Hi,
I need to align a trajectory (residues 2 to 169) to a reference pdb
(residues :3-170) and then calculate rmsd of a loop (residues 28 to 35) in
the trajectory to residues 29-36 in the reference pdb. I tried the
following:
align :2-169&!.H= reference :3-170&!.H= mass
rmsd p1-atoms :28-35&!.H= reference :29-36&!.H= out rmsd_v10.dat
I doubt that the loops are being aligned before rmsd reporting and
not the protein part. As I mentioned I need to align the protein part and
then calculate rmsd of the loop part after alignment.
I need help forming the cpptraj script for executing this.
Regards
Abhilash
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Received on Fri Jan 19 2024 - 14:00:02 PST
