A New Jmol Interface for Handling and Visualizing
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Open Babel Documentation Release 2.3.1
Open Babel Documentation Release 2.3.1 Geoffrey R Hutchison Chris Morley Craig James Chris Swain Hans De Winter Tim Vandermeersch Noel M O’Boyle (Ed.) December 05, 2011 Contents 1 Introduction 3 1.1 Goals of the Open Babel project ..................................... 3 1.2 Frequently Asked Questions ....................................... 4 1.3 Thanks .................................................. 7 2 Install Open Babel 9 2.1 Install a binary package ......................................... 9 2.2 Compiling Open Babel .......................................... 9 3 obabel and babel - Convert, Filter and Manipulate Chemical Data 17 3.1 Synopsis ................................................. 17 3.2 Options .................................................. 17 3.3 Examples ................................................. 19 3.4 Differences between babel and obabel .................................. 21 3.5 Format Options .............................................. 22 3.6 Append property values to the title .................................... 22 3.7 Filtering molecules from a multimolecule file .............................. 22 3.8 Substructure and similarity searching .................................. 25 3.9 Sorting molecules ............................................ 25 3.10 Remove duplicate molecules ....................................... 25 3.11 Aliases for chemical groups ....................................... 26 4 The Open Babel GUI 29 4.1 Basic operation .............................................. 29 4.2 Options ................................................. -
The Alexandria Library, a Quantum-Chemical Database of Molecular Properties for Force field Development 9 2017 Received: October 1 1 1 Mohammad M
www.nature.com/scientificdata OPEN Data Descriptor: The Alexandria library, a quantum-chemical database of molecular properties for force field development 9 2017 Received: October 1 1 1 Mohammad M. Ghahremanpour , Paul J. van Maaren & David van der Spoel Accepted: 19 February 2018 Published: 10 April 2018 Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules. Design Type(s) data integration objective • molecular physical property analysis objective Measurement Type(s) physicochemical characterization Technology Type(s) Computational Chemistry Factor Type(s) Sample Characteristic(s) 1 Uppsala Centre for Computational Chemistry, Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden. Correspondence and requests for materials should be addressed to D.v.d.S. (email: [email protected]). -
Chemical File Format Conversion Tools : a N Overview
International Journal of Engineering Research & Technology (IJERT) ISSN: 2278-0181 Vol. 3 Issue 2, February - 2014 Chemical File Format Conversion Tools : A n Overview Kavitha C. R Dr. T Mahalekshmi Research Scholar, Bharathiyar University Principal Dept of Computer Applications Sree Narayana Institute of Technology SNGIST Kollam, India Cochin, India Abstract— There are a lot of chemical data stored in large different chemical file formats. Three types of file format databases, repositories and other resources. These data are used conversion tools are discussed in section III. And the by different researchers in different applications in various areas conclusion is given in section IV followed by the references. of chemistry. Since these data are stored in several standard chemical file formats, there is a need for the inter-conversion of II. CHEMICAL FILE FORMATS chemical structures between different formats because all the formats are not supported by various software and tools used by A chemical is a collection of atoms bonded together the researchers. Therefore it becomes essential to convert one file in space. The structure of a chemical makes it unique and format to another. This paper reviews some of the chemical file gives it its physical and biological characteristics. This formats and also presents a few inter-conversion tools such as structure is represented in a variety of chemical file formats. Open Babel [1], Mol converter [2] and CncTranslate [3]. These formats are used to represent chemical structure records and its associated data fields. Some of the file Keywords— File format Conversion, Open Babel, mol formats are CML (Chemical Markup Language), SDF converter, CncTranslate, inter- conversion tools. -
Package Name Software Description Project
A S T 1 Package Name Software Description Project URL 2 Autoconf An extensible package of M4 macros that produce shell scripts to automatically configure software source code packages https://www.gnu.org/software/autoconf/ 3 Automake www.gnu.org/software/automake 4 Libtool www.gnu.org/software/libtool 5 bamtools BamTools: a C++ API for reading/writing BAM files. https://github.com/pezmaster31/bamtools 6 Biopython (Python module) Biopython is a set of freely available tools for biological computation written in Python by an international team of developers www.biopython.org/ 7 blas The BLAS (Basic Linear Algebra Subprograms) are routines that provide standard building blocks for performing basic vector and matrix operations. http://www.netlib.org/blas/ 8 boost Boost provides free peer-reviewed portable C++ source libraries. http://www.boost.org 9 CMake Cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software http://www.cmake.org/ 10 Cython (Python module) The Cython compiler for writing C extensions for the Python language https://www.python.org/ 11 Doxygen http://www.doxygen.org/ FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created. It supports the most obscure ancient formats up to the cutting edge. No matter if they were designed by some standards 12 ffmpeg committee, the community or a corporation. https://www.ffmpeg.org FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and 13 fftw complex data (as well as of even/odd data, i.e. -
Quantum Chemical Calculations of NMR Parameters
Quantum Chemical Calculations of NMR Parameters Tatyana Polenova University of Delaware Newark, DE Winter School on Biomolecular NMR January 20-25, 2008 Stowe, Vermont OUTLINE INTRODUCTION Relating NMR parameters to geometric and electronic structure Classical calculations of EFG tensors Molecular properties from quantum chemical calculations Quantum chemistry methods DENSITY FUNCTIONAL THEORY FOR CALCULATIONS OF NMR PARAMETERS Introduction to DFT Software Practical examples Tutorial RELATING NMR OBSERVABLES TO MOLECULAR STRUCTURE NMR Spectrum NMR Parameters Local geometry Chemical structure (reactivity) I. Calculation of experimental NMR parameters Find unique solution to CQ, Q, , , , , II. Theoretical prediction of fine structure constants from molecular geometry Classical electrostatic model (EFG)- only in simple ionic compounds Quantum mechanical calculations (Density Functional Theory) (EFG, CSA) ELECTRIC FIELD GRADIENT (EFG) TENSOR: POINT CHARGE MODEL EFG TENSOR IS DETERMINED BY THE COMBINED ELECTRONIC AND NUCLEAR WAVEFUNCTION, NO ANALYTICAL EXPRESSION IN THE GENERAL CASE THE SIMPLEST APPROXIMATION: CLASSICAL POINT CHARGE MODEL n Zie 4 V2,k = 3 Y2,k ()i,i i=1 di 5 ATOMS CONTRIBUTING TO THE EFG TENSOR ARE TREATED AS POINT CHARGES, THE RESULTING EFG TENSOR IS THE SUM WITH RESPECT TO ALL ATOMS VERY CRUDE MODEL, WORKS QUANTITATIVELY ONLY IN SIMPLEST IONIC SYSTEMS, BUT YIELDS QUALITATIVE TRENDS AND GENERAL UNDERSTANDING OF THE SYMMETRY AND MAGNITUDE OF THE EXPECTED TENSOR ELECTRIC FIELD GRADIENT (EFG) TENSOR: POINT CHARGE MODEL n Zie 4 V2,k = 3 Y2,k ()i,i i=1 di 5 Ze V = ; V = 0; V = 0 2,0 d 3 2,±1 2,±2 2Ze V = ; V = 0; V = 0 2,0 d 3 2,±1 2,±2 3 Ze V = ; V = 0; V = 0 2,0 2 d 3 2,±1 2,±2 V2,0 = 0; V2,±1 = 0; V2,±2 = 0 MOLECULAR PROPERTIES FROM QUANTUM CHEMICAL CALCULATIONS H = E See for example M. -
Pipenightdreams Osgcal-Doc Mumudvb Mpg123-Alsa Tbb
pipenightdreams osgcal-doc mumudvb mpg123-alsa tbb-examples libgammu4-dbg gcc-4.1-doc snort-rules-default davical cutmp3 libevolution5.0-cil aspell-am python-gobject-doc openoffice.org-l10n-mn libc6-xen xserver-xorg trophy-data t38modem pioneers-console libnb-platform10-java libgtkglext1-ruby libboost-wave1.39-dev drgenius bfbtester libchromexvmcpro1 isdnutils-xtools ubuntuone-client openoffice.org2-math openoffice.org-l10n-lt lsb-cxx-ia32 kdeartwork-emoticons-kde4 wmpuzzle trafshow python-plplot lx-gdb link-monitor-applet libscm-dev liblog-agent-logger-perl libccrtp-doc libclass-throwable-perl kde-i18n-csb jack-jconv hamradio-menus coinor-libvol-doc msx-emulator bitbake nabi language-pack-gnome-zh libpaperg popularity-contest xracer-tools xfont-nexus opendrim-lmp-baseserver libvorbisfile-ruby liblinebreak-doc libgfcui-2.0-0c2a-dbg libblacs-mpi-dev dict-freedict-spa-eng blender-ogrexml aspell-da x11-apps openoffice.org-l10n-lv openoffice.org-l10n-nl pnmtopng libodbcinstq1 libhsqldb-java-doc libmono-addins-gui0.2-cil sg3-utils linux-backports-modules-alsa-2.6.31-19-generic yorick-yeti-gsl python-pymssql plasma-widget-cpuload mcpp gpsim-lcd cl-csv libhtml-clean-perl asterisk-dbg apt-dater-dbg libgnome-mag1-dev language-pack-gnome-yo python-crypto svn-autoreleasedeb sugar-terminal-activity mii-diag maria-doc libplexus-component-api-java-doc libhugs-hgl-bundled libchipcard-libgwenhywfar47-plugins libghc6-random-dev freefem3d ezmlm cakephp-scripts aspell-ar ara-byte not+sparc openoffice.org-l10n-nn linux-backports-modules-karmic-generic-pae -
1 Introduction – the Basic Computational Environment This Chapter Provides You with Some Basic Introduction to Your 'Computational Work Desk'
The Basic Computational Environment 1 1 Introduction – The Basic Computational Environment This chapter provides you with some basic introduction to your 'Computational Work desk'. It is structured into three parts. The first one consists of some quick tutorial how to login into your machine. The second part deals with basic steps in a UNIX-like environment and introduces the 'SHELL', the UNIX command line. In the third part two of the most used editors are presented in order to enable the user to manipulate text files at will. 1.1 Login Into Your Computer Before you can login it is essential that you haven been provided with a username and a password. Usually these are provided by your chemistry department or your system administrator. The first thing you will see is the 'login-screen', asking you to type in your username. Figure 1: a typical login screen The screen might look somewhat different, but it should be similar to the one shown above. Once you typed in your username and pressed the <RETURN> key, the system will ask you for your password, which you are expected to type, again followed by <RETURN>. (The pressing of the <RETURN> key after typing in some commands or other things is assumed from now on.) Having succeeded in providing the correct password you are provided with your graphical desktop. All your actions will take place in this environment. The next thing to do is to open a window containing a command- line, which is usally called a 'shell'. This is nothing else than a window where you can type in your commands. -
Is a Package for Displaying Molecular Density DESCRIPTION MOLDEN Is
Molden 1 MOLDEN FUNCTION Molden - is a package for displaying Molecular Density DESCRIPTION MOLDEN is a package for displaying molecular density. It is tuned to the Ab Initio packages GAMESS* and GAUSSIAN. It can read all the information it needs from a GAMESS or GAUSSIAN outputfile. In this form it has been running on a Convex C-120, an Apollo DN10000, an IRIS 4d/70gt, a DECstation 5000 and a SUN, and in slightly adapted versions on a VAX and a Cray-YMP. It should run smoothly on most Unix machines. See section INSTALLATION GUIDE on how to install MOLDEN.(* The GAMESS version referred to here is the european version maintaned by M.F. Guest et al not to be confused with the american version maintained by M.W. Schmidt et al) MOLDEN was written by: G. Schaftenaar CAOS/CAMM Center Nijmegen Toernooiveld, Nijmegen The Netherlands (1991) e-mail adress : [email protected] FILES MOLDEN reads two files, these are: Inputfile File holding the title and keyword lines ( FORTRAN unit 5 ) GAMESS/GAUSSIAN Outputfile A file produced by running GAMESS/GAUSSIAN. The name of this file must be defined with the keyword file . This must be the output of a single GAMESS/GAUSSIAN run. Care must be taken not to turn off printing of vectors and/or basis set in the case of GAMESS. In the case of GAUSSIAN printing of basis set information has to be turned on by the use of the keyword GFINPUT. Printing of MO coefficients has to be turned on by use of the keyword IOP(6/7=1).( FORTRAN unit 30 ) MOLDEN writes two files, these are: Outputfile Results file. -
Computational Chemistry: a Practical Guide for Applying Techniques to Real-World Problems
Computational Chemistry: A Practical Guide for Applying Techniques to Real-World Problems. David C. Young Copyright ( 2001 John Wiley & Sons, Inc. ISBNs: 0-471-33368-9 (Hardback); 0-471-22065-5 (Electronic) COMPUTATIONAL CHEMISTRY COMPUTATIONAL CHEMISTRY A Practical Guide for Applying Techniques to Real-World Problems David C. Young Cytoclonal Pharmaceutics Inc. A JOHN WILEY & SONS, INC., PUBLICATION New York . Chichester . Weinheim . Brisbane . Singapore . Toronto Designations used by companies to distinguish their products are often claimed as trademarks. In all instances where John Wiley & Sons, Inc., is aware of a claim, the product names appear in initial capital or all capital letters. Readers, however, should contact the appropriate companies for more complete information regarding trademarks and registration. Copyright ( 2001 by John Wiley & Sons, Inc. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic or mechanical, including uploading, downloading, printing, decompiling, recording or otherwise, except as permitted under Sections 107 or 108 of the 1976 United States Copyright Act, without the prior written permission of the Publisher. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 605 Third Avenue, New York, NY 10158-0012, (212) 850-6011, fax (212) 850-6008, E-Mail: PERMREQ @ WILEY.COM. This publication is designed to provide accurate and authoritative information in regard to the subject matter covered. It is sold with the understanding that the publisher is not engaged in rendering professional services. If professional advice or other expert assistance is required, the services of a competent professional person should be sought. -
User's Guide Terachem V1.9
User’s Guide TeraChem v1.9 PetaChem, LLC 26040 Elena Road Los Altos Hills, CA 94022 http://www.petachem.com August 16, 2017 TeraChem User’s Guide Contents 1 Introduction 3 1.1 Obtaining TeraChem.........................................4 1.2 Citing TeraChem...........................................4 1.3 Acknowledgements..........................................5 2 Getting started 6 2.1 System requirements.........................................6 2.2 Installation..............................................6 2.3 Environment Variables........................................7 2.4 Licensing...............................................8 2.4.1 Node-locked Licenses.....................................8 2.4.2 IP-Checkout Licenses....................................9 2.4.3 HTTP Forwarding......................................9 2.5 Command Line Options....................................... 10 2.6 Running sample jobs......................................... 12 3 TeraChem I/O file formats 17 3.1 Input files............................................... 17 3.2 Atomic coordinates.......................................... 17 3.3 Basis set file format......................................... 17 3.3.1 Mixing basis sets - Custom Basis File Method....................... 20 3.3.2 Mixing Basis Sets - Multibasis Method........................... 21 3.4 Fixing Atoms in Molecular Dynamics................................ 21 3.5 Ab Initio Steered Molecular Dynamics (AISMD)......................... 22 3.6 Specifying Values of the Hubbard Parameter for DFT+U................... -
Chey Marcel Jones
Chey Marcel Jones CURRICULUM VITAE 350 Sharon Park Dr, Menlo Park, CA 94025 [email protected] | (570) 449-7329 EDUCATION Stanford University Stanford, CA Doctor of Philosophy, Chemistry Expected 2022 Research Advisor: Todd Martínez Temple University Philadelphia, PA Bachelor of Science with Honors, Chemistry Aug. 2013 – May 2017 Summa Cum Laude, Distinction in Major Research Advisor: Spiridoula Matsika Cumulative GPA: 3.94/4.00 AWARDS AND HONORS 2017-2022, National Science Foundation Graduate Research Fellowship National Science Foundation 2017-2022, Stanford Graduate Fellowship in Science and Engineering Stanford University – Department of Chemistry 2017-2022, Enhancing Diversity in Graduate Education (EDGE) Doctoral Fellowship Stanford University 2017, ACS Scholastic Achievement Award in Chemistry American Chemical Society, Philadelphia Section 2017, Stanford Summer Fellowship Stanford University 2016, ACS 252nd National Meeting Outstanding Undergraduate Poster Award American Chemical Society, Division of Physical Chemistry 2016, Leadership Alliance Summer Research-Early Identification Program (SR-EIP) Scholar Stanford University 2016-2017, Albert B. Brown Chemistry Award Temple University – Main Campus 2015-2016, Albert B. Brown Chemistry Award Temple University – Main Campus 2015-2017, Maximizing Access to Research Careers – Undergraduate Student Training in Academic Research (MARC U-STAR) Award National Institutes of Health, Temple University – Main Campus 2013-2017, Honors Provost Scholarship Award Temple University – Main Campus RESEARCH EXPERIENCE Undergraduate Research Advisor: Spiridoula Matsika Sep. 2014 - May 2017 Temple University – Main Campus • Electronic structure and behavior of a molecular photochromic switch were investigated for applications in nanotechnology and optical data storage. Photo-physical pathways were modeled, using multi-reference methods, to elucidate reaction pathways through conical intersections, based on ground-state and excited-state character. -
Lecture 2: Standard Software and Visualization Tools
The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble. P. A. M. Dirac, 1929. Lecture 2: standard software and visualization tools A brief overview of simulation and visualization software in current use Dr Ilya Kuprov, University of Southampton, 2012 (for all lecture notes and video records see http://spindynamics.org) Expert level packages: Gaussian Notable Pro Notable Contra Excellent internal coordinate module supporting very Very expensive, carries severe sophisticated scans, constraints and licensing restrictions. energy surface analysis. Does not scale to more than 4 Excellent solvation and reaction (CISD) to 32 (DFT) cores, even on field support. shared memory systems. Very user-friendly, clear and A real pain to install. forgiving input syntax. Gaussian is not the most %Mem=16GB CPU-efficient package in exis- %NProcShared=8 #p opt=tight rb3lyp/cc-pVDZ scf=(tight,dsymm) tence, but it takes much less integral=(grid=ultrafine) time to set up a Gaussian job than a job for any other Flavin anion geometry optimization expert level package. -1 1 N.B.: CPU time is £0.06 an C 0.00000000 0.00000000 0.00000000 hour, brain time is £25+ an C 0.00000000 0.00000000 1.41658511 C 1.23106864 0.00000000 2.09037416 hour. C 2.43468421 0.00000000 1.39394037 http://www.gaussian.com/g_prod/g09_glance.htm Expert level packages: GAMESS Notable Pro Notable Contra Three distinct code branches (UK, US, PC) with Excellent configuration interaction module.