VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jun 02 2020 - 12:43:54 CDT

The VMD hydrogen bonds plugin is a GUI to access the "measure hbonds"
script command.

That command expects atom data consistent with the CHARMM force field,
specifically hydrogen atoms are recognized by their (string format) atom
type.
also, you seem to be misunderstanding the purpose of the selections. those
are to encompass the hydrogen bond donors and acceptors (which does *NOT*
include the hydrogen atoms, but the one that they are bound to and to which
they form a hydrogen bond, they may be the same, e.g. in the case of water)--00000000000028bbf005a71d75af--