MD analysis using Python

Question

I am trying to run this command:

python3 traj_orientation-group.py -g fnIII-9_ps20_Nchain6_T298_nw.gro -x fnIII-9_ps20_Nchain6_T298_nw.xtc -o fnIII-9_ps20_Nchain6_run1.phrsn-orientation --protein_res_start 1 --protein_res_stop 89 –group 51 52 53 54 55

This is for MD analysis. I got this following error below:

usage: traj_orientation-group.py [-h] [-g GROFILE] [-x XTCFILE] [-o OUTFILE] [--protein_res_start PROTEIN_RES_START] [--protein_res_stop PROTEIN_RES_STOP] [--group GROUP [GROUP ...]] traj_orientation-group.py: error: unrecognized arguments: –group 51 52 53 54 55

How can I resolve this?

For more context, see the mailing list thread https://groups.google.com/g/mdnalysis-discussion/c/J8oJ0M9Rjb4/m/vHsPjXC1DQAJ — orbeckst, Dec 23 '21 at 19:17
The solution here was to use `--group` instead of `-group`, so this question can be closed as "Typo". — halfer, Mar 18 '23 at 12:17

score 1 · Answer 1 · edited Mar 18 '23 at 12:15

1

You are providing an argument –group 51 52 53 54 55 and it seems that the only option in the source script is --group (so a double dash is needed)

I will also mention that -g and --group are equivalent and you already provided some arguments to -g here -> -g fnIII-9_ps20_Nchain6_T298_nw.gro

edited Mar 18 '23 at 12:15

halfer

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answered Dec 23 '21 at 09:47

w_sz

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Hi, it worked with --group. Thanks a lot – Viswa Vittal Dec 23 '21 at 12:43
please accept the best answer if it worked :) – w_sz Dec 23 '21 at 14:07

MD analysis using Python

1 Answers1