AMBER Archive (2004)

Subject: AMBER: ptraj and hbond

From: Nelson Fonseca (nfonseca_at_dq.ua.pt)
Date: Thu Aug 26 2004 - 04:50:39 CDT

Experience is what you get when you don't get what you
want.
        
                      -- Dan Stanford--

Dear all,

I would like to know the exact meaning of the angle cutoff
option of hbond command. If Im not wrong, the distance
cutoff for a hydrogen bond of the type O-H...O is defined
as the distance between the two heavy atoms of oxygen, but
Im having strange results when I change the value of the
angle cutoff. For example when I define a value of 60º ,
in the output I get all the angles above 60º but when I
define the cutoff to be 100º I get all my angles under
100º ! This behavior is somewhat contradictory.
How can I get for example all the interactions between
pairs ignoring the angle cutoff?

Thanks in advance.

Regards,

Nelson Fonseca
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