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marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
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Protein with too many chains #406

Open outihaa opened 2 years ago

outihaa commented 2 years ago

When one has a protein with 200 individual chains, how can one read it into martinize2? There are not enough characters in the alphabet to name the individual chains.

pckroon commented 2 years ago

Tricky :) I don't think you strictly need to specify the chain ID in your pdb. This should be accounted for automatically based on connectivity. Alternatively, you can put TER records between your chains to signify they're different molecules. You may want to test this on something small though, maybe 200 chains consisting of 1 atom each :)

fgrunewald commented 2 years ago

@outihaa chain identifiers only really matter for the elastic network, if you want have the elastic network (EN) only within the same chain for example. As @pckroon pointed out there is no real solution for this (other than using the TER record) and martinize2 should work as expected when you have the same identifier for almost all other cases. Let us know if it works or doesn't work what you are trying to do.

pckroon commented 2 years ago

One last word of warning regarding TER records: make sure that any disulfide bonds are specified as CONECT records. And check them by hand once martinize is done.

fgrunewald commented 2 years ago

@outihaa were you able to solve your issue?