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rebelot / schrodinger_utils

Various integrations to the Schrodinger ecosystem. With major interest on analysis tools for Molecular Dynamics simulations run with Desmond.
MIT License
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How to execute #1

Open debanjansen48 opened 5 months ago

debanjansen48 commented 5 months ago

I am interested in kerseq2hills.py. Kindly guide how to execute the script.

unable to add Desmond scripts using maestro. How to execute them?

rebelot commented 5 months ago

desmond scripts are meant to be used from the command line using the terminal.

e.g. 

$SCHRODINGER/run my_script.py ...

kerseq2hills.py however does not utilize any of the schrodinger API, so you can run it with any python3 interpreter

to see options and invocation

python kerseq2hills.py -h
debanjansen48 commented 5 months ago

Receiving following errors

I am interested in the conversion of desmond metadynamics data to plumed colver and hill file

(base) @.:/media/debanjan/DS-1TB/Acinetobacter_baumannii/MD-Relibactam/MD-1/desmond_metadynamics_MD-1$ python3 kerseq2hills.py desmond_metadynamics_MD-1.kerseq HILLS.out usage: kerseq2hills.py [-h] [-kT KT] [-T T] kerseq out header kerseq2hills.py: error: the following arguments are required: header (base) @.:/media/debanjan/DS-1TB/Acinetobacter_baumannii/MD-Relibactam/MD-1/desmond_metadynamics_MD-1$ python3 -kT KT kerseq2hills.py desmond_metadynamics_MD-1.kerseq HILLS.out Unknown option: -k usage: python3 [option] ... [-c cmd | -m mod | file | -] [arg] ... Try python -h' for more information. (base) ***@***.***:/media/debanjan/DS-1TB/Acinetobacter_baumannii/MD-Relibactam/MD-1/desmond_metadynamics_MD-1$ python3 -kT KT kerseq2hills.py -c desmond_metadynamics_MD-1.kerseq HILLS.out Unknown option: -k usage: python3 [option] ... [-c cmd | -m mod | file | -] [arg] ... Trypython -h' for more information. (base) @.***:/media/debanjan/DS-1TB/Acinetobacter_baumannii/MD-Relibactam/MD-1/desmond_metadynamics_MD-1$ python3 kerseq2hills.py h usage: kerseq2hills.py [-h] [-kT KT] [-T T] kerseq out header kerseq2hills.py: error: the following arguments are required: out, header

On Fri, Apr 26, 2024 at 4:29 PM Tommaso Laurenzi @.***> wrote:

desmond scripts are meant to be used from the command line using the terminal.

e.g.

$SCHRODINGER/run my_script.py ...

kerseq2hills.py however does not utilize any of the schrodinger API, so you can run it with any python3 interpreter

to see options and invocation

python kerseq2hills.py -h

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