AMBER Archive (2005)

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

From: haixiao jin (jinhx952_at_gmail.com)
Date: Thu Oct 20 2005 - 05:49:29 CDT

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_at_O :173_at_OD1 out distance.list

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

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

Mask [:173_at_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_at_O]. thanks for your attention!
Any suggestion will be helpful.
  haixiaojin

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