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A. pKa calculation (Theory)

• About pKa calcualtion


• OmpF pKa calculation (Science paper) : pKa_calc_porin.pdf


• About pKa calculation in UHBD Manual p16-p20: UHBD_Manual.pdf

B. Performing pKa calculation (Practice)

Aftre login to your account in bio.gsnu.ac.kr, follow this pKa Calculation Procedure.

Summary for the procedures:

• 1) Copy the 6 basic files from /class/pka into your working directory.
• 2) Prepare your pdb file (from RCSB or NCBI...).
• 3) Name change your pdb file to pkaS.pdb
• 4) Edit the pkaS.pdb file (remove extra lines except for ATOM lines).
• 5) Count number of HIS and CYS for editing pkaS-doinp.inp
• 6) Editing pkaS-doinp.inp files based on your PDB file.
• 7) Add H atoms using ./pkaS-addH command.
• 8) Editing pkaS-dops.inp files for final pKa calculation.
• 9) Run ./pkaS-dosbs > pKa.log for pKa calculation.
• 10) Analyze the result in hybrid.out & hybrid.chart