Dear Amber Users,
I have learned that the total size of the periodic cell (i.e., the number
of atoms in the system produced by LEAP) significantly depends on the
initial orientation of the protein structure - in my case the size can vary
within a range from 107 000 to 138 000 atoms for an identical protein
molecule. It seems that the original XYZ axes of a cell are fixed in LEAP,
so if the protein molecule is oriented diagonally with respect to XYZ then
the cell size would be the largest.
My question - is there any parameter in LEAP to automatically adjust the
cell to the dimensions of an input protein molecule (i.e., automatically
rotate the XYZ axes) so that the size of the periodic system in water is
the smallest?
Thank you.
Dmitry
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Received on Sat Nov 04 2017 - 03:00:03 PDT
