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I already know the protonation state of a residue. How can I make PDB2PQR aware of it?

PDB2PQR has the ability to recognize certain protonation states and keep them fixed during optimization. To use this feature manually rename the residue name in the PDB file as follows:
  • Neutral ASP: ASH
  • Negative CYS: CYM
  • Neutral GLU: GLH
  • Neutral HIS: HIE/HID/HSD/HSE
  • Positive HIS: HIP/HSP
  • Neutral LYS: LYN
  • Negative TYR: TYM
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