Support NCAA in protonate_stru

ChemBioHTP / EnzyHTP

EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling

https://enzyhtp-doc.readthedocs.io

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Open shaoqx opened 1 year ago

shaoqx commented 1 year ago

Current engine (PDB2PQR) in protonate_stru does not support modified AA. It will just delete them in the output.

shaoqx commented 1 year ago

Here are several solutions

temp solution: modify the code of PDB2PQR like this https://github.com/Electrostatics/pdb2pqr/discussions/244 A more longterm solution will be if PDB2PQR updated to a version that support these changes by just supplying files.
Interface H++ and provide as an alternative engine
Dig into PROPKA3 or DeepKa to if they support NCAA and protonate it ourselves.