Hello Everyone,
I did a trajectory alignment using ptraj a couple of days ago. My
reference structure was one frame of a trajectory, and this reference was
used to align another trajectory. It seemed to me that the alignment
brought all frames of the aligned trajectory together, but all their
coordinates are far away from both the reference and where they are in
the original trajectory. I will show the resultant coordinate below.
I brought up this question again now because I'd really like to make
sure if ptraj works in a way rather than my setting.
In a case if ptraj only works for alignment of a trajectory to the first
frame of this trajectory, then I need to make my reference to join the
trajectory as its first frame, is this doable? My reference frame was
saved as a pdb file after other manipulation - it can be converted to be
"restart" format, but not trajectory frame - does this bring problem
putting the reference into another trajectory?
Here is the ptraj setting:
trajin MDtraj1 1 1000 100
reference my_reference_snap
trajout aligned_traj
rms my_reference_snap out rms .P
strip :WAT
strip :Cl-
strip :Na+
go
Below is the resultant coordinates:
ref.pdb
ATOM 1 H5T RG5 1 38.720 16.214 81.045
aligned10.pdb
ATOM 1 H5T RG5 1 -4.310 27.117 -20.806 0.00 0.00
aligned110.pdb
ATOM 1 H5T RG5 1 -4.448 27.235 -16.973 0.00 0.00
Thanks,
Wen
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Received on Fri Apr 01 2005 - 18:53:01 PST
