the goodman group
university of cambridge  

Chemical Information Laboratory


Short scripts to help with common tasks

  • batq
    List all jobs on the batch queues, including those submitted by other people (note atq and at -l only list your own jobs. The information is up to fifteen minutes out of date.
  • bminbat
    Put a MacroModel job on the batch queue
  • boltz
    This program processes the log file from a MacroModel to calculate all the Boltzmann factors for a series of compounds
  • boltzfile
    Boltzmann factors from a file containing a series of energies in kJ/mol
  • boltzout
    Boltzmann factors from a MacroModel .out file
  • c2mm
    Cadpac output to MacroModel format
  • cluster
    Schrodinger's clustering program
  • cos2ead
    Cosmic output to MacroModel format
  • gam2mm
    GAMESS to MacroModel format
  • jag2molden
    Jaguar to Molden format
  • jagbat
    Submit a jaguar input file to the batch queue
  • jagck
    Running Jaguar jobs have files in a temporary directory as well as the current directory. This command extracts the convergence information from one file and the latest energy from another. It supercedes jagdfck and jaghfck
    jagck filename
  • jagfreq
    Take a Jaguar frequency calculation and create a molden file which can visualise the normal mode vibrations.
  • jagfreqanalysis
    Take a jaguar frequency calculation and project the vibrational modes onto the bonds. This suggests associations between frequencies and particular bond vibrations
    jagfreqanalysis filename
  • jagplot
    Create a jaguar input file, containing plotting commands, to visualise orbitals, etc. The command takes an input file as an argument which must have its structure in Cartesian coordinates, not as a Z-matrix.
  • jagresults
    Summaries the results from a Jaguar output file
  • javamol
    Display a mol file
  • lfcrsortout
    When transferring files between computers, sometimes carriage returns change to a different character, so the file has just one long line. This command can fix the problem.
  • lfcrsortoutbatch
    As above, but works for multiple files
  • mm2cad
    MacroModel to Cadpac format
  • mm2gam
    MacroModel to GAMESS format
  • mm2mop
    MacroModel to MOPAC format
  • mm2mopG
    MacroModel to MOPAC format with geometry optimisation
  • mm2mopM
    MacroModel to MOPAC format with geometry optimisation
  • mmck
    Running MacroModel jobs have files in a temporary directory as well as the current directory. This command shows the current status of a conformation search calculation.
    mmck filename
  • mop2mm
    MOPAC to MacroModel format
  • mop2mmall
    MOPAC to MacroModel format
  • mult2mop
    All structures in a MacroModel file to separate MOPAC files
  • nao2ead
  • QRC
  • rungamess
    Run a GAMESS job - but use rungms instead to put it on batch queue
  • rungms
    Put a GAMESS job on the batch queue

© Goodman Group, 2005-2024; privacy; last updated July 18, 2024

department of chemistry University of Cambridge