Last I knew, it aligns to principal axes before solvating. So e.g. if
you solvate a box, it will first turn it onto a corner.
On 11/4/17 2:34 AM, Dmitry Suplatov wrote:
> 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 - 03:00:04 PDT
