tleap failed for protein
Opened this issue · 2 comments
kexul commented
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 commented
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 commented
Thanks, I'll submit an issue there.