Hi,
I have simulated a dimer (A: 1-370, B: 371-540)
Now, I want to study the motion of 1 monomer with respect to the second
monomer.
For the same, I want to align the dimer to the chain "A" before i calculate
the rmsd values.
How should I do that?
parm mol.parm
trajin traj.nc
#align to first frame, backbone atoms
reference :1:1-370.CA,N,C,O
rms ref out rmsd.dat :1-370.CA,C,N,O
rms ref out rmsd.dat :371-540.CA,C,N,O
Am I doing anything wrong?
Thanks,
Hirdesh
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Received on Mon May 27 2019 - 12:00:02 PDT
