A user has to provide the different inputs for the PyRED program in a single archive file. An archive file is generally compressed allowing a fast upload of large input 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 Project.config and/or System.config 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 for a PyRED job.
• If OPT_Calc = Off is defined in the System.config file, Mol_red'$n'-'$c'.log QM geometry optimization output file(s) [generated by the GAMESS, Firefly or Gaussian QM program; '$n' and '$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 that case.
• If Re_Fit = On is defined in the System.config file, QM geometry optimization and MEP computation output files have also to be included in the Data-R.E.D.Server/Mol_m'$n' directories; see examples below to create the archive file in that 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: generated by using such a command: ' 7zr a archive inputs/Mol_red1.pdb inputs/Project.config inputs/System.config '
• 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 *.config frcmod.user '
• One can also use the graphical environment of the operating system to generate a 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 also 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).
• If OPT_Calc = Off:
  - tar.bz2 or .tbz2: generated by using ' tar -jcvf archive Mol_red?.pdb Mol_red?-?.log Project.config System.config '
  - zip: generated by using ' zip -r archive Mol_red* *.config frcmod.user '
• If Re_Fit = On:
  One has to provide a previous PyRED job:
  - tar.bz2 or .tbz2: generated by using ' tar -jcvf archive Mol_red?.pdb Project.config System.config Data-R.E.D.Server/Mol_m?/JOB1-*.out Data-R.E.D.Server/Mol_m?/JOB2-*.out '
  - zip: generated by using ' zip -r archive Mol_red*.pdb *.config frcmod.user Data-R.E.D.Server/Mol_m*/JOB?-*.out '
  - In case of a large archive file (to excluse the useless 'back' files): ' tar -jcvf archive `ls -v Mol_red*.pdb *.config frcmod.user Data-R.E.D.Server/Mol_m*/JOB?-*.out | grep -v back` '
  - In case of a previous job executed with the ' MOD_GAUSSIAN_JOB = Complex ' keyword, be sure to include the symbolic links present in the original archive file (and not empty files).

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...

Last update of this page: September 5th, 2023.

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