AMBER Archive (2004)

Subject: Re: AMBER: hbond in ptraj

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Fri May 07 2004 - 14:15:15 CDT

> As I know donor should provide hydrogen. And acceptor accepts
> hydrogen. But donor command in ptraj only need one heavy atom
> to be specified, while acceptor need both heavy atom and hydrogen
> to be specified.
> Or may be the HBond donor means providing electron and acceptor
> means receiving electron?

Yes, if you are intending to measure hydrogen bonds, the donor is the
electron pair donor (-O, N:, ...) and the acceptor is the electron pair
acceptor (-O-H, -N-H, ...). This is semantically opposite to
the way most people think about it, but for some reason I always thought
about it as electron pair donors and acceptors rather than hydrogen
donor/acceptors.

Note that this command is rather general however in that you do not
necesarily have to measure traditional D--H-A distances but could do X-Y
distances...

  donor RES X
  acceptor RES Y Y

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