HETERATOMS cause NAMD issues

[adw62]

The ATOMS in the PDB are renamed to HETERATOM here:https://github.com/UCL-CCS/TIES20/blob/62f2dac4911824cf6b257f33e898a74e8a655b97/ties/generator.py#L285

I thought it was for all atoms but it only renames the ligand atoms to HETERATOM this might be more correct(?) but none the less it makes NAMD crash with 'FATAL ERROR: number of pdb and psf atoms are not the same' (OpenMM is unaffected)

The best fix is to make parmed write ATOM otherwise we can add a post processing function to correct?

[bieniekmateusz]

That makes sense so it's parmed. Maybe parmed has something like str.residue.type and it is not set. We can modify that on the fly when we read the file for the first time, or at the end I guess.

I can't see in the documentation any mention of HETERATOM renaming. I can check in the evening. Thanks

ps. I can see it in the files now that you mention it. Interestingly the 'no_fep' appears normal?

[adw62]

Yh 'no_fep' happens before parmed. Thats what helped me find the culprit haha

[bieniekmateusz]

Heya, a fix to the issue in parmed which by default treats them as non-standard residue: https://parmed.github.io/ParmEd/html/api/parmed/parmed.structure.html#parmed.structure.Structure.write_pdb