Computational Biology(계산생물학)
Prof. Keun Woo Lee (이근우 교수)



pKa Calculations



A. pKa calculation (Theory)

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


과 목: 계산생물학/생물정보학 (경상대학교 생화학과)
담당교수: 이근우 (kwlee@gnu.ac.kr)


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