Prepare.py Inputs and Arguments

The prepare.py program takes a Model Input File as input and generates the files necessary to run a SEEKR2 calculation.

usage:

python prepare.py [-h] [-f] [-s] MODEL_INPUT_FILE

Required Arguments

MODEL_INPUT_FILE

The name of a model input XML file for a SEEKR2 calculation. Samples model files can be found in the following locations:

seekr2/seekr2/data/sample_input_mmvt_openmm.xml
seekr2/seekr2/data/sample_input_mmvt_namd.xml
seekr2/seekr2/data/sample_input_elber_openmm.xml
seekr2/seekr2/data/trypsin_benzamidine_files/input_tryp_ben_mmvt.xml
seekr2/seekr2/data/trypsin_benzamidine_files/input_tryp_ben_elber.xml

Also, an entire page of documentation is dedicated to explaining the inputs of the model input file.

Optional Arguments

-h, –help

show help message and exit

-f, –force_overwrite

Toggle whether to overwrite existing simulation output files within any anchor that might have existed in an old model that would be overwritten by generating this new model. If not toggled while attempting to overwrite an old model with a new model, this program will throw an exception instead of performing any such overwrite.

-s, –skip_checks

By default, pre-simulation checks will be run after the preparation is complete, and if the checks fail, prepare.py will terminate and the SEEKR2 model will not be saved. This argument bypasses those checks and allows the model to be generated regardless of check outcomes.