Hi,
If you give ptraj or cpptraj a reference structure you can do
distance-based mask parsing based on that reference structure, e.g.:
reference initial
trajin traj
rms first reference out rmsd.dat :LIG<:5.0
Will get the RMSD of all residues within 5.0 angstroms of residue LIG
based on the structure in 'initial'. See the manual for more details
on distance-based mask parsing.
-Dan
On Tue, Feb 5, 2013 at 6:40 AM, HM <scienceamber.gmail.com> wrote:
> Hi All,
> I am interested in calculating the rmsd of the active site region i.e. 5 A
> around bound ligand. But as the number of those residues changes from
> trajectories to trajectories, I am not sure how to tell ptraj or cpptraj to
> calculate rmsd for active site region.
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> 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 Tue Feb 05 2013 - 08:00:02 PST
