Ligand parameterization

[LucianoPenaTejo]

Hello, greetings to all.

I am trying to get the PQR of a protein-ligand complex (TREK2-NFX). However I have not been able to do it. In the PDB file, the residue name is NFX, therefore, the PDB2PQR skips it when parameterizing:

Unable to find amino or nucleic acid definition for NFX. Parsing as new residue.

Finally I get a PQR of the protein alone. I read the documentation and tried with the examples provided (1HPV and 1ABF), but the result was the same, only the protein is obtained. I was looking at the other issues, but I couldn't solve the problem either. I have tried both on the web server, and on command line. The line I am using is:

pdb2pqr --ff CHARMM --ligand=sNFX_charged.mol2 --nodebump --noopt TREK2_1NFX.pdb TREK2_1NFX.pqr
I generated the mol2 file with antechamber. Apparently it is well read by the software, however it does not read that kind of residue from the TREK2_1NFX.pdb file. Attached are the outputs and inputs for the command.

On the other hand, I also have the doubt how I can finally generate a PQR with more than one ligand. I need 2 ligands attached to my protein. From what I saw, PDB2PQR is only able to process one structure.

Thanks in advance.

sNFX_charged_mol2.txt
TREK2_1NFX_log.txt
TREK2_1NFX_pdb.txt
TREK2_1NFX_pqr.txt