VMD-L Mailing List

From: Souvik Sinha (souvik.sinha893_at_gmail.com)
Date: Mon Jul 30 2018 - 04:28:54 CDT

If you are interested in aligning only, I don't think you need to split it
up unless you have something to do with the separate files. For aligning,
you just need to load you trajectory file in vmd and use the "RMSD
Trajectory Tool" interface. There you can set your reference frame or even
a separate structure as your reference for alignment.

On Mon, Jul 30, 2018 at 2:44 PM, <abhik.ghosh_at_bose.res.in> wrote:

> > 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
> >
> Dear Souvik
> Thank you. It works very well. Now do you have any idea if I want to
> allign all one by one and want to save final coordinate as single pdb. ANy
> idea how that can be done using pymol or vmd?
> Thanking you.
> Regards
> Abhik
>
> 

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