I'm having some problems loading .pdb files into the APBS/Pdb2pqr programs. My pub files are generated using the FoldX suite, and apparently this is a non-standard .pdb file.
The error is mostly when translating using the pdb2pqr.
I would really appreciate any help or clues to my problem! Thank you
INFO:Checking and transforming input arguments.
INFO:Loading topology files.
INFO:Loading molecule: 001_pMHC_NLMEVMPNI.pdb
ERROR:Error parsing line: 'FoldX'
ERROR:<FoldX generated pdb file>
ERROR:Truncating remaining errors for record type:FoldX
WARNING:Warning: 001_pMHC_NLMEVMPNI.pdb is a non-standard PDB file.
ERROR:['FoldX']
INFO:Setting up molecule.
INFO:Created biomolecule object with 0 residues and 0 atoms.
INFO:Setting termini states for biomolecule chains.
INFO:Loading forcefield.
INFO:Loading hydrogen topology definitions.
CRITICAL:No biomolecule heavy atoms found and no ligand present. Unable to proceed. You may also see this message if PDB2PQR does not have parameters for any residue in your biomolecule.
CRITICAL:Giving up.