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marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
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Sequential distance between two residues for elastic network #392

Closed toontun closed 2 years ago

toontun commented 2 years ago

Hello,

I wonder what is the cutoff that will permits to connect two residues in the elastic network (Rubber Band) ? Is it residue i+2 ? i+4? I mean on the linear sequence.

Thank you,

pckroon commented 2 years ago

From: https://github.com/marrink-lab/vermouth-martinize/blob/master/vermouth/processors/apply_rubber_band.py There is a minimum distance between residues after which elastic bonds will be applied (default 2, can be overriden with the -ermd CLI flag). From the CLI you can also set a minimum and maximum elastic bond length (in nm (or A?)) with -el and -eu. There is also a minimum forceconstant for elastic bands: if they're weaker than that they'll be removed. You can set that with -em. See also martinize2 -h, and specifically the Protein elastic network section.

Now, a bit more on the minimum distance between residues: This is /not/ limited to the linear sequence, but will also take e.g. disulphide bonds into account. Note that this behaviour differs from how martinize1 works!

toontun commented 2 years ago

OK, very clear, thank you!