VMD-L Mailing List

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Mon Jul 30 2018 - 02:36:23 CDT

I think you can use 'split' command in any linux shell to process your
trajectory pdb and get separate pdb for each frame. You can use something
like this:

split -l (no of lines per pdb) -d -a 4 --additional-suffix=.pdb
trajectory.pdb

so if you have say 100 lines per frame in your trajectory, the above
command will split the trajectory pdb into files (.pdb) having 100 lines
each.

Regards,
Souvik

On Mon, Jul 30, 2018 at 11:31 AM, <abhik.ghosh_at_bose.res.in> wrote:

> > Hello. I think you can try the script available here
> >
> > http://www.ks.uiuc.edu/Research/vmd/script_library/
> scripts/splitmultiframepdb/
> > Best,
> > Amin.
> >
> > On Mon, 30 Jul 2018 at 7:40 AM, <abhik.ghosh_at_bose.res.in> wrote:
> >
> >> Hello All
> >> I have a simulated trajectory of a protein in pdb file format. I have
> >> nearly 100000 frame in the pdb file. Now I want to split this file into
> >> separate files having separated pdb. Each pdb has one frame. How is it
> >> possible. Any suggestions are welcome.
> >> Thanking you.
> >> Regards
> >> Abhik Ghosh
> >>
> >>
> >
> Dear Amin
> I have tried it. But nothing is happened. Actually I have pdb file. Is
> this script is applicable for other than pdf format? I have load the pdb
> file in vmd then I have run the script in tk console window. But nothing
> has happened.
> Thanking you.
> Regards
> Abhik
>
> 

-- 
Souvik Sinha
Research Fellow
Bioinformatics Centre (SGD LAB)
Bose Institute
Contact: 033 25693275