AMBER Archive (2006)

Subject: AMBER: ptraj grid output

From: Vlad Cojocaru (
Date: Thu Jan 19 2006 - 12:25:49 CST

Dear ambers,
  I am trying to analyze the waters around and inside a protein by using
the grid command in ptraj (as described by Thomas -- I have a question
about the output density....
  As far as I understood the output gives the number of selected atoms
that lie on the grid point during the traj... I am processing a 1000
frames trajectory and I have 1 water that is present in the same spot
all the time. The biggest value in the output density is about 165 (I
visualized the density with Chimera) and corresponds to the water that
is always there. However, I thought that in such a case, the number
should be close to 1000 since I have 1000 frames that have the water on
the same spot, thus about 1000 atoms (oxygens) lying on the same spot or
very close to it ... Either I am doing something wrong or I completely
misunderstood the meaning of the output ...
  Could somebody explain in a bit more detail what is actually output by
the grid command?


The ptraj input is:

center :1-461 mass origin
image origin center familiar

grid wat.grid 200 0.5 200 0.5 200 0.5 :WAT_at_O

Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298

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