OSError: Can't parse line 8 in section '[]' because the section is unknown

[ddesh5208660]

Hi everyone,

I tried to run this tutorial both in the virtual environment and locally. Both didn't seem to work for me. Pls, guide me to run this tutorial.

[fgrunewald]

@ddesh5208660 can you provide the contents of your topology file?

[ddesh5208660]

@fgrunewald Here is the topology file.

[fgrunewald]

which OS are you working on?

[ddesh5208660]

MacOS

[fgrunewald]

I don't know what's exactly going on, but somehow it considers line 8 to be a non-empty section directive. Can you delete the empty line and see what it then says. Also I assume you have the ffbonded.itp and ffnonbonded.itp files in your toplevel folder

[ddesh5208660]

Yes, I do have both files in my top level folder. Line 8 of which "file" I should delete ?

[fgrunewald]

Line 8 of the topology file. The error says that it considers line 8 to be an empty section, which is strange because it should skip that empty line.

[ddesh5208660]

U r right ! But ,Even after deletion, same error appeared as earlier.

here is the topology file after deletion of line 8 along with stated error.

[fgrunewald]

It could be related to Python 10 or there is an obvious mistake I'm not seeing at the moment. Anyways I don't have time to look into this further right now. The best I can suggest is to run the tutorial in google-collab jupyter notebook.

[fgrunewald]

here is an example notebook https://colab.research.google.com/drive/14PKyyUnt_aycyYFALhm0FlBKP1LKeO-9?usp=sharing

[pckroon]

Could you try to remove the commas from the system name?

Also check the lines 8 of the files you include. I'm not 100% sure about which file it's complaining about.

[ddesh5208660]

@pckroon I removed commas but showed the same "OSError". I am also wondering which file it is complaining about.

[ddesh5208660]

It could be related to Python 10 or there is an obvious mistake I'm not seeing at the moment. Anyways I don't have time to look into this further right now. The best I can suggest is to run the tutorial in google-collab jupyter notebook.

I think you could try to build this in MacOS.

[ddesh5208660]

@fgrunewald @pckroon I think in the following block (line 235) there is some issue. Any thoughts on those?

[fgrunewald]

It could be related to Python 10 or there is an obvious mistake I'm not seeing at the moment. Anyways I don't have time to look into this further right now. The best I can suggest is to run the tutorial in google-collab jupyter notebook.

I think you could try to build this in MacOS.

On my Mac I never had issues but it runs python 3.9

[fgrunewald]

@ddesh5208660 can you zip your files and sent them to me by mail f.grunewald[at]rug.nl

[ddesh5208660]

Sure. Sending now.

[fgrunewald]

@ddesh5208660 I figured out what is going wrong. It appears that the forcefield.itp was not properly downloaded. At last in the archive I have an html text instead of a plain text file in itp format. If you include the actual itp file it should work

[fgrunewald]

@pckroon to avoid these things in future it might make sense to return the line with the error that is raised by parse_section. That would make it easier to spot incorrectly formatted files

[ddesh5208660]

@fgrunewald Thanks. Yeah, you were right. I should have checked those files in the VIM editor. Here is the result.