Utility Programs

Dabble comes with a few utility programs that I've found helpful for system preparation and analysis. They all use the Dabble API and are invoked from the command line. They should be in your $PATH if you installed Dabble using conda.

Obtaining restraint masks for AMBER

To restrain specific residues when conducting simulations with AMBER, the residue number is used. However, in the prmtop file format, any resid information (corresponding to PDB numbering) is not retained, with the system instead being numbered starting from zero. This can make the selection of restraint masks challening.

As Dabble outputs intermediate files containing resid info (most notably the psf, when obtaining a prmtop with CHARMM parameters), the get_restraint_mask.py script can help you convert resids into a restraint mask suitable for your mdin file.

NOTE: The way this script works requires a psf file corresponding to your system. As the project I wrote the script for was using CHARMM parameters, Dabble had generated a psf output file in addition to the prmtop used in AMBER. If you're using AMBER parameter sets you won't get this intermediate file and will need to use a different approach.

There are no command-line arguments, just invoke the script and it will prompt you for the psf and restraint selection.

# TODO sample output from this script