From Jacobson Lab Wiki
pKa is a top level plop command used to assign protonation states.
The protonation states of Asp, Glu, His, Tyr, Cys, Lys, and phosphorylated residue side chains can vary depending on the pH and the local environment of the residue, and in principle more than one protonation state could have nontrivial populations under a given set of conditions. Clearly, utilizing an incorrect protonation state for a polarizable side chain can lead to substantial errors in the electrostatic energies, and thus incorrect predictions.
For automatic protonation state prediction, use ICDA
Manual modification of protonation states is supported using the following command:
pka change residue type
where "residue" is a particular Asp/Glu/His residue, specified with the usual "chain:residue" format, and "type" is a 3 letter code (all caps) specifying which protonation state should be used. For the relevant codes, click plop residues. As an example,
pka change A:123 HIP
would change the protonation state of residue 123 in chain A, which must be a histidine, to the doubly protonated, positively charged form. Note that the protonation states of the N-terminal amino and C-terminal carboxy groups cannot be modified at present (unfortunately).
 pKa second level commands
chan[ge] clust ! ICDA hydrogen assignments corr eval swi_his ! switch N/O atoms in HIS switch ! switch N/O atoms in ASN/GLN
 pKa command options
adjust - yes/no, applies correction term(s) to some residues angle_cut_1 - angle_cut_2 check_flip - yes/no check_his - dist_cut - defaults to 3.1 fastpka - defaults to true (according to comment ignores crystal symmetry) gbup - ICDA_min - msol onthefly - yes/no params - refener[gy] - restart - make a restart file, defaults to true skip_arg - yes/no, skip arginine residues skip_het - yes/no update - use_restart path - reads in the restart file specified verb[ose] - verbose output