Re: [AMBER] extraction of specific region of the trajectory file using ptraj

From: Jason Swails <>
Date: Wed, 24 Jul 2013 08:13:19 -0400

On Wed, Jul 24, 2013 at 2:38 AM, Puspita Halder <> wrote:

> Hi,
> I need to extraxt the coordinates of the active site (e.g. 10 to 12
> Angstrom from the central metal atom) of my protein from its dcd trajectory
> file. My first question is: can I do that by using ptraj? I am not very
> familiar with all the functionalities of ptraj since I stated using that
> very recently. If anyone of you used ptraj for similar kind of analysis
> please let me know the required commands to do so using ptraj.

Most commands allow you to specify a portion of the system to perform that
analysis on (e.g., RMSD, RMSF, PCA, etc.) without needing to extract just
those coordinates into another file. Look at the Amber mask syntax
(described in Appendix C of the Amber12 manual) which describes how to use
the mask syntax to select atoms (masks are the main way that atoms are
selected in all/most Amber programs). Masks allow for (static)
distance-based criteria. (Static meaning that the selection is determined
from the first coordinate frame and is fixed for the rest of the analysis.)

If you insist on creating a stripped set of coordinates, you can use the
"strip" command (but you will have to create a matching prmtop if you wish
to do any analyses with programs like VMD or ptraj).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jul 24 2013 - 05:30:02 PDT
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