Hello everyone, I am trying to obtain the RMSD value between a docked ligand I got with Autodock Vina (PDBQT file) and a crystal ligand structure i downloaded from rcsb.org (PDB file).
The thing is when I open the crystal ligand file on PyMOL this error appears: Warning: Invalid characters in 'MLN_Cristalizado_PDB' have been replaced or stripped ObjectMolecule: Read crystal symmetry information. CmdLoad: "" loaded as "MLN_Cristalizado_PDB". And when I try to run the rms command this error appears: PyMOL>rms MLN_Cristalizado_PDB (crystal ligand), MLN_H-4760_prueba21R4L (docked ligand) ExecutiveRMS-Error: No atoms selected. Previously running the rms command, I run these commands: alter all, segi="" alter all, chain="" How can I get an easier way of solving this problem? Can I get an approximate RMSD value with another command? I attach the two files for you to try for yourselves if you want to. I want to add that when i open the two files on the notepad the identifiers of the atoms are different, I have also gotten the error of mismatched identifiers before too. Thanks in advance to anyone who replies, good luck!
MLN Cristalizado PDB.pdb
Description: Binary data
MLN_H-4760_prueba21R4L.pdbqt
Description: Binary data
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