CHAMI F. wrote:
> Dear all,
>
> I need to extract the box dimensions from an mdcrd trajectory file to each frame in a pdb file :
> i can have this ::::::::::::::::::::::::::::::::
> MODEL 1
> BOX x y z ang1 ang2 ang3
> REMARK 1 PDB file generated by ptraj (set 1)
> ATOM 1 C6 STE 1 4.692 3.040 48.736 0.00 0.00
> ATOM 2 H8 STE 1 4.625 3.445 49.766 0.00 0.00
> ATOM 3 H9 STE 1 4.473 3.914 48.032 0.00 0.00
Dear Fatima,
If your trajectory has been saved in the netcdf format, you can extract
the cell lengths and angles using the netcdf tool, ncdump:
ncdump -v cell_lengths mdcrd.nc
ncdump -v cell_angles mdcrd.nc
Under Ubuntu, this can be installed with:
sudo apt-get install netcdf-bin
You should be able to incorporate this into some form of script, perhaps
using a combination of sed and awk, to obtain what you desire as
outlined above.
Regards,
Mark
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Received on Wed Sep 07 2011 - 07:00:07 PDT
