Excluding C and N terminus from Isoelectric calculation

I'm currently trying to calculate the isoelectric value for amino acid sequences, but excluding the N terminus and C terminus from the calculation. I tried running the isoelectric function with a custom .pk file

isoArr{z, 1} = isoelectric(seq, 'PKVals', 'file.pK');

where file.pk is

N_term 0.0

K 10.53

R 12.48

H 6

D 3.86

E 4.25

C 8.33

Y 10.07

C_term 0.0

However, that did not output the correct values, and deleting the Nterm and Cterm lines gave me an error. I was wondering if there was an easy way to exclude both of these from the calculation or if I basically have to write my own isoelectric function.

Answer 1

[Arthur Goldsipe]

I think you want to set the N_term and C_term entries to 7.0 rather than 0.0, since 7.0 is the the "neutral" pK value.