[gmx-users] I want only coordinates in md.xtc/md.pdb

[Chandan Choudhury]

For any text file, use your favorite editor to delete all your water
molecules. It will load very fast. For the xtc/trr files, use trjconv with
an index file to write a new xtc/trr file without water molecules. Index
file should contain the atom nos. of the molecules you want.

trjconv -s a.tpr -f a.xtc/trr -n a.ndx -o b.xtc/trr

chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Thu, Dec 8, 2011 at 10:56 AM, Saba Ferdous <saba.bsbi154 at iiu.edu.pk>wrote:

> Dear Sir,
> I need to ask you that if I want only pdb coordinates in the resultant
> md-noPBC.xtc/md-noPBC.pdb file rather than the solvant atoms and
> coordinates then what should I do. because the water box causes very delay
> in loading of frames and its difficult to viualize the trajectory. kindly
> help me to get out of the broblem. I only want that my protein get display
> in vmd rather than the water box.
> the size of md-noPBC.xtc is 612 Mb
> md-noPBC.pdb  is 13.2 GB
>
> analysis is getting very slow and system is hanging. kindly help me out to
> fix this problem.
>
> Regards
> Thanks
>
>
> --
> Saba Ferdous
> Research Scholar (M. Phil)
> National Center for Bioinformatics
> Quaid-e-Azam University, Islamabad
> Pakistan
>
>
> --
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