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propka.cfg
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propka.cfg
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# PropKa configuration file
version version_A
# Model pKa values
model_pkas C- 3.20
model_pkas ASP 3.80
model_pkas GLU 4.50
model_pkas HIS 6.50
model_pkas CYS 9.00
model_pkas TYR 10.00
model_pkas LYS 10.50
model_pkas ARG 12.50
#model_pkas SER 14.20 Jack Kyte: Structure in Protein Chemistry, 1995, Garland Publishing, Inc New York and London
model_pkas N+ 8.00
model_pkas CG 11.50
model_pkas C2N 11.50
model_pkas N30 10.00
model_pkas N31 10.00
model_pkas N32 10.00
model_pkas N33 10.00
model_pkas NAR 5.00
model_pkas OCO 4.50
model_pkas SH 10.00
model_pkas OP 6.00
# Custom ligand pKa values
# P. Acharya, P. Cheruku, S. Chatterjee, S. Acharya, and, J. Chattopadhyaya:
# Measurement of Nucleobase pKa Values in Model Mononucleotides
# Shows RNA-RNA Duplexes To Be More Stable than DNA-DNA Duplexes
# Journal of the American Chemical Society 2004 126 (9), 2862-2869
#
custom_model_pkas DA-N1 3.82
custom_model_pkas DA-N3 3.82
custom_model_pkas DA-N7 3.82
custom_model_pkas DA-OP1 1.00
custom_model_pkas DA-OP2 1.00
custom_model_pkas DG-N1 9.59
custom_model_pkas DG-N3 9.59
custom_model_pkas DG-N7 9.59
custom_model_pkas DG-OP1 1.00
custom_model_pkas DG-OP2 1.00
custom_model_pkas DC-N3 4.34
custom_model_pkas DC-OP1 1.00
custom_model_pkas DC-OP2 1.00
custom_model_pkas DT-N3 10.12
custom_model_pkas DT-OP1 1.00
custom_model_pkas DT-OP2 1.00
# protein group mapping
protein_group_mapping ASP-CG COO
protein_group_mapping GLU-CD COO
protein_group_mapping HIS-CG HIS
protein_group_mapping CYS-SG CYS
protein_group_mapping TYR-OH TYR
protein_group_mapping LYS-NZ LYS
protein_group_mapping ARG-CZ ARG
#protein_group_mapping SER-OG SER
protein_group_mapping THR-OG1 ROH
protein_group_mapping SER-OG ROH#
protein_group_mapping ASN-CG AMD
protein_group_mapping GLN-CD AMD
protein_group_mapping TRP-NE1 TRP
# matrix for propka interactions
# 'N' non-iterative interaction
# 'I' iterative interaction
# '-' no interaction
#CYS
interaction_matrix CYS I#N+
interaction_matrix N+ N I#HIS
interaction_matrix HIS I N I#LYS
interaction_matrix LYS N N N I#AMD
interaction_matrix AMD N - N - -#COO
interaction_matrix COO I N I N N I#ARG
interaction_matrix ARG N N N N - N I#TRP
interaction_matrix TRP N - - - - N - -#ROH
interaction_matrix ROH N - - - - N - - -#TYR
interaction_matrix TYR N I I I N N N N N I#SER
interaction_matrix SER N N N N N N I N N N I #CG
interaction_matrix CG N N N N - N I - - N I I#C2N
interaction_matrix C2N N N N N - N I - - N I I I#N30
interaction_matrix N30 N I N N - N N - - I N I I I#N31
interaction_matrix N31 N I N N - N N - - I N I I I I#N32
interaction_matrix N32 N I N N - N N - - I N I I I I I#N33
interaction_matrix N33 N I N N - N N - - I N I I I I I I#NAR
interaction_matrix NAR I N I I N I N - - I N N N N N N N I#OCO
interaction_matrix OCO I N I N N I N N N N N N N N N N N I I#NP1
interaction_matrix NP1 N - N - - N - - - N N - - - - - - N N -#OH
interaction_matrix OH N - - - - N - - - N N - - - - - - - N - -#O3
interaction_matrix O3 N - N - - N - - - N N - - - - - - N N - - -#CL
interaction_matrix CL N - N - - N - - - N N - - - - - - N N - - - -#F
interaction_matrix F N - N - - N - - - N N - - - - - - N N - - - - -#NAM
interaction_matrix NAM N - N - - N - - - N N - - - - - - N N - - - - - -#N1
interaction_matrix N1 N - N - - N - - - N N - - - - - - N N - - - - - - -#O2
interaction_matrix O2 N - N - - N - - - N N - - - - - - N N - - - - - - - -#OP
interaction_matrix OP I N I N N I N N N N N N N N N N N I I N N N N N N N N I#SH
interaction_matrix SH I N N N N N N N N N N I I I I I I N N N N N N N N N N N I
# Cutoff values for side chain interactions
# default value
sidechain_cutoffs default 3.0 4.0
# COO
sidechain_cutoffs COO COO 2.5 3.5
Sidechain_cutoffs COO SER 2.65 3.65
sidechain_cutoffs COO ARG 1.85 2.85
sidechain_cutoffs COO LYS 2.85 3.85
sidechain_cutoffs COO HIS 2.0 3.0
sidechain_cutoffs COO AMD 2.0 3.0
sidechain_cutoffs COO TRP 2.0 3.0
sidechain_cutoffs COO ROH 2.65 3.65
sidechain_cutoffs COO TYR 2.65 3.65
sidechain_cutoffs COO N+ 2.85 3.85
sidechain_cutoffs COO CG 1.85 2.85
sidechain_cutoffs COO C2N 1.85 2.85
sidechain_cutoffs COO N30 2.85 3.85
sidechain_cutoffs COO N31 2.85 3.85
sidechain_cutoffs COO N32 2.85 3.85
sidechain_cutoffs COO N33 2.85 3.85
sidechain_cutoffs COO NAR 2.0 3.0
sidechain_cutoffs COO OCO 2.5 3.5
sidechain_cutoffs COO OH 2.65 3.65
sidechain_cutoffs COO NAM 2.0 3.0
# SER
sidechain_cutoffs SER SER 3.5 4.5
sidechain_cutoffs SER ARG 2.5 4.0
sidechain_cutoffs SER HIS 2.0 3.0
sidechain_cutoffs SER AMD 2.5 3.5
sidechain_cutoffs SER CYS 3.5 4.5
sidechain_cutoffs SER TRP 2.5 3.5
sidechain_cutoffs SER ROH 3.5 4.5
sidechain_cutoffs SER CG 2.5 4.0
sidechain_cutoffs SER C2N 2.5 4.0
sidechain_cutoffs SER NAR 2.0 3.0
sidechain_cutoffs SER OH 3.5 4.5
sidechain_cutoffs SER SH 3.5 4.5
sidechain_cutoffs SER TYR 3.5 4.5
sidechain_cutoffs SER N+ 3.0 4.5
sidechain_cutoffs SER NAM 2.5 3.5
# ARG
sidechain_cutoffs ARG CYS 2.5 4.0
sidechain_cutoffs ARG TYR 2.5 4.0
sidechain_cutoffs ARG OCO 1.85 2.85
sidechain_cutoffs ARG SH 2.5 4.0
# HIS
sidechain_cutoffs HIS AMD 2.0 3.0
sidechain_cutoffs HIS TYR 2.0 3.0
sidechain_cutoffs HIS OCO 2.0 3.0
# CYS
sidechain_cutoffs CYS CYS 3.0 5.0
sidechain_cutoffs CYS TRP 2.5 3.5
sidechain_cutoffs CYS ROH 3.5 4.5
sidechain_cutoffs CYS AMD 2.5 3.5
sidechain_cutoffs CYS TYR 3.5 4.5
sidechain_cutoffs CYS N+ 3.0 4.5
sidechain_cutoffs CYS CG 2.5 4.0
sidechain_cutoffs CYS C2N 2.5 4.0
sidechain_cutoffs CYS N30 3.0 4.5
sidechain_cutoffs CYS N31 3.0 4.5
sidechain_cutoffs CYS N32 3.0 4.5
sidechain_cutoffs CYS N33 3.0 4.5
sidechain_cutoffs CYS OH 3.5 4.5
sidechain_cutoffs CYS NAM 2.5 3.5
sidechain_cutoffs CYS SH 3.0 5.0
# TYR
sidechain_cutoffs TYR TYR 3.5 4.5
sidechain_cutoffs TYR N+ 3.0 4.5
sidechain_cutoffs TYR AMD 2.5 3.5
sidechain_cutoffs TYR TRP 2.5 3.5
sidechain_cutoffs TYR ROH 3.5 4.5
sidechain_cutoffs TYR CG 2.5 4.0
sidechain_cutoffs TYR C2N 2.5 4.0
sidechain_cutoffs TYR OCO 2.65 3.65
sidechain_cutoffs TYR NAR 2.0 3.0
sidechain_cutoffs TYR OH 3.5 4.5
sidechain_cutoffs TYR NAM 2.5 3.5
sidechain_cutoffs TYR SH 3.5 4.5
# N+
sidechain_cutoffs N+ OCO 2.85 3.85
sidechain_cutoffs N+ SH 3.0 4.5
# LYS
sidechain_cutoffs LYS OCO 2.85 3.85
# OCO
sidechain_cutoffs OCO OCO 2.5 3.5
sidechain_cutoffs OCO TRP 2.0 3.0
sidechain_cutoffs OCO ROH 2.65 3.65
sidechain_cutoffs OCO AMD 2.0 3.0
sidechain_cutoffs OCO CG 1.85 2.85
sidechain_cutoffs OCO C2N 1.85 2.85
sidechain_cutoffs OCO N30 2.85 3.85
sidechain_cutoffs OCO N31 2.85 3.85
sidechain_cutoffs OCO N32 2.85 3.85
sidechain_cutoffs OCO N33 2.85 3.85
sidechain_cutoffs OCO NAR 2.0 3.0
sidechain_cutoffs OCO OH 2.65 3.65
sidechain_cutoffs OCO NAM 2.0 3.0
# NAR
sidechain_cutoffs NAR AMD 2.0 3.0
# SH
sidechain_cutoffs SH ROH 3.5 4.5
sidechain_cutoffs SH TRP 2.5 3.5
sidechain_cutoffs SH AMD 2.5 3.5
sidechain_cutoffs SH NAM 2.5 3.5
sidechain_cutoffs SH CG 2.5 4.0
sidechain_cutoffs SH C2N 2.5 4.0
sidechain_cutoffs SH OH 3.5 4.5
sidechain_cutoffs SH SH 3.0 5.0
# Maximal interaction energies for side chains
sidechain_interaction 0.85
# Angular dependent sidechain interactions
angular_dependent_sidechain_interactions HIS
angular_dependent_sidechain_interactions ARG
angular_dependent_sidechain_interactions AMD
angular_dependent_sidechain_interactions TRP
# exception interaction values
COO_HIS_exception 1.60
OCO_HIS_exception 1.60
CYS_HIS_exception 1.60
CYS_CYS_exception 3.60
# Coulomb interaction parameters
coulomb_cutoff1 4.0
coulomb_cutoff2 10.0
coulomb_diel 80.0
# Backbone hydrogen bond parameters
backbone_NH_hydrogen_bond COO -0.85 2.00 3.00
#backbone_NH_hydrogen_bond C- -0.85 2.00 3.00
backbone_NH_hydrogen_bond CYS -0.85 3.00 4.00
backbone_NH_hydrogen_bond TYR -0.85 2.20 3.20
backbone_NH_hydrogen_bond OCO -0.85 2.00 3.50
backbone_NH_hydrogen_bond NAR -0.85 2.00 3.50
backbone_CO_hydrogen_bond HIS 0.85 2.00 3.00
backbone_CO_hydrogen_bond OCO 0.85 3.00 4.00
backbone_CO_hydrogen_bond CG 0.85 2.00 4.00
backbone_CO_hydrogen_bond C2N 0.85 2.00 4.00
backbone_CO_hydrogen_bond N30 0.85 2.00 4.00
backbone_CO_hydrogen_bond N31 0.85 2.00 4.00
backbone_CO_hydrogen_bond N32 0.85 2.00 4.00
backbone_CO_hydrogen_bond N33 0.85 2.00 4.00
backbone_CO_hydrogen_bond NAR 0.85 2.00 3.50
# Group charges
charge COO -1
charge HIS +1
charge CYS -1
charge TYR -1
charge LYS +1
charge ARG +1
charge N+ +1
charge C- -1
charge OCO -1
charge SER -1
charge CG +1
charge C2N +1
charge N30 +1
charge N31 +1
charge N32 +1
charge N33 +1
charge NAR +1
charge SH -1
charge OP -1
# list of acids
acid_list ASP
acid_list GLU
acid_list CYS
acid_list TYR
acid_list SER
acid_list C-
acid_list OCO
acid_list OP
acid_list SH
# list of bases
base_list ARG
base_list LYS
base_list HIS
base_list N+
base_list CG
base_list C2N
base_list N30
base_list N31
base_list N32
base_list N33
base_list NAR
# list of groups used in backbone reorganisation calculations
backbone_reorganisation_list ASP
backbone_reorganisation_list GLU
# Residues that should be ignored
ignore_residues HOH
ignore_residues H2O
ignore_residues HOH
ignore_residues SO4
ignore_residues PO4
ignore_residues PEG
ignore_residues EPE
#ignore_residues NAG
ignore_residues TRS
# Relative Van der Waals volume parameters for the radial volume model
# Radii adopted from Bondi, A. (1964). "Van der Waals Volumes and Radii". J. Phys. Chem. 68 (3): 441-51
VanDerWaalsVolume C 1.40 # radius: 1.70, volume: 20.58 all 'C' and 'CA' atoms
VanDerWaalsVolume C4 2.64 # 38.79 hydrodphobic carbon atoms + unidentified atoms
VanDerWaalsVolume N 1.06 # radius: 1.55, volume: 15.60 all nitrogen atoms
VanDerWaalsVolume O 1.00 # radius: 1.52, volume: 14.71 all oxygen atoms
VanDerWaalsVolume S 1.66 # radius: 1.80, volume: 24.43 all sulphur atoms
VanDerWaalsVolume F 0.90 # raidus: 1.47, volume: 13.30 for fluorine
VanDerWaalsVolume Cl 1.53 # radius: 1.75, volume: 22.44 for chlorine
VanDerWaalsVolume P 1.66 # radius: 1.80, volume: 24.42 for phosphorus
# Other desolvation parameters
desolvationSurfaceScalingFactor 0.25
desolvationPrefactor -13.0
desolvationAllowance 0.0
desolv_cutoff 20.0
buried_cutoff 15.0
Nmin 280
Nmax 560
# Ligand groups
ligand_typing groups
min_bond_distance_for_hydrogen_bonds 4
# covalent coupling
coupling_max_number_of_bonds 3
shared_determinants 0
common_charge_centre 0
remove_penalised_group 1
# non-covalent coupling
max_intrinsic_pKa_diff 2.0
min_interaction_energy 0.5
max_free_energy_diff 1.0
min_swap_pka_shift 1.0
min_pka 0.0
max_pka 10.0
pH variable
reference neutral
# ions
ions 1P 1 # generic charged atoms
ions 2P 2
ions 1N -1
ions 2N -2
ions MG 2 #Magnesium Ion
ions CA 2 #Calcium Ion
ions ZN 2 #Zinc Ion
ions NA 1 #Sodium Ion
ions CL -1 #Chloride Ion
ions MN 2 #Manganese (ii) Ion
ions K 1 #Potassium Ion
ions CD 2 #Cadmium Ion
ions FE 3 #Fe (iii) Ion
ions SR 2 #Strontium Ion
ions CU 2 #Copper (ii) Ion
ions IOD -1 #Iodide Ion
ions HG 2 #Mercury (ii) Ion
ions BR -1 #Bromide Ion
ions CO 2 #Cobalt (ii) Ion
ions NI 2 #Nickel (ii) Ion
ions FE2 2 #Fe (ii) Ion
# write out order of residues
write_out_order ASP
write_out_order GLU
write_out_order C-
write_out_order HIS
write_out_order CYS
write_out_order TYR
write_out_order LYS
write_out_order ARG
write_out_order SER
write_out_order N+
write_out_order CG
write_out_order C2N
write_out_order N30
write_out_order N31
write_out_order N32
write_out_order N33
write_out_order NAR
write_out_order OCO
write_out_order SH
write_out_order OP