N-ter Pro always charged

[amjjbonvin]

Describe the bug

The N-ter and C-ter charge state is defined by using different linkage files:

• protein-allhdg5-4-noCter.link : uncharged C-ter
• protein-allhdg5-4-noNter.link : uncharged N-ter
• protein-allhdg5-4-noter.link : uncharged N- and C-ter
• protein-allhdg5-4.link : charged termini

There is however in the noter and noNter still PRO-related statements that cause a N-terminal PRO (and also HYP and HY3, two hydroproline residues) to be charged.

The solution is to remove the following lines from the noter and noNter files:

first PROP tail + PRO end
first PROP tail + HYP end
first PROP tail + HY3 end

Additional context

Was discovered thanks to a user question of the BioExcel forum:

https://ask.bioexcel.eu/t/capping-residues/4445