In [1]:

    

import mdtraj as md
liganded = md.load('sang/liganded.pdb')
unliganded = md.load('sang/unliganded.pdb')


    

In [3]:

    

liganded


    

    
Out[3]:





<mdtraj.Trajectory with 1 frames, 4000 atoms, 401 residues, and unitcells at 0x7f960c0a30d0>

In [4]:

    

unliganded


    

    
Out[4]:





<mdtraj.Trajectory with 1 frames, 4003 atoms, 401 residues, and unitcells at 0x7f95ec110e90>

In [2]:

    

rmsds = md.rmsd(liganded, unliganded, 0)


    

    




---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-2-87694c3bd5fe> in <module>()
----> 1 rmsds = md.rmsd(liganded, unliganded, 0)

_rmsd.pyx in _rmsd.rmsd (mdtraj/rmsd/_rmsd.c:1957)()

ValueError: Input trajectories must have same number of atoms. found 4000 and 4003.

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