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User's Manual User’s manual: Ruby script for analysis of FMO output (RbAnalysisFMO) (Windows / Unix version) Editor: Takaki Tokiwa Last update: 2019/02/18 1 Contents 0. First of all ..................................................................................................................................... 2 0.1 Copyright notice ...................................................................................................................... 2 0.2 Citation ................................................................................................................................... 2 1. Introduction .................................................................................................................................. 3 2. Preparation ................................................................................................................................... 5 2.1 Required programs .................................................................................................................. 5 2.2 Installation .............................................................................................................................. 8 2.2.1 Installation of PV and Paics ................................................................................................ 8 2.2.2 Installation of Ruby compiler ............................................................................................. 8 2.2.3 Installation of Nokogiri library in Ruby using gem command............................................. 10 2.2.5 Installation of gs (Ghostscript) .......................................................................................... 15 3. Analysis ...................................................................................................................................... 19 3.1 What is needed....................................................................................................................... 19 3.2 Option list.............................................................................................................................. 23 3.3. Analysis from the Paics out file .............................................................................................. 30 3.3.1 “Selected-pairs” mode in “one-dimensional table” ............................................................. 30 3.3.1.1 Comannd line mode without options (standard streams on command-line or terminal) . 30 3.3.1.2 In-line mode (Using options on command-line or terminal) .......................................... 38 3.3.2 “All-pairs” mode in “two-dimensional table” .................................................................... 39 3.3.2.1 Comannd line mode without options (standard streams on command-line or terminal) . 39 3.3.2.2 In-line mode (Using options on command-line or terminal) .......................................... 45 4. References .................................................................................................................................. 46 Appendix ........................................................................................................................................ 47 A – Preparation to install PV and Paics ........................................................................................ 47 B – Installation of gcc/g++ compiler on Ubuntu............................................................................. 47 C – Installation of gfortran compiler on Ubuntu ........................................................................... 47 D – Installation of Intel C and Intel Fortran compiler ................................................................... 47 E – Installation of MPI (Message Passing Interface) ...................................................................... 49 F – Installation of other softwares (freeglut, glut, LaTeX, and tcl/tk) .............................................. 49 G – Installation of PV .................................................................................................................. 52 H – Installation of Paics ............................................................................................................... 54 2 0. First of all 0.1 Copyright notice The Ruby source code (RbAnalysisFMO) is copyrighted, but you can freely use and copy it as long as you don't change or remove any of the copyright notices. This Ruby program (RbAnalysisFMO) is Copyright (C) 2016 by Takaki Tokiwa. All Rights Reserved Permission to use, copy, modify, distribute, and distribute modified versions of this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies and that both the copyright notice and this permission notice appear in supporting documentation, and that the name(s) of the author(s) not be used in advertising or publicity pertaining to distribution of the software without specific, written prior permission. THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. 0.2 Citation Please cite the following paper when using this analysis program (AnalysisFMO toolkit)! - Authors: Takaki Tokiwa, Shogo Nakano, Yuta Yamamoto, Takeshi Ishikawa, Sohei Ito, Vladimir Sladek, Kaori Fukuzawa, Yuji Mochizuki, Hiroaki Tokiwa, Fuminori Misaizu, and Yasuteru Shigeta - Title: Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations - Journal name: Journal of Chemical Information and Modeling - Vol., Issue, pp. year: Vol. 59, Issue 1, pp. 25-30 - DOI: 10.1021/acs.jcim.8b00649 3 1. Introduction This manual provides a first introduction to ruby script (RbAnalysisFMO in AnalysisFMO Toolkit [1]) for analysis the output file (*.out or *.log, and so on) of the fragment molecule orbital (FMO) calcualtion packages (GAMESS (the general atomic and molecular electronic structure system) [2], Paics (the parallelized ab initio calculation system) [3], and ABINIT-MP (the ABINT ab initio multi-processor) [4,5]). The output file of FMO calculation is composed of various data in an ASCII (text) format: run time parameter, atomic coordinate, and inter fragment interaction energies (IFIEs) and/or pair interaction energies (PIEs). It is necessary to extract IFIEs or PIEs from the FMO output file due to analyze and visualize. RbAnalysisFMO is able to analyze and extract IFIEs or PIEs from the FMO output file. The GAMESS program package can calculate PIEs [2] and The PAICS program package can calculate IFIEs [3]. ABINIT-MP program package can calculate IFIEs [4] but ABINIT-MP Open series can calculate IFIEs and PIEs [5]. There are two analysis modes in this ruby script as following: ・”Selected-pairs” mode in “one-dimensional table”: This ruby script using “Selected-pairs” mode analyzes IFIEs or PIEs as fragments-target (target means fragment, ligand, peptide, H2O and so on) interaction from the FMO output file. In the PAICS case, this mode analyzes data from the result of PAICS calculation with the “frag_calc_pair” option (selection of the fragment pairs, such as fragment number 1-100 (ALL) and fragment number 101 (target)). The details of the this option is described in P. 14 the Chapter2 “INPUT” at http://www.paics.net/pdf/manual.pdf/. In the GAMESS case, result is the GAMESS calculation with the “MOLFRG” option (The details of the this option is described in P. 276 the Section 2 – “Input Description” at http://fisica.ufpr.br/bettega/input_GAMESS.pdf/ or “$FMO group (optional, activates FMO option)” at http://myweb.liu.edu/~nmatsuna/gamess/input/FMO.html/). But, ABINIT-MP and ABINIT-MP Open series (Ver. 1 Rev. 10) do not calculate this mode, as of September in 2018. This mode saves as a CSV (Comma-Separated Values format, *.csv) and TXT (ASCII (text) format, *.txt) files in one-dimensional table. IFIEs data is plotted bar graph using the gnuplot program (http://www.gnuplot.info/ (accessed September 26th, 2018)). The PS file is converted the PDF file using ps2pdf program attached to Ghostscript (https://www.ghostscript.com/ (accessed September 26th, 2018)) after this plotted graph is saved as the PS file by gnuplot. ・”All-pairs” mode in “two-dimensional table”: This ruby script using “All-pairs” mode analyzes IFIEs or PIEs as fragments-fragments (which may be included ligand, peptide, H2O and so on) interaction from the FMO output file. In the PAICS case, this mode analyzes data from the result of PAICS calculation without the “frag_calc_pair” option (that is, results of PAICS for all fragment calculation). In the GAMESS case, result is the GAMESS calculation without the “MOLFRG” option. This mode saves as a CSV (*.csv) and TXT (*.txt) files in two-dimensional table and can plot 2D interaction map from IFIE or PIE data using Gnuplot. 4 In addition, the RbAnalysisFMO requires several Ruby libraries: Logger and Nokogiri (sparklemotion/nokogiri. GitHub. https://github.com/sparklemotion/nokogiri/blob/master/LICENSE.md (accessed September 26th, 2018)), which is Rubygen providing HTML and XML. The manual is subdivided in two sections. The first one covers the basic preparation
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