Remove duplicate propka.cfg file.
This commit is contained in:
Nathan Baker
398
propka.cfg
398
propka.cfg
@@ -1,398 +0,0 @@
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# PropKa configuration file
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version version_A
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# Model pKa values
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model_pkas C- 3.20
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model_pkas ASP 3.80
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model_pkas GLU 4.50
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model_pkas HIS 6.50
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model_pkas CYS 9.00
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model_pkas TYR 10.00
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model_pkas LYS 10.50
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model_pkas ARG 12.50
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#model_pkas SER 14.20 Jack Kyte: Structure in Protein Chemistry, 1995, Garland Publishing, Inc New York and London
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model_pkas N+ 8.00
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model_pkas CG 11.50
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model_pkas C2N 11.50
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model_pkas N30 10.00
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model_pkas N31 10.00
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model_pkas N32 10.00
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model_pkas N33 10.00
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model_pkas NAR 5.00
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model_pkas OCO 4.50
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model_pkas SH 10.00
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model_pkas OP 6.00
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# Custom ligand pKa values
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# P. Acharya, P. Cheruku, S. Chatterjee, S. Acharya, and, J. Chattopadhyaya:
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# Measurement of Nucleobase pKa Values in Model Mononucleotides
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# Shows RNA-RNA Duplexes To Be More Stable than DNA-DNA Duplexes
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# Journal of the American Chemical Society 2004 126 (9), 2862-2869
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#
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custom_model_pkas DA-N1 3.82
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custom_model_pkas DA-N3 3.82
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custom_model_pkas DA-N7 3.82
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custom_model_pkas DA-OP1 1.00
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custom_model_pkas DA-OP2 1.00
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custom_model_pkas DG-N1 9.59
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custom_model_pkas DG-N3 9.59
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custom_model_pkas DG-N7 9.59
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custom_model_pkas DG-OP1 1.00
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custom_model_pkas DG-OP2 1.00
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custom_model_pkas DC-N3 4.34
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custom_model_pkas DC-OP1 1.00
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custom_model_pkas DC-OP2 1.00
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custom_model_pkas DT-N3 10.12
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custom_model_pkas DT-OP1 1.00
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custom_model_pkas DT-OP2 1.00
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# protein group mapping
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protein_group_mapping ASP-CG COO
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protein_group_mapping GLU-CD COO
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protein_group_mapping HIS-CG HIS
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protein_group_mapping CYS-SG CYS
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protein_group_mapping TYR-OH TYR
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protein_group_mapping LYS-NZ LYS
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protein_group_mapping ARG-CZ ARG
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#protein_group_mapping SER-OG SER
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protein_group_mapping THR-OG1 ROH
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protein_group_mapping SER-OG ROH#
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protein_group_mapping ASN-CG AMD
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protein_group_mapping GLN-CD AMD
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protein_group_mapping TRP-NE1 TRP
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# matrix for propka interactions
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# 'N' non-iterative interaction
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# 'I' iterative interaction
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# '-' no interaction
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#CYS
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interaction_matrix CYS I#N+
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interaction_matrix N+ N I#HIS
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interaction_matrix HIS I N I#LYS
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interaction_matrix LYS N N N I#AMD
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interaction_matrix AMD N - N - -#COO
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interaction_matrix COO I N I N N I#ARG
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interaction_matrix ARG N N N N - N I#TRP
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interaction_matrix TRP N - - - - N - -#ROH
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interaction_matrix ROH N - - - - N - - -#TYR
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interaction_matrix TYR N I I I N N N N N I#SER
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interaction_matrix SER N N N N N N I N N N I #CG
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interaction_matrix CG N N N N - N I - - N I I#C2N
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interaction_matrix C2N N N N N - N I - - N I I I#N30
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interaction_matrix N30 N I N N - N N - - I N I I I#N31
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interaction_matrix N31 N I N N - N N - - I N I I I I#N32
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interaction_matrix N32 N I N N - N N - - I N I I I I I#N33
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interaction_matrix N33 N I N N - N N - - I N I I I I I I#NAR
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interaction_matrix NAR I N I I N I N - - I N N N N N N N I#OCO
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interaction_matrix OCO I N I N N I N N N N N N N N N N N I I#NP1
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interaction_matrix NP1 N - N - - N - - - N N - - - - - - N N -#OH
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interaction_matrix OH N - - - - N - - - N N - - - - - - - N - -#O3
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interaction_matrix O3 N - N - - N - - - N N - - - - - - N N - - -#CL
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interaction_matrix CL N - N - - N - - - N N - - - - - - N N - - - -#F
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interaction_matrix F N - N - - N - - - N N - - - - - - N N - - - - -#NAM
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interaction_matrix NAM N - N - - N - - - N N - - - - - - N N - - - - - -#N1
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interaction_matrix N1 N - N - - N - - - N N - - - - - - N N - - - - - - -#O2
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interaction_matrix O2 N - N - - N - - - N N - - - - - - N N - - - - - - - -#OP
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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
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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
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# Cutoff values for side chain interactions
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# default value
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sidechain_cutoffs default 3.0 4.0
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# COO
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sidechain_cutoffs COO COO 2.5 3.5
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Sidechain_cutoffs COO SER 2.65 3.65
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sidechain_cutoffs COO ARG 1.85 2.85
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sidechain_cutoffs COO LYS 2.85 3.85
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sidechain_cutoffs COO HIS 2.0 3.0
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sidechain_cutoffs COO AMD 2.0 3.0
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sidechain_cutoffs COO TRP 2.0 3.0
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sidechain_cutoffs COO ROH 2.65 3.65
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sidechain_cutoffs COO TYR 2.65 3.65
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sidechain_cutoffs COO N+ 2.85 3.85
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sidechain_cutoffs COO CG 1.85 2.85
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sidechain_cutoffs COO C2N 1.85 2.85
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sidechain_cutoffs COO N30 2.85 3.85
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sidechain_cutoffs COO N31 2.85 3.85
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sidechain_cutoffs COO N32 2.85 3.85
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sidechain_cutoffs COO N33 2.85 3.85
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sidechain_cutoffs COO NAR 2.0 3.0
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sidechain_cutoffs COO OCO 2.5 3.5
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sidechain_cutoffs COO OH 2.65 3.65
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sidechain_cutoffs COO NAM 2.0 3.0
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# SER
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sidechain_cutoffs SER SER 3.5 4.5
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sidechain_cutoffs SER ARG 2.5 4.0
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sidechain_cutoffs SER HIS 2.0 3.0
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sidechain_cutoffs SER AMD 2.5 3.5
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sidechain_cutoffs SER CYS 3.5 4.5
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sidechain_cutoffs SER TRP 2.5 3.5
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sidechain_cutoffs SER ROH 3.5 4.5
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sidechain_cutoffs SER CG 2.5 4.0
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sidechain_cutoffs SER C2N 2.5 4.0
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sidechain_cutoffs SER NAR 2.0 3.0
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sidechain_cutoffs SER OH 3.5 4.5
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sidechain_cutoffs SER SH 3.5 4.5
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sidechain_cutoffs SER TYR 3.5 4.5
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sidechain_cutoffs SER N+ 3.0 4.5
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sidechain_cutoffs SER NAM 2.5 3.5
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# ARG
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sidechain_cutoffs ARG CYS 2.5 4.0
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sidechain_cutoffs ARG TYR 2.5 4.0
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sidechain_cutoffs ARG OCO 1.85 2.85
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sidechain_cutoffs ARG SH 2.5 4.0
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# HIS
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sidechain_cutoffs HIS AMD 2.0 3.0
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sidechain_cutoffs HIS TYR 2.0 3.0
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sidechain_cutoffs HIS OCO 2.0 3.0
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# CYS
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sidechain_cutoffs CYS CYS 3.0 5.0
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sidechain_cutoffs CYS TRP 2.5 3.5
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sidechain_cutoffs CYS ROH 3.5 4.5
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sidechain_cutoffs CYS AMD 2.5 3.5
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sidechain_cutoffs CYS TYR 3.5 4.5
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sidechain_cutoffs CYS N+ 3.0 4.5
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sidechain_cutoffs CYS CG 2.5 4.0
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sidechain_cutoffs CYS C2N 2.5 4.0
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sidechain_cutoffs CYS N30 3.0 4.5
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sidechain_cutoffs CYS N31 3.0 4.5
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sidechain_cutoffs CYS N32 3.0 4.5
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sidechain_cutoffs CYS N33 3.0 4.5
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sidechain_cutoffs CYS OH 3.5 4.5
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sidechain_cutoffs CYS NAM 2.5 3.5
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sidechain_cutoffs CYS SH 3.0 5.0
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# TYR
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sidechain_cutoffs TYR TYR 3.5 4.5
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sidechain_cutoffs TYR N+ 3.0 4.5
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sidechain_cutoffs TYR AMD 2.5 3.5
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sidechain_cutoffs TYR TRP 2.5 3.5
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sidechain_cutoffs TYR ROH 3.5 4.5
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sidechain_cutoffs TYR CG 2.5 4.0
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sidechain_cutoffs TYR C2N 2.5 4.0
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sidechain_cutoffs TYR OCO 2.65 3.65
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sidechain_cutoffs TYR NAR 2.0 3.0
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sidechain_cutoffs TYR OH 3.5 4.5
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sidechain_cutoffs TYR NAM 2.5 3.5
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sidechain_cutoffs TYR SH 3.5 4.5
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# N+
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sidechain_cutoffs N+ OCO 2.85 3.85
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sidechain_cutoffs N+ SH 3.0 4.5
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# LYS
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sidechain_cutoffs LYS OCO 2.85 3.85
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# OCO
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sidechain_cutoffs OCO OCO 2.5 3.5
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sidechain_cutoffs OCO TRP 2.0 3.0
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sidechain_cutoffs OCO ROH 2.65 3.65
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sidechain_cutoffs OCO AMD 2.0 3.0
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sidechain_cutoffs OCO CG 1.85 2.85
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sidechain_cutoffs OCO C2N 1.85 2.85
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sidechain_cutoffs OCO N30 2.85 3.85
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sidechain_cutoffs OCO N31 2.85 3.85
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sidechain_cutoffs OCO N32 2.85 3.85
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sidechain_cutoffs OCO N33 2.85 3.85
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sidechain_cutoffs OCO NAR 2.0 3.0
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sidechain_cutoffs OCO OH 2.65 3.65
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sidechain_cutoffs OCO NAM 2.0 3.0
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# NAR
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sidechain_cutoffs NAR AMD 2.0 3.0
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# SH
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sidechain_cutoffs SH ROH 3.5 4.5
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sidechain_cutoffs SH TRP 2.5 3.5
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sidechain_cutoffs SH AMD 2.5 3.5
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sidechain_cutoffs SH NAM 2.5 3.5
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sidechain_cutoffs SH CG 2.5 4.0
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sidechain_cutoffs SH C2N 2.5 4.0
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sidechain_cutoffs SH OH 3.5 4.5
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sidechain_cutoffs SH SH 3.0 5.0
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# Maximal interaction energies for side chains
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sidechain_interaction 0.85
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# Angular dependent sidechain interactions
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angular_dependent_sidechain_interactions HIS
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angular_dependent_sidechain_interactions ARG
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angular_dependent_sidechain_interactions AMD
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angular_dependent_sidechain_interactions TRP
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# exception interaction values
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COO_HIS_exception 1.60
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OCO_HIS_exception 1.60
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CYS_HIS_exception 1.60
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CYS_CYS_exception 3.60
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# Coulomb interaction parameters
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coulomb_cutoff1 4.0
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coulomb_cutoff2 10.0
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coulomb_diel 80.0
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# Backbone hydrogen bond parameters
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backbone_NH_hydrogen_bond COO -0.85 2.00 3.00
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#backbone_NH_hydrogen_bond C- -0.85 2.00 3.00
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backbone_NH_hydrogen_bond CYS -0.85 3.00 4.00
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backbone_NH_hydrogen_bond TYR -0.85 2.20 3.20
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backbone_NH_hydrogen_bond OCO -0.85 2.00 3.50
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backbone_NH_hydrogen_bond NAR -0.85 2.00 3.50
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backbone_CO_hydrogen_bond HIS 0.85 2.00 3.00
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backbone_CO_hydrogen_bond OCO 0.85 3.00 4.00
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backbone_CO_hydrogen_bond CG 0.85 2.00 4.00
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backbone_CO_hydrogen_bond C2N 0.85 2.00 4.00
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backbone_CO_hydrogen_bond N30 0.85 2.00 4.00
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backbone_CO_hydrogen_bond N31 0.85 2.00 4.00
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backbone_CO_hydrogen_bond N32 0.85 2.00 4.00
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backbone_CO_hydrogen_bond N33 0.85 2.00 4.00
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backbone_CO_hydrogen_bond NAR 0.85 2.00 3.50
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# Group charges
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charge COO -1
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charge HIS +1
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charge CYS -1
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charge TYR -1
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charge LYS +1
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charge ARG +1
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charge N+ +1
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charge C- -1
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charge OCO -1
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charge SER -1
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charge CG +1
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charge C2N +1
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charge N30 +1
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charge N31 +1
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charge N32 +1
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charge N33 +1
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charge NAR +1
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charge SH -1
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charge OP -1
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# list of acids
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acid_list ASP
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acid_list GLU
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acid_list CYS
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acid_list TYR
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acid_list SER
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acid_list C-
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acid_list OCO
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acid_list OP
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acid_list SH
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# list of bases
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base_list ARG
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base_list LYS
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base_list HIS
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base_list N+
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base_list CG
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base_list C2N
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base_list N30
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base_list N31
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base_list N32
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base_list N33
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base_list NAR
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# list of groups used in backbone reorganisation calculations
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backbone_reorganisation_list ASP
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backbone_reorganisation_list GLU
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# Residues that should be ignored
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ignore_residues HOH
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ignore_residues H2O
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ignore_residues HOH
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ignore_residues SO4
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ignore_residues PO4
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ignore_residues PEG
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ignore_residues EPE
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#ignore_residues NAG
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ignore_residues TRS
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# Relative Van der Waals volume parameters for the radial volume model
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# Radii adopted from Bondi, A. (1964). "Van der Waals Volumes and Radii". J. Phys. Chem. 68 (3): 441-51
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VanDerWaalsVolume C 1.40 # radius: 1.70, volume: 20.58 all 'C' and 'CA' atoms
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VanDerWaalsVolume C4 2.64 # 38.79 hydrodphobic carbon atoms + unidentified atoms
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VanDerWaalsVolume N 1.06 # radius: 1.55, volume: 15.60 all nitrogen atoms
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VanDerWaalsVolume O 1.00 # radius: 1.52, volume: 14.71 all oxygen atoms
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VanDerWaalsVolume S 1.66 # radius: 1.80, volume: 24.43 all sulphur atoms
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VanDerWaalsVolume F 0.90 # raidus: 1.47, volume: 13.30 for fluorine
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VanDerWaalsVolume Cl 1.53 # radius: 1.75, volume: 22.44 for chlorine
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VanDerWaalsVolume P 1.66 # radius: 1.80, volume: 24.42 for phosphorus
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# Other desolvation parameters
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desolvationSurfaceScalingFactor 0.25
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desolvationPrefactor -13.0
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desolvationAllowance 0.0
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desolv_cutoff 20.0
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buried_cutoff 15.0
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Nmin 280
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Nmax 560
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# Ligand groups
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ligand_typing groups
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min_bond_distance_for_hydrogen_bonds 4
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# covalent coupling
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coupling_max_number_of_bonds 3
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shared_determinants 0
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common_charge_centre 0
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remove_penalised_group 1
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# non-covalent coupling
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max_intrinsic_pKa_diff 2.0
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min_interaction_energy 0.5
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max_free_energy_diff 1.0
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min_swap_pka_shift 1.0
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min_pka 0.0
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max_pka 10.0
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pH variable
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reference neutral
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# ions
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ions 1P 1 # generic charged atoms
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ions 2P 2
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ions 1N -1
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ions 2N -2
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ions MG 2 #Magnesium Ion
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ions CA 2 #Calcium Ion
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ions ZN 2 #Zinc Ion
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ions NA 1 #Sodium Ion
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ions CL -1 #Chloride Ion
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ions MN 2 #Manganese (ii) Ion
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ions K 1 #Potassium Ion
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ions CD 2 #Cadmium Ion
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ions FE 3 #Fe (iii) Ion
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ions SR 2 #Strontium Ion
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ions CU 2 #Copper (ii) Ion
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ions IOD -1 #Iodide Ion
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ions HG 2 #Mercury (ii) Ion
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ions BR -1 #Bromide Ion
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ions CO 2 #Cobalt (ii) Ion
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ions NI 2 #Nickel (ii) Ion
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ions FE2 2 #Fe (ii) Ion
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# write out order of residues
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write_out_order ASP
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write_out_order GLU
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write_out_order C-
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write_out_order HIS
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write_out_order CYS
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write_out_order TYR
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write_out_order LYS
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write_out_order ARG
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write_out_order SER
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write_out_order N+
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write_out_order CG
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write_out_order C2N
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write_out_order N30
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write_out_order N31
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write_out_order N32
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write_out_order N33
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write_out_order NAR
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write_out_order OCO
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write_out_order SH
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write_out_order OP
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