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jvermaas / LigninBuilder

VMD Plugin and associated scripts to build lignin structures from topological specifications
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combined final state #6

Open ashomali opened 2 years ago

ashomali commented 2 years ago

Dear all,

Thanks for the helpful code. Is there any way to combine all the pdb/psf files after the minimization with namd?

jvermaas commented 2 years ago

My recommendation would be to use TopoTools to mash them together into a single psf/pdb pair. See the topotools documentation for examples of how to combine different molecules from VMD together. LigninBuilder also has some code in there to try and do an initial separation that then needs to be minimized again (see the separatelignins procedure within ligninbuilder.tcl).