Dear Mark,
thank you so much for your email.
I managed to use the netcdf tool ..it is straightforward to get box size than the VMD plugin
pbc get -molid 9 -all
{40.500000 40.491001 40.471001 90.000000 90.000000 90.000000} {40.508999 40.500000 40.480000 90.000000 90.000000 90.000000} {40.391998 40.382999 40.362999 90.000000 90.000000 90.000000} {40.348999 40.340000 40.320000 90.000000 90.000000 90.000000} {40.334999 40.326000 40.306000 90.000000 90.000000 90.000000} {40.396999 40.388000 40.368000 90.000000 90.000000 90.000000} {40.236000 40.227001 40.207001 90.000000 90.000000 90.000000} {40.370998 40.362000 40.341999 90.000000 90.000000 90.000000} {40.355999 40.347000 40.327000 90.000000 90.000000 90.000000} {40.351002 40.341999 40.321999 90.000000 90.000000 90.000000} {40.408001 40.398998 40.379002 90.000000 90.000000 90.000000} {40.277000 40.268002 40.248001 90.000000 90.000000 90.000000} {40.277000 40.268002 40.248001 90.000000 90.000000 90.000000}
I will proceed to scripting using sed
best wishes
Fatima
-----Original Message-----
From: Mark Williamson [mailto:mjw.mjw.name]
Sent: Wed 07/09/2011 14:51
To: AMBER Mailing List
Subject: Re: [AMBER] writing box info to pdb file extracted from an mdcrd trajectory
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 - 09:30:04 PDT
