Hi,
On Wed, Aug 21, 2013 at 10:53 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
> However, this script gives me the output,
>
> #Frame RMSD_00001
> 1 0.0000
Are the reference structure and the input trajectory the same
structure? If so the 0.0 makes sense.
> should the line be rms reference :1-138.CA ? Also I want to compute the rmsd of
> subunit B wrt subunit A.
If you want to align subunit A over subunit B and get the RMSD then
you just need to use a reference mask in the RMS command. Note that
you *must* ensure the same number of atoms is selected in the target
mask and the reference mask (otherwise the RMSD makes no sense).
rms reference <Target Mask> <Ref Mask> out rms.dat
The first mask pertains to the 'target' (i.e. input coordinates), the
second mask pertains to the reference structure. So the command is
saying 'give me the best-fit RMSD of atoms in <Target Mask> of my
input coordinates to atoms in <Ref Mask> of my reference trajectory.
Hopefully this is all clear, let me know if not.
-Dan
--
-------------------------
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 Aug 21 2013 - 22:00:03 PDT
