Hi,
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,
-Dan
On Wed, Jul 24, 2013 at 6:13 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Jul 24, 2013 at 2:38 AM, Puspita Halder <puspitah.gmail.com> 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
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Jul 24 2013 - 08:30:03 PDT
