From chemistry-request@server.ccl.net Fri Apr 18 07:37:18 2003 Received: from marilyn.uochb.cas.cz ([147.231.120.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3IBbHE31319 for ; Fri, 18 Apr 2003 07:37:17 -0400 Received: from iveta.uochb.cas.cz (iveta.uochb.cas.cz [147.231.120.176]) by marilyn.uochb.cas.cz (8.11.6/8.11.6) with ESMTP id h3IBbJs14653 for ; Fri, 18 Apr 2003 13:37:19 +0200 Received: from svozil by iveta.uochb.cas.cz with local (Exim 3.35 #1 (Debian)) id 196UB6-000187-00 for ; Fri, 18 Apr 2003 13:37:12 +0200 Date: Fri, 18 Apr 2003 13:37:12 +0200 To: chemistry@ccl.net Subject: Molecular transformation language Message-ID: <20030418113712.GA4321@iveta.uochb.cas.cz> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.28i From: Daniel Svozil Hi, I am doing some calculations with the molecules differently oriented each to other and a lot of time takes to prepare the coordinate files for those system. So I started looking for some possibility how to automatize this process as much as possible. Do you know, is there any programming language or library of the existing language that offers this functionality? Here are some my ideas what should such a system include: - easy, but powerful way how to select atoms for the transformations (e.g. select the whole backbone, select all waters in system, select atoms number 1,3,6, select atoms that are not further than 3 angstroms from the given atom/point, select all carbons, etc., etc.) - some sort of clever coordinate systems, so I can say e.g. rotate this H atom in H2O around the axis defined by thos OH bond, etc. - the possibility to read/wite at least PDB, XYZ would be also nice - possibility to calculate different geometric characteristics (bond lenghts, angles, dihedrals) for the given set of atoms - simple molecular viewer to check the transformed system (e.g. just wireframe, with scene rotation/translation/zooming, with the possibility to measure lengths/angles/dihedrals) - the language should be interpreted, not compiled So far I went through VMD, PyMol, NAB and currently I am ivestigating MMTK package. VMDs functionality is much broader and I didn't figure out, how to perform some transformation tasks, though I am sure it can be done. PyMol has very poor documentation, especially transformation procedure seem to be undocumented. NAB (http://www.scripps.edu/case/casegr-sh-2.2.html) is a manipulation language for DNA/proteins, but it could probably be used for other systems as well. Unfortunately, I didn't suceed with the compilation under Linux (though I am sure I'll resolve it eventually). Also, NAB is compiled language, which I find as a disadvantage. MMTK (http://starship.python.net/crew/hinsen/MMTK/) is probably also capable of the molecular transformations, but it is general molecular mechanics system, so it has a lot of other features. So to summarize, I didn't find any simple scriptable molecular transformation system so far. I am sure that such a software would be interesting for a lot people. Maybe I am looking in the wrong direction. Any help would be more than appreciated. Regards Dan -- Daniel Svozil, PhD Institute of Organic Chemistry and Biochemistry and Center for Complex Molecular Systems and Biomolecules http://www.molecular.cz/ Czech Republic phone: +420-2-20 183 263 From chemistry-request@server.ccl.net Thu Apr 17 16:17:13 2003 Received: from celebris04.cetem.gov.br ([200.20.105.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3HKHCE03414 for ; Thu, 17 Apr 2003 16:17:13 -0400 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Thu, 17 Apr 2003 16:33:02 -0300 Message-ID: <216FE3CA3D4DD611AE2600105AD16BDFD56B1B@correio.cetem.gov.br> From: Ian Hovell To: =?iso-8859-1?Q?Chemistry_=28Correio_eletr=F4nico=29?= Subject: Jcamp formatted spectra in hyperchem Date: Thu, 17 Apr 2003 16:32:58 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) 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 h3HKHDE03415 Hi CLLers, Does anyone know of a program that converts Jcamp-DX (*.jdx *.dx) formatted spectra into script files readable by Hyyperchem or Gaussian? Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Ciência e da Tecnologia- MCT Avenida Ipê, No 900 - Cidade Universitaria Ilha do Fundão Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell@cetem.gov.br From chemistry-request@server.ccl.net Fri Apr 18 08:13:56 2003 Received: from admin.cnrs-orleans.fr ([163.9.1.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3ICDtE32054 for ; Fri, 18 Apr 2003 08:13:55 -0400 Received: from chinon (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.12.9/jtpda-5.4) with ESMTP id h3ICCKDl014710 ; Fri, 18 Apr 2003 14:12:20 +0200 (MET DST) Content-Type: text/plain; charset="iso-8859-1" From: Konrad Hinsen To: Daniel Svozil , chemistry@ccl.net Subject: Re: CCL:Molecular transformation language Date: Fri, 18 Apr 2003 14:16:36 +0200 User-Agent: KMail/1.4.3 References: <20030418113712.GA4321@iveta.uochb.cas.cz> In-Reply-To: <20030418113712.GA4321@iveta.uochb.cas.cz> MIME-Version: 1.0 Message-Id: <200304181416.36968.hinsen@cnrs-orleans.fr> X-MailScanner: Found to be clean Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h3ICDuE32055 On Friday 18 April 2003 13:37, Daniel Svozil wrote: > Do you know, is there any programming language or library of the existing > language that offers this functionality? You are already looking at MMTK, which can do most of what you need. Only visualization needs to be delegated to external viewers. However, with a VRML viewer, you can set up any visualization that you like. > Here are some my ideas what should such a system include: > - easy, but powerful way how to select atoms for the transformations > (e.g. select the whole backbone, select all waters in system, select Rather straightforward in any object-oriented system. > atoms number 1,3,6, select atoms that are not further than 3 angstroms > from the given atom/point, select all carbons, etc., etc.) Two to three lines of Python code for any of these. > - some sort of clever coordinate systems, so I can say e.g. rotate this > H atom in H2O around the axis defined by thos OH bond, etc. molecule.rotateAroundAxis(molecule.O.position(), molecule.H1.position(), 45.*Units.deg) > - the possibility to read/wite at least PDB, XYZ would be also nice PDB is there, XYZ takes four lines of Python code. > - possibility to calculate different geometric characteristics (bond > lenghts, angles, dihedrals) for the given set of atoms All there. > - simple molecular viewer to check the transformed system (e.g. just > wireframe, with scene rotation/translation/zooming, with the > possibility to measure lengths/angles/dihedrals) VMD and PyMol are fine for all that and can be used from MMTK scripts. > MMTK > (http://starship.python.net/crew/hinsen/MMTK/) is probably also capable of > the molecular transformations, but it is general molecular mechanics > system, so it has a lot of other features. Indeed. But the people on the MMTK mailing list will help you find the things you need for your project. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Apr 18 11:05:58 2003 Received: from oz.che.rochester.edu ([128.151.211.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3IF5vE03283 for ; Fri, 18 Apr 2003 11:05:57 -0400 Received: (from janeou@localhost) by oz.che.rochester.edu (8.11.6+Sun/8.11.6) id h3IF68F22772 for CHEMISTRY@ccl.net; Fri, 18 Apr 2003 11:06:08 -0400 (EDT) Date: Fri, 18 Apr 2003 11:06:08 -0400 (EDT) From: Jane-Jane Ou Message-Id: <200304181506.h3IF68F22772@oz.che.rochester.edu> To: CHEMISTRY@ccl.net Subject: CCL:Freguency job with Gaussian98:Summary The question asked: I am currently running a frequency job with Gaussian98 after optimization. The optimization job did not take very long, however, the frequency job is going very slowly with warnings: **** Warning!!: The largest alpha MO coefficient is 0.10268903D+02 **** Warning!!: The smallest alpha delta epsilon is 0.84363472D-01 What do these warnings mean? <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< The responses: 1: As usual frequency jobs lasts longer than optimization jobs if you have started with a suitable geometry. Those warnings are internal remainds that Gaussian (any version) does and consequetively changes its way of calculations, if i am not wrong its integral calculations. It does not mean that calculation goes wrong. In spite of this remaind your calculation will be completed unless any other error occur. 2: I had the same question like yours so i send a query form to gaussian team in order to give an explanation about the warnig message which you receive. So i attach the response from them "Gaussian tests the values of the MO coefficients and orbital energies after each SCF calculation. When you get a warning about the smallest delta epsilon, the warning is referring to the difference between orbital energies. Since some of the equations in post-HF methods include a term in the numerator which has the MO coefficients to some positive integer and a difference in orbital energies in the denominator, the calculations can become numerically unstable if the numerator is too large (e.g. MO coefficients too large) or the denominator is too small (orbital energy difference too small). So, this is a warning that the post-HF results may be affected. However, the criteria for these warnings are fairly strict, so the vast majority of the calculations that have these warning messages do not actually suffer from numerical instabilities. If you have results that don't seem to make sense, and these warnings are present, it would be a good idea to repeat the calculation with a different basis set (these problems tend to be worse for basis sets with many diffuse functions) to verify the results." 3: Freqs often take longer, sometimes maybe 5 times longer, than optimizations. The warning seems to be most applicable to post-hartree-Fock level calculations and arises from near-linear-dependence of the basis set functions (ideally, they should be linearlylinearly independent). For more information see the summary in the CCL archives, 23 April 2002. Thank you for all the responses. Sincerely yours, Jane Ou