Re: [AMBER] Ptraj Translate Error

From: Daniel Roe <>
Date: Tue, 8 Feb 2011 00:09:51 -0500

I think what has happened here is you want to write new.rst as an
Amber restart file but are actually writing it as an Amber trajectory
(you can double check your ptraj output to see if this is the case).
If no format keywords are specified with the 'trajout' command it
defaults to Amber trajectory. Try:

trajout new.rst restart

and see if that works. Also, I don't think you need the brackets in
the 'translate' command.


On Tue, Feb 8, 2011 at 12:02 AM, Hirdesh Kumar <> wrote:
> Hi All,
> I was trying to change the coordinate of one of the atom in my trajectory
> file using ptraj. Below mentioned is the script for same:
>  *trajin min2.rst
>  translate .5258 [x -0.294] [y 0] [z 0]
>  trajout new.rst
>  go*
> I want atom number 5258 to change in 3d for its X coordinate. When I check
> for the property of input and output file I found
>  *  min2.rst  ---> 2392805 Byte
>   new.rst    ---> 1593018 Byte*
> I have done something wrong as just the change in one coordinate cant change
> the file size to this much extent. To further check the result, I prepared
> the pdb file using output trajectory, But it is showing error and it not
> converted into pdb.
> Please suggest me my error.
> Thanks
> Hirdesh
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Received on Mon Feb 07 2011 - 21:30:03 PST
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