For each charged residue you have to define both the pKa value and the potential charge. The pKa values have to be between 0.1 and 14.0, and the charge (Ch.) can be either -1 or 1. A value of 0 in either the pKa or the Ch. column will result in the value being ignored in the pI and charge calculations.
If you click on the ‘Transfer pKa’ button, you will be given the choice of transferring the pKa values from the built-in list of either Skoog and Wichman, free amino acid residues or Rickard et al. This makes it easier to edit the table, as in most cases it is likely that you will only change a single or few values (e.g. Cys if modified).
You cannot set the pKa value of either termini as this is defined for each individual residue in the program.
Remember to save the file before closing GPMAW.
pKa values in the modification file:
In the modification file (Edit | Edit modification file) you define pKa values in a similar way as for the mass file. A difference is that you can load and save different modifcation files directly from the Edit box.
Like for the mass file you have to define both the pKa value to be larger than 0.1 and the charge to be either -1 or +1. The ‘Term’ column directs the modification to either the N-terminal or the C-terminal residue (the ‘Valid residues’ have also to be correct) and has no influence on the other columns.
Remember to save the changed modification file before closing the program.