Re: [AMBER] saving pdb and rst at specific frames in trajectory

From: Daniel Roe <>
Date: Mon, 22 Mar 2021 10:43:42 -0400


The input you gave should have given you 2 pdb files named
out_frame.pdb.1 and out_frame.pdb.2000 - is this not the case?

Also, If all you want to do is save the pdb/restart files at regular
intervals just use 'trajin' to read in frames with an offset. Also if
you want to remove box info you can just use the box action with
'nobox', e.g.

parm complex.prmtop
box nobox
trajin 1 last 500
trajout out_frame.pdb pdb multi
trajout out_frame.rst7 restart

Note though that this will give you frames 1, 501, 1001, etc.

Hope this helps,


On Wed, Mar 17, 2021 at 9:23 AM Sadaf Rani <> wrote:
> Dear Amber users
> Please correct me on how should I save PDB and rst file at a specific
> frame. I have a trajectory of 2000 frames and I want to save PDB files at
> e.g first, 500, 1500, and 2000 frames.
> I used the following command to save at first and 2000 frames however when
> I load pdb in vmd it is loaded as a complete trajectory. Could anyone
> please correct me?
> I used the following command in cpptraj:-
> parm complex.prmtop
> trajin
> trajout out_frame.pdb pdb multi nobox onlyframes 1,2000
> Regards
> Sadaf
> _______________________________________________
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Received on Mon Mar 22 2021 - 08:00:03 PDT
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