Dear Amber developer and users,
Thank you for usual support and giving a comments.
I am now trying to identify small ligand cluster.
Here I use "checkoverlap" in ptraj modules.
Using the command,
I am feeling that "checkoverlap" checks not only real cell but also image
cell.
For example, in the situation where I calculate the distance between
molecule A and B,
If distance between A in real cell and B in real cell is larger than that
between
A in real cell and B in image cell, the later would be written down as a
value.
I am most grateful if you give me some comments on my guess.
Yours sincerely,
Ikuo Kurisaki
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Received on Mon Oct 24 2011 - 05:30:08 PDT
