AMBER: ptraj and hbond

From: Nelson Fonseca <nfonseca.dq.ua.pt>
Date: Thu, 26 Aug 2004 10:50:39 +0100

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 60 ,
in the output I get all the angles above 60 but when I
define the cutoff to be 100 I get all my angles under
100 ! 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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Received on Thu Sep 02 2004 - 01:15:11 PDT
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