AMBER: trouble in calculating the distance between O atom of water molecule and atom of residue

From: haixiao jin <>
Date: Thu, 20 Oct 2005 18:49:29 +0800

Dear all,

I try to calculate a distance between the center of mass of the oxygen atom
of structural water molecule and the center of mass of a atom of residue,
the input script is showed bellow:

 trajin 1npt.mdcrd

distance 1 :342.O :173.OD1 out distance.list

 but the :342.O that represents the O atom of water molecule is unregonized..
The message is showed that:

 Mask [:342.O] represents O atoms!!!!! NO ATOMS DETECTED!!!

Mask [:173.OD1] represents 1 atoms

 How could it happen!
To carry out the hydrogen bond analysis of water molecule, it is OK to
represent O atom of water molecule in [:342.O]. thanks for your attention!
Any suggestion will be helpful.

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Received on Thu Oct 20 2005 - 12:53:01 PDT
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