Re: [AMBER] Extracting PDBs every 'N" ns

From: Daniel Roe <>
Date: Mon, 3 Dec 2018 14:14:20 -0500


On Mon, Dec 3, 2018 at 5:25 AM Jag Silwal <> wrote:
> Thank you for your email. 'autoimage' seems to work for this.I just want to
> check to make sure I am ding it right. So if I want to extract the PDB at
> one particular time, lets say at 800 ns, can I just use the following
> command then?
> parm x.prmtop
> trajin final.mdcrd
> autoimage
> outtraj snapshot1.pdb onlyframes 800000

Assuming your trajectory was saved at a frequency of 1 frame every ps,
this would work. If all you want is that single frame, the following
will be faster:

parm x.prmtop
trajin final.mdcrd 800000 800000
trajout snapshipt1.pdb

> and if I am saving frames every 20 ns for a total of 800 ns and want to
> extract frames every 20 ns as PDB, I would use
> parm x.prmtop
> trajin final.mdcrd 20000 last 20000
> trajout MyFrames.pdb multi

Yes, again assuming your trajectory was saved 1 frame/ps. Don't forget
to autoimage.


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Received on Mon Dec 03 2018 - 11:30:03 PST
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