Thanks Daniel for your all time support. :-)
HM
On Tue, Feb 5, 2013 at 6:20 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Feb 05 2013 - 11:30:03 PST
