I’m trying to make the pdb2pqr tool fit my needs. I have a .pdb file that I modified by acetylating it using a PyMOL plug-in at the level of a Lys residue, turning it into Aly (acetyl lysine). For this purpose, I’m using the CHARMM36 force field.

However, when I pass my acetylated pdb file through pdb2pqr, it doesn’t recognize “Aly” as a canonical residue and generates a pqr file skipping the recognition of “Aly”. I used the following command:

pdb2pqr --ff=charmm --ffout=charmm inputfilename.pdb outputfilename.pqr

I found a topology file containing values for Aly recognizable by CHARMM36, which is “toppar_all36_prot_modify_res.str”, but I don’t know how to extend the use of pdb2pqr to non-canonical amino acids, as in my case.

Any suggestions?