tleap failed for protein

[kexul]

Hi, here is code to reproduce:

protein = Protein('6VTN', ligand_ref='1001')
protein.filter(ligands=None, waters='chain', simple_anions=None,
                      complex_anions=None,
                      chains=['A'])
protein.prepare()
protein.parametrise()

Error:

OSError: Error while calling command 'tleap'

tleap.log

FATAL:  Atom .R<CHIE 375>.A<HD1 19> does not have a type.

[msuruzhon]

This is a long-standing issue with PDB2PQR, where the terminal histidines are not renamed properly. I don't know of a workaround, if you have any suggestions how to handle this or alternatively get in touch with the PDB2PQR developers about whether this can be circumvented, we could then modify the workflow.

[kexul]

Thanks, I'll submit an issue there.