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protocaller / ProtoCaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS
http://protocaller.readthedocs.io
GNU General Public License v3.0
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tleap failed for protein #39

Open kexul opened 3 years ago

kexul commented 3 years ago

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 3 years ago

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 3 years ago

Thanks, I'll submit an issue there.