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

From: Daniel Roe <>
Date: Wed, 24 Jul 2013 09:17:57 -0600


Just to expand on Jason's advice a bit, the 'strip' command can be
used with a distance-based mask but it will base those distances on
the active reference frame only. The 'mask' command can extract
coordinates to PDB files using distance-based masks on a
frame-by-frame basis, but unless the site is very stable be aware you
will likely end up with a collection of PDBs that have differing
numbers of atoms.

If you specify what kinds of analysis you'd like to do we can provide
more specific advice. Hope this helps,


On Wed, Jul 24, 2013 at 6:13 AM, Jason Swails <> wrote:
> 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).
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Jul 24 2013 - 08:30:03 PDT
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