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marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
Apache License 2.0
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-govs-include no longer present? #603

Closed BartBruininks closed 3 months ago

BartBruininks commented 3 months ago

Dear martinizers,

We have been working on an alternative Go implementation and it is currently in publication, however, when I try to run our scripts with the current Martinize2 it seems the -govs-include flag does not exist anymore. We have a custom script that allows for arbitrary copy numbers for homooligomers. Is there a suggested workaround or are we now stuck at an older version (if so, which one?). It would be nice if the old behavior would still be supported.

PREVIOUSLY WORKING COMMAND: martinize2 -f protein.pdb -o output.top -x protein_cg.pdb -dssp /path/to/dssp -p backbone -ff martini3001 -govs-include -govs-moltype protein_name -scfix

pckroon commented 3 months ago

-govs-include has been superseded by -go, with changed semantics in #550. The previous flag will not be restored. I strongly suggest adapting your new model to the new flags, since it'll be better for your sanity.

BartBruininks commented 3 months ago

Yhea I was on the same track.