Error in AtomMapping with more than 100 atoms

Hi everyone

I am trying to use the pmx atomMapping, to create a hybrid topology for ligands. Whenever I try to do the mapping with more than 100 atoms (including hydrogens) it fails and shows the following error:
Cannot determine element for PDB atom #100

I use the following line:
pmx atomMapping -i1 mol1.pdb -i2 mol2.pdb -o1 pairs1.out -o2 pairs2.out -opdb1 out_pdb1.pdb -opdb2 out_pdb2.pdb -score out_score.dat

Is there a way to do the mapping and hybrid topology for this “big” ligands?

Thank you!

Angelica S.

Hi Angelica,

That seems like an issue with reading the PDB file.
Could you check if the file format (and element name) is fine?
Could you also share the files for reproducing the error?


Hi Sudarshan,

Thank you for your reply.
Yes, there was a issue in the PDB with the atom naming. I renamed the atoms and now it works.
I can’t share the original file but, basically I made the following change for all the atoms with a naming over X99:

ATOM 100 H100 171 1 131.718 139.293 94.299 1.00 0.00 XXXX

ATOM 100 H10 171 1 131.718 139.293 94.299 1.00 0.00 XXXX


Angelica S.