How to execute

[debanjansen48]

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]

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]

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] ... Try python -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

— Reply to this email directly, view it on GitHub https://github.com/rebelot/schrodinger_utils/issues/1#issuecomment-2079162350, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOJ7Q4WGWBWBUAYB7VJJSVLY7IXP5AVCNFSM6AAAAABGZ7DHI2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANZZGE3DEMZVGA . You are receiving this because you authored the thread.Message ID: @.***>