Creation of the archive file

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A user has to provide the different input files for the PyRED program in a single archive file. An archive file is generally compressed allowing a fast upload of large files. The maximum size for an uploaded archive file is set to 90 MB at R.E.D. Server Development (see here for help for creating an archive file).

To be recognized by PyRED, the input files must have the following names in the archive file:

• 'n' consecutive PDB input file(s) has/have to be provided [filename(s): Mol_red'n'.pdb; 'n' is an integer representing the input molecule(s), which is incremented: 'n' > 0]
• The System.config and Project.config configuration input files can also be included to overwrite the default tasks carried out by PyRED and/or to perform additional tasks
• The frcmod.user input file can also be included to provide missing force field parameters (see the Amber file formats)
• If OPT_Calc = Off is defined in the System.config file, Mol_red'n'-'c'.log QM geometry optimization output file(s) [generated with the GAMESS, Firefly or Gaussian QM program by using another computer cluster; 'n' and 'c' are two integers representing the input molecule(s) and their conformation(s), respectively: 'n' > 0 and 'c' > 0] has/have also to be provided as input file(s) (see examples below to create the archive file in this case)
• If Re_Fit = On is defined in the System.config file, QM geometry optimization and MEP computation output files generated from a previous PyRED job have also to be included (these files must be found in the Data-R.E.D.Server/Mol_m'n' directories; see examples below to create the archive file in this case)

The PyRED program does NOT recognize the MOL2, P2N and ENT input file formats! Use instead the PDB file format with the '.pdb' file extension for your input molecule(s).

Various types of archive files are automatically recognized by R.E.D. Server Development (input files in the archive file can be in the working directory or in a sub-directory):

• 7-zip (has a high compression ratio): generated by using such a command: ' 7zr/7za a archive dir_inputs/Mol_red1.pdb dir_inputs/System.config dir_inputs/Project.config dir_inputs/frcmod.user '
  (the System.config, Project.config and frcmod.user files are not mandatory; 'dir_inputs': the PyRED input and configuration files may be included in a directory or may be directly present in the working directory)
• zip: generated by using: ' zip -r archive data/Mol_red?.pdb data/*.config data/frcmod.user '
  ('?' = a single character and '*' = multiple characters)
• rar: generated by using: ' rar a archive Mol_red*.pdb *.config '
• tar.gz or .tgz: generated by using: ' tar -zcvf archive Mol_red?.pdb *.config '
• tar.bz2 or .tbz2: generated by using: ' tar -jcvf archive Mol_red?.pdb *.config '
• tar: generated by using: ' tar -cvf archive Mol_red*.pdb '
• The graphical environment of the operating system can also be used to generate the compressed archive file: first select the list of input files by keep pushing the 'Ctrl' button of the keyboard, and by clicking on the left button of the mouse; then right click using the mouse, and choose "Create an archive..." or "Compress..." to create the archive.
• A single PDB input file can be directly uploaded without the need of creating an archive file (see the readme.txt file to pass System.config and Project.config keywords in the PDB input files).
• A single QM output file (Gaussian, GAMESS, Firefly file formats are handled) can also be directly uploaded without the need of creating an archive file.

• If OPT_Calc = Off is defined in the System.config file:
  ▲ tar.bz2 or .tbz2: generated by using: ' tar -jcvf archive inp_data/Mol_red*.pdb inp_data/Mol_red*.log inp_data/System.config inp_data/Project.config inp_data/frcmod.user '
  (the Project.config and frcmod.user files are not mandatory)
  ▲ zip: generated by using: ' zip -r archive Mol_red* *.config '

• If Re_Fit = On is defined in the System.config file, QM data generated in a previous PyRED job have to be also provided:
  ▲ tar.bz2 or .tbz2: generated by using: ' tar -jcvf archive Mol_red*.pdb System.config Project.config frcmod.user Data-R.E.D.Server/Mol_m*/JOB1-ga?_*.* Data-R.E.D.Server/Mol_m*/JOB2-ga?_*.* '
  ('ga?' = 'gau' is used to identify Gaussian files, while 'gam' is used for GAMESS/Firefly ones; the Project.config and frcmod.user' files are not mandatory).
  ▲ zip: generated by using: ' zip -r archive Mol_red*.pdb *.config frcmod.user Data-R.E.D.Server/Mol_m*/JOB?-*.* '
  ('?' = '1' and '2' for the QM JOB1*.* geometry optimization and MEP computation JOB2*.* files)
  ▲ In the case of the archive file is too large (i. e. to remain below the 90 MB limit defined by the web server and to exclude the useless 'back' files): ' tar -jcvf archive `ls -v Mol_red*.pdb *.config frcmod.user Data-R.E.D.Server/Mol_m*/JOB?-*.* | grep -v back` '
  ▲ In the case of the previous job was executed with the ' MOD_GAUSSIAN_JOB = Complex ' keyword, be sure to include the symbolic links present in the archive file (and not empty files).
  ▲ If the GAMESS/Firefly program was used in the previous job, MEP data are in the JOB2-gam_m*.dat punch file(s)!

The name and extension of the archive file do not matter: the filename of the uploaded archive is automatically renamed into "ArchiveFile".

The molecule(s) involved in a PyRED job corresponds to the Mol_red'n'.pdb file(s) available in the uploaded archive file. The molecule order used in force field generation also corresponds to that defined in the archive file.

We regularly extend the process of recognition of the archive file and of the files available in this archive by R.E.D. Server Development/PyRED based on the problems encoutered by the users...

QM = quantum mechanics; MEP = molecular electrostatic potential

Last update of this page: November 30th, 2024.

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