VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 07 2018 - 14:34:53 CST

Hi,
  It sounds like you're using the PDB to contain a trajectory.
For the purpose of writing out the reduced/trimmed trajectory, I'd
suggest you might try the "catdcd" tool that is made available in some
recent versions of VMD. You can use VMD to get a list of the atom
indices you want to keep, and eliminate all of the others, writing
out a new trajectory file. If you search the VMD-L archive
there should be many examples of 'catdcd' usage, in addition
to its built-in help and documentation.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Nov 07, 2018 at 01:03:10PM +0530, Abhik Ghosh Moulick wrote:
> Dear All
> I have pdb file of 1000 frame. My protein has 76 number of residue. I want
> to make separate pdb only contains 'N' and 'HN' atom for all frames. How
> it can be done.
> In my case all frames are alligned w.r.t initial frame.
> Thanking you.
> Regards
>
>
> --
> Abhik Ghosh Moulick (JRF)
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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