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utilities
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Utilities
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 The information is up to fifteen minutes out of date.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
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