I have a simulation trajectory from DFTB+ for 1 NaNO3 in 32 H2O molecules. The trajectory is in xyz format and I converted a frame of xyz to pdb using openbabel to serve as topology input.
I am following the instructions from the solvation analysis package documentation. However, I keep getting an assertion error
All residues must have the same length
I don't know how to get past this. My codes are pasted below from my Jupyter notebook.
import MDAnalysis as mdau=mda.Universe("./single-frame-1NaNO3-32-H2O.pdb", "./nano3-1-water-32-some-frames.xyz")import solvation_analysisnano3Atoms=u.atoms.select_atoms("id 1 or id 2 or id 3 or id 4 or id 5")oAtomsWater=u.atoms.select_atoms("type O and resname HOH")hAtomsWater=u.atoms.select_atoms("type H and resname HOH")solventAtoms=u.atoms - nano3Atomsfrom solvation_analysis.solute import SolutesoluteObject=Solute.from_atoms(nano3Atoms,{"Wat":solventAtoms},solute_name="salt")All the intermediate steps seem to present reasonable outputs with nano3Atoms showing all atoms that correspond to NaNO3. The last step when soluteObject is defined is when the assertion error is thrown. Any help would be greatly appreciated.
A pdb file and some frames from the simulation output are presented here.Thank you,