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

From: Gustaf Olsson <>
Date: Wed, 17 Mar 2021 13:48:58 +0000

I’m just guessing here, though the syntax from what I remember is start, stop, step

Meaning you would want 500,500,1, 1500,1500,1 ….

> trajout out_frame.pdb pdb multi nobox onlyframes 1,2000

trajout out_frame-500.pdb pdb multi nobox onlyframes 500,500,1
trajout out_frame-1500.pdb pdb multi nobox onlyframes 1500,1500,1
trajout out_frame-2000.pdb pdb multi nobox onlyframes 2000,2000,1

One PDB for each frame. You don’t need any rst file for a PDB.

I am quite sure there are shorthands for “first” and “last” and potentially a better way to print each frame to a separate PDB. Though this should work and is as much as I could guess without looking in the manual.

Best regards
// Gustaf

> On 17 Mar 2021, at 14:23, 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 Wed Mar 17 2021 - 07:00:02 PDT
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