Hi,
On Thu, Aug 22, 2013 at 8:25 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
> align subunit B on subunit A, then compute the rmsd between subunit C and
> subunit B. I tried the following but the results seems a little odd.
>
> trajin ./decamer.pdb.25
> reference ./decamer.pdb.25
> rms reference :maskB.CA :maskA.CA
> rms reference :maskC.CA :maskB.CA out rms.dat nofit
Maybe I'm not understanding what you're trying to do, but if you're
trying to obtain the RMSD between subunits B and C why not just do
what you did for subunits A and B, e.g.:
rms reference <maskC> <maskB>
In what you're doing now you're first fitting target subunit B to
reference subunit A, then taking the no-fit RMSD of target subunit C
to reference subunit B, which will probably be quite large. Note that
reference coordinates are not moved during RMSD calculations.
Maybe what you wanted to do was fit target subunit B to ref subunit A,
fit target subunit C to ref subunit A, then take the no-fit RMSD of
subunits B to A? This is slightly more involved but can be done. The
following example makes use of COORDS data sets in cpptraj (V13.X),
which is different from the normal batch operation; see the AmberTools
13 manual for more details on this. It also assumes everything is one
frame; it could also be done with multiple frames by skipping the
'reference' command and using the 'reftraj' keyword in the final rms
command.
# Load topology file
parm topology.parm7
# Load traj as COORDS data set for B
loadcrd ./decamer.pdb.25 subB
# Load traj as COORDS data set for C
loadcrd ./decamer.pdb.25 subC
# Fit subB on ref A
crdaction subB rms reference <maskB> <maskA>
# Fit subC on ref A
crdaction subC rms reference <maskC> <maskA>
# Save fit subB to disk
crdout subB subB.ref.rst7
# Read fit subB back in as a reference; tag as refB
reference subB.ref.rst7 [refB]
# Calculate no-fit rms of fit subC to fit subB
crdaction subC rms ref [refB] <maskC> <maskB> nofit out rms-fitC-fitB.dat
Hope this helps,
-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 Fri Aug 23 2013 - 09:00:03 PDT
