I am using pdb2pqr from pip to convert residue naming to an AMBER compatible format. When the PDB contains a HIP residue (example attached), it gets converted to HI+ which is not compatible with the AMBER force field. Using the server instead I get the correct PQR with HIP residues left intact.
I'm using pdb2pqr ver 3.6.2, with the command
pdb2pqr --ff AMBER --ffout PARSE --titration-state-method=propka --with-ph=7 receptor.pdb receptor.pqr
I am using pdb2pqr from pip to convert residue naming to an AMBER compatible format. When the PDB contains a HIP residue (example attached), it gets converted to HI+ which is not compatible with the AMBER force field. Using the server instead I get the correct PQR with HIP residues left intact.
I'm using pdb2pqr ver 3.6.2, with the command
pdb2pqr --ff AMBER --ffout PARSE --titration-state-method=propka --with-ph=7 receptor.pdb receptor.pqrreceptor.pdb.zip
EDIT: found the issue, removing --ffout PARSE fixed it.