On Oct 10, 2013, at 8:49 PM, Saleem Ayaz <saleemayaz_hu at yahoo.com> wrote:
> Dear users
> When I make structure file for QE calculation I convert cif file to XYZ
> format and take the atomic positions from there but these atomic positions
> are not look to be in angstrom. for example some atomic positions of amino
> acid.
> The correct atomic positions of first C atom are 0.442, 0.612, 0.803 (Ang) .
With respect to which reference system? Maybe you should rather check for atomic
distances and angles.
> Can I use these positions?
Yes, if they correspond to the system you would like to study.
> ATOMIC_POSITIONS {?}
> C 11.861079793 2.966803800 8.127280110
> O 12.509781978 3.985469800 7.796265486
> O 11.516617567 2.651456000 9.302285237
> C 11.377184932 2.032458000 7.026801667
> H 11.452545578 1.096162600 7.340394469
> N 12.229684621 2.211333800 5.820824411
> H 13.094780045 2.076324000 6.097637810
> H 12.186990774 3.124234000 5.410443708
> H 11.963240449 1.545058000 5.294298226
> ...........
> _______________________________________________
>
By looking to the positions you list using a visualisation software, they do
look
reasonable. So maybe they could be just those you want but shifted/rotated.
Giovanni
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