ValueError: PDB Error: All MODELs must contain the same number of ATOMs

[MohaiminDev]

Hi,

Thanks for such a useful repository. I was trying to extract features of protein-ligand complex using generate_feature.py. But, I am getting the following error "ValueError: PDB Error: All MODELs must contain the same number of ATOMs".

Do you know how to solve this error ??

It will be a great help.

Thanks in advance

[zhenglz]

Thanks for using this repo. Mdtraj gives the error. The input pdb file could be problematic. Please send me a sample receptor PDB file you used and a ligand file to me ([email protected]), thus I could revert the issue.

[zhenglz]

A potential issue would be, your ligand molecule in the pdb file is not well named. I mean that the residue name (col: 18-20) in the pdb file should be something like "LIG". PDB file format: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM