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marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
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-ss input_file.ssd for martinize2 #367

Open philipford opened 3 years ago

philipford commented 3 years ago

When I prepare a ssd file with the required secondary structure for martinize.py, I can get all the input files correctly. However, martinize2 shows an error of 'The length of the sequence (12) does not match the number of residues in the selection (2372)'. Can we still use input ssd file for the -ss option in martinize2? Any help will be appreciated.

pckroon commented 3 years ago

It looks like that option was removed! I guess it is because when working with ssd files it becomes a bit tricky/ambiguous to figure out which residue (in the ssd file) corresponds to which residue (in the molecule(s)). @jbarnoud any insights here?

jbarnoud commented 3 years ago

The -ss option takes a secondary structure sequence as a string. It seems I omitted that martinize 1 could take a file.

philipford commented 3 years ago

Thanks, pckroon and jbarnoud. As mentioned in 1UBQ tutorial (http://md.chem.rug.nl/index.php/tutorials-general-introduction-gmx5/82-tutorial2-gmx5?start=3), martinize 1 could deal with ssd input file. Hopefully, this option will be kept in martinize2.

pckroon commented 3 years ago

It seems I omitted that martinize 1 could take a file.

Omitted/forgot, or left-out on purpose? As for implementing it, it should not be too hard since all the relevant code is already there: it's just plumbing that's missing. That said, I currently have negative amounts of time available :(