Hi,
On Wed, Aug 21, 2013 at 7:25 PM, <moitrayee.mbu.iisc.ernet.in> wrote:
> trajin ./decamer-rep-57ns.pdb.1
> reference decamer-rep-57ns.pdb.1 :1-138.CA -> to define reference
> rms :139-277.CA reference -> to align subunit B on A
> rms :139-277.CA reference out rmsAB.dat nofit -> to calculate rmsd of B wrt A.
For the following I'm assuming here residues 1-138 are subunit A, and
139-277 are subunit B.
First, you're reading in your reference with a mask; the effect of
this is to strip the reference structure so 'only' the atoms in the
mask remain; in this case CA atoms from residues 1 to 138. Then you're
trying to fit residues 139-277 in your input trajectory to the
reference; but since those residues were stripped from the reference
you should have received an error like:
Error: rmsd: No reference atoms selected for parm...
(If you did not receive an error message please tell me what version
of cpptraj you are running).
I think maybe what you want is to first fit on subunit A, then take
the no-fit RMSD of subunit B, e.g.:
trajin ./decamer-rep-57ns.pdb.1
reference decamer-rep-57ns.pdb.1
# Align subunit A in trajectory to A in reference
rms reference :1-277.CA
# Get the no-fit RMSD of subunit B in trajectory to B in reference;
still fit on A
rms nofit reference :139-277.CA out rmsAB.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 Wed Aug 21 2013 - 21:30:03 PDT
