Ruby script (RbAnalysisFMO in AnalysisFMO Toolkit) 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), Paics (the parallelized ab initio calculation system),
and ABINIT-MP (the ABINT ab initio multi-processor)). 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 and The PAICS program package
can calculate IFIEs. ABINIT-MP program package can calculate IFIEs but
ABINIT-MP Open series can calculate IFIEs and PIEs.
Note that this analyzed csv file (*.csv) is visualized on PyMOL program by PyPaics, PyGAMESS, or PyABINIT-MP programs and developed by Shogo Nakano.
There are two analysis modes in this ruby script as following:
・”Selected-pairs” mode in “one-dimensional table”:
This mode can be analyzed energies as fragments-target interaction from the FMO out file. Target is fragment, ligand, peptide, H2O, ion, and so on. In the case of Paics calculation, it is used “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 “frag_calc_pair” option are described in P. 14 the Chapter2 “INPUT” at http://www.paics.net/pdf/manual.pdf. This mode saves as a CSV (Comma-Separated Values format, *.csv) and TXT (ASCII (text) format, *.txt) files in one-dimensional table. Energy data is plotted bar graph using the gnuplot program. The PS file is converted the PDF file using ps2pdf program after this plotted graph is saved as the PS file by gnuplot.
・”All-pairs” mode in “two-dimensional table”:
This mode can be analyzed energies as (all) fragments-(all) fragments, which may be included ligand, peptide, H2O and so on, interaction from the FMO out file. In the case of PAICS calculation, it is not used “frag_calc_pair” option (that is, results of PAICS for all fragment calculation). This mode saves as a CSV (Comma-Separated Values format, *.csv) and TXT (ASCII (text) format,, *.txt) files in two-dimensional table. And, Energy data is plotted 2D graph using gnuplot program.
The detail of how to use RbPaics is described in the attached manual in
Supporting operating system: Windows, Linux (Unix), (Not tested and check on Mac OS)
Supporting Ruby language version: Ruby 1.9.3, Ruby 2.x
Ruby library: open3, fileutils, logger, Nokogiri (sparklemotion/nokogiri. GitHub. https://github.com/sparklemotion/nokogiri/blob/master/LICENSE.md (accessed September 26th, 2018))
Required programs to use these ruby scripts
→ Please check section 2 in the manual on this web-page.
RbPaics could be downloaded from following links.
Manual of RbPaics could be downloaded from following link.