 0 x3 c4 1.5 c5 90. c6 -90. 0 x4 c5 1.5 c6 90. c1 -90. 0 x5 c6 1.5 c1 90. c2 -90. 0 x6 c1 1.5 c2 90. c3 -90. 0 h1 c6 h1c6 c1 120. x6 -90. 0 h2 c1 h2c1 c2 120. x1 -90. 0 h3 c2 h3c2 c3 120. x2 -90. 0 h4 c3 h4c3 c4 120. x3 -90. 0 h5 c4 h5c4 c5 120. x4 -90. 0 h6 c5 h6c5 c6 120. x5 -90. variables: d1=3D1.40585969 d2=3D1.38805889 d3=3D1.40479196 d4=3D1.40323351 d5=3D1.38686601 h1c6=3D1.08160985 h2c1=3D1.08108159 h3c2=3D1.36420291 h4c3=3D1.08174779 h5c4=3D1.0823553 h6c5=3D1.08236572 constants: a2 60.0 $END BUT: get following error message: RUN TITLE --------- optimisation benzene:rob3lyp THE POINT GROUP OF THE MOLECULE IS CNV THE ORDER OF THE PRINCIPAL AXIS IS 6 **** ERROR READING VARIABLE NGAUSS CHECK COLUMN 4 c6 x 1.40304 = ....V....1....V....2....V....3....V....4....V....5....V....6....V....7...= .V.... 8 **** ERROR READING VARIABLE SCFAC CHECK COLUMN 4 c6 x 1.40304 = ....V....1....V....2....V....3....V....4....V....5....V....6....V....7...= .V.. Im not sure what Im doing wrong! Any help is gratefully received. Many thanks Helen ------=_NextPart_000_0011_01C27AE9.729262C0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Many thanks to those of you who replied = to my=20 previous request. Only now I have another one!!
My test input is this (in internal = coords as I=20 want to modify molecule later): 
 $control coord=3Dzmt units=3Dangs = scftyp=3DROB3LYP=20 runtyp=3Doptimize chrg=3D0
mult=3D1 $basis=3D31=20 ngauss=3D4
 $zmat
 $END
 $DATA
optimisation=20 benzene:rob3lyp
cnv 6
 
x
c6 x 1.40304
c1 c6 d1 x=20 a2
c2           = ;       =20 c1   d2       = c6   =20 120.     x    =20 0.      =20 0
c3           =        =20 c2   d3       = c1   =20 120.     x    =20 0.      =20 0
c4           =        =20 c3   d4       = c2   =20 120.     x    =20 0.      =20 0
c5           =        =20 c4   d5       = c3   =20 120.     x    =20 0.      =20 0
x1           =        =20 c2   1.5       = c3   =20 90.      c4  =20 -90.     =20 0
x2           =        =20 c3   1.5       = c4   =20 90.      c5  =20 -90.     =20 0
x3           =        =20 c4   1.5       = c5   =20 90.      c6  =20 -90.     =20 0
x4           =        =20 c5   1.5       = c6   =20 90.      c1  =20 -90.     =20 0
x5           =        =20 c6   1.5       = c1   =20 90.      c2  =20 -90.     =20 0
x6           =        =20 c1   1.5       = c2   =20 90.      c3  =20 -90.     =20 0
h1           =        =20 c6   h1c6       = c1   =20 120.     x6   = -90.     =20 0
h2           =        =20 c1   h2c1       = c2   =20 120.     x1   = -90.     =20 0
h3           =        =20 c2   h3c2       = c3   =20 120.     x2   = -90.     =20 0
h4           =        =20 c3   h4c3       = c4   =20 120.     x3   = -90.     =20 0
h5           =        =20 c4   h5c4      c5   =20 120.     x4   = -90.     =20 0
h6           =        =20 c5   h6c5        =20 c6    120.     x5  =20 -90.
variables:
d1=3D1.40585969
d2=3D1.38805889
d3=3D1.404791= 96
d4=3D1.40323351
d5=3D1.38686601
h1c6=3D1.08160985
h2c1=3D1= .08108159
h3c2=3D1.36420291
h4c3=3D1.08174779
h5c4=3D1.0823553h6c5=3D1.08236572
constants:
a2=20 60.0
 $END
 
BUT: get following error = message:
RUN TITLE
    =20 ---------
 optimisation
benzene:rob3lyp
 

 THE POINT GROUP OF THE = MOLECULE IS=20 CNV
 THE ORDER OF THE PRINCIPAL AXIS IS    =20 6
 **** ERROR READING VARIABLE NGAUSS   CHECK = COLUMN =20 4
 c6 x 1.40304
 
 ....V....1....V....2....V....3....V....4....V....5....V...= .6....V....7....V....
8
 ****=20 ERROR READING VARIABLE SCFAC    CHECK COLUMN  = 4
 c6=20 x 1.40304
 
 ....V....1....V....2....V....3....V....4....V....5....V...= .6....V....7....V..
 
Im not sure what Im doing wrong! Any = help is=20 gratefully received.
Many thanks
Helen
------=_NextPart_000_0011_01C27AE9.729262C0-- From chemistry-request@server.ccl.net Wed Oct 23 19:38:44 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9NNciS15774 for ; Wed, 23 Oct 2002 19:38:44 -0400 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id g9NNcjb03441; Wed, 23 Oct 2002 19:38:45 -0400 (EDT) Date: Wed, 23 Oct 2002 19:38:44 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net, microelectronics@asdn.net Subject: ACS Symposium on Computational Nanotechnology (Nov. 15, 2002, Abstract deadline) (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Wed, 23 Oct 2002 15:14:08 -0700 From: Mario Blanco To: jkl@ccl.net Cc: "wag@wag.caltech.edu" Subject: ACS Symposium on Computational Nanotechnology (Nov. 15, 2002, Abstract deadline) [....] CALL FOR PAPERS Computational Nanotechnology A Symposium to be held at the 225th ACS National Meeting Computers in Chemistry Division March 23-27, 2003 New Orleans, Louisiana Co-Organizers: William A. Goddard III (wag@wag.caltech.edu) & Mario Blanco (mario@wag.caltech.edu) Beckman Institute 139-74 California Institute of Technology Pasadena, CA 91125 Summary This symposium focuses on the computer modeling and simulation of molecular based nanotechnology components and devices. Papers on computational methods, currently under use or under development, which have been applied towards the support of chemical synthesis of molecular components (bottom-up) and/or fabrication of devices incorporating molecular components (top-down), are strongly encouraged. Papers on molecular computer aided design (molecular CAD) and molecular analysis tools in support of nanotechnology applications are greatly encouraged. Papers on massively parallel molecular dynamics formulations, suitable for the simulation of large molecular assemblies as well as multi-scale (Quantum to molecular dynamics, coupled particle/continuum) simulation methods are also encouraged. New designs of molecular devices acting as switches, nano-electromechanical actuators (NEMS), nano-fluidics, electrically, optically, and/or chemically driven motors, molecular based artificial muscle fibers, carbon-nanotube and fullerenes based devices, computational bio-nanotechnology concepts and devices incorporating DNA, proteins, GPCR's, olfactory receptors, peptides, self-assembled nanotubes and membrane channels and combinations thereof are also strongly encouraged. Abstract Deadline: November 15, 2002 Abstract Submission Procedure: Abstracts must be submitted via the ACS OASys system by the deadline date. The abstract should arouse interest in the paper and do it justice. Succinctly state the purpose of the paper and mention important results and conclusions. Abstracts are submitted on line at http://oasys.acs.org/acs/225nm/comp/papers/index.cgi . Follow instructions and choose this symposium. Once inside write down your abstract ID and passcode for future reference. Notice that for this symposium all presentations are oral. For more information visit http://www.acs.org/meetings or contact one of the co-organizers above. Mario Blanco, PhD e-mail:mario@wag.caltech.edu Director, Molecular Process Simulations fax: (626) 585-0918 California Institute of Technology BI 139-74 phone: (626) 395-2754 Pasadena, CA 91125