Dear amber users
in amber manual, there is [ The optional "distance" keyword specifies the
cutoff distance for the pair interactions
and the optional "angle" keyword specifies the angle cutoff for the hydrogen
bond. The default is no angle cutoff and a distance of 3.5 angstroms.]
I think that in hb (D-H...A) distance of 3.5 angstroms = distance between D
and A.
is my think true?
what means of no angle cutoff? donor–hydrogen-acceptor or acceptor-
donor–hydrogen?
if I want following criterion for hydrogen bond analysis, is [ hbond
distance 3.5 angle 135 series] in ptraj file true?
donor-acceptor distance (dDA) ≤ 3.5 Å and the donor–hydrogen-acceptor angle
(αDHA) ≥ 135°.
any help will highly appreciated.
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Received on Sat Jul 30 2011 - 05:30:03 PDT
