VMD-L Mailing List

From: abhik.ghosh_at_bose.res.in
Date: Mon Jul 30 2018 - 04:14:26 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
>
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