Oops. It has been pointed out to me that I made a bit of a mistake in
the script I gave; you shouldn't give both 'first' and 'reference' to
an RMS command ('first' will always take priority). This:
reference initial
trajin traj
rms reference out rmsd.dat :LIG<:5.0
is indeed what I meant. That's what happens when I write commands
before finishing my coffee. However, note that you could also do:
reference initial
trajin traj
rms first out rmsd.dat :LIG<:5.0
This will use 'initial' for the distance-based mask parsing, but the
first frame for RMSD.
-Dan
On Tue, Feb 5, 2013 at 8:37 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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.
>> _______________________________________________
>> AMBER mailing list
>> 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)
--
-------------------------
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 - 09:30:03 PST
