Hi,
I would like to run constant pH and Redox Potential to analyze changes in the redox potential of a cysteine pair. I checked titratable_residues.py and CYS does not have an electrostatic correction. Can someone confirm if I could proceed by just adjusting eleccnt=0 and typ="phredox"
# Cysteine
refene1 = _ReferenceEnergy(igb2=77.4666763, igb5=76.2588331, igb8=71.5804519)
refene1.solvent_energies(igb2=77.6041407, igb5=76.2827217)
refene1.dielc2_energies(igb2=38.090523, igb5=37.454637)
refene1.dielc2.solvent_energies(igb2=38.489170)
# Copying the reference energy to be printted on the old CPIN format
refene1_old = _ReferenceEnergy(igb2=77.4666763, igb5=76.2588331, igb8=71.5804519)
refene1_old.solvent_energies(igb2=77.6041407, igb5=76.2827217)
refene1_old.dielc2_energies(igb2=38.090523, igb5=37.454637)
refene1_old.dielc2.solvent_energies(igb2=38.489170)
refene1_old.set_pKa(8.5, deprotonated=False)
refene2 = _ReferenceEnergy(igb2=0, igb5=0, igb8=0)
refene2.solvent_energies(igb1=0, igb2=0, igb5=0, igb7=0, igb8=0)
refene2.dielc2_energies(igb2=0, igb5=0, igb8=0)
refene2.dielc2.solvent_energies(igb1=0, igb2=0, igb5=0, igb7=0, igb8=0)
CYS = TitratableResidue('CYS', ['N', 'H', 'CA', 'HA', 'CB', 'HB2', 'HB3', 'SG',
'HG', 'C', 'O'], pka=8.5, typ="phredox")
CYS.add_state(protcnt=1, eleccnt=0, refene=refene1, refene_old=refene1_old, pka_corr=8.5, # protonated
charges=[-0.4157, 0.2719, 0.0213, 0.1124, -0.1231, 0.1112, 0.1112,
-0.3119, 0.1933, 0.5973, -0.5679])
CYS.add_state(protcnt=0, eleccnt=0, refene=refene2, refene_old=refene2, pka_corr=0.0, # deprotonated
charges=[-0.4157, 0.2719, 0.0213, 0.1124, -0.3593, 0.1122, 0.1122,
-0.8844, 0.0, 0.5973, -0.5679])
CYS.check()
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Received on Fri Oct 27 2023 - 23:30:02 PDT
