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Re: [IMP-dev] CHARMM topology question



On 8/15/12 11:57 AM, Dina Schneidman wrote:
I want to add bonds, angles and dihedrals to my structure. It has some
missing atoms, but I don't want them there on purpose.
When I create the topology, those atoms are automatically added to the
structure.
Is there a way to tell it not to add any missing atoms?

When in doubt, read the documentation. ;)

topology->setup_hierarchy(mhd_);

This is for the common use case "tidy up the hierarchy so it matches the topology, by adding/removing atoms as necessary". If you don't want to do that, call the functions it calls yourself, leaving out add_missing_atoms().

	Ben
--
                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle