Hi,
I am trying to calculate rmsd between my trajectory and a pdb file.
Here is what I have done:
parm parm1.prmtop
trajin all.nc
parm parm2.prmtop [ref2parm]
reference ref.pdb parm [ref2parm] [ref2]
rms ref [ref2] out test.dat
I have stripped all the atoms from trajectories and pdb (and associated
prmtops) so that there is an equal number of atoms.
For a sanity check, I got a few frames from the trajectory and compared the
rmsd using Chimera.
My issues is, that amber calculates the rmsd to be around 7 and Chimera
around 1. Since the structures are very similar, Chimera is right.
Any idea as to what am I doing wrong?
Thank you very much
L.
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Received on Fri Sep 20 2019 - 12:30:02 PDT
