Commit 32007a49 authored by Leonardo Solis's avatar Leonardo Solis
Browse files

added pdbs for testing


Former-commit-id: f5e9dd7d
parent fa98a210
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1CBR_REA_A_200
RCSB PDB01141506563D
Coordinates from PDB:1CBR:A:200 Model:1 without hydrogens
22 22 0 0 0 0 999 V2000
5.0920 2.4270 -10.7940 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0790 1.2390 -10.8790 C 0 0 0 0 0 0 0 0 0 0 0 0
7.4570 1.5880 -11.3400 C 0 0 0 0 0 0 0 0 0 0 0 0
8.1090 2.6160 -10.4790 C 0 0 0 0 0 0 0 0 0 0 0 0
7.1710 3.7700 -10.1040 C 0 0 0 0 0 0 0 0 0 0 0 0
5.8090 3.6640 -10.1590 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8670 4.7410 -9.7870 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0090 5.6850 -8.8490 C 0 0 0 0 0 0 0 0 0 0 0 0
4.0490 6.7120 -8.5120 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3830 7.6020 -7.5550 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5130 8.6700 -7.1050 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9620 9.5090 -6.1670 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1640 10.5920 -5.6370 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7030 11.3990 -4.6890 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0710 12.5430 -4.0160 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9070 2.0000 -9.9190 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5820 2.7980 -12.2130 C 0 0 0 0 0 0 0 0 0 0 0 0
7.9800 4.9390 -9.5360 C 0 0 0 0 0 0 0 0 0 0 0 0
2.7160 6.8010 -9.2660 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7300 10.7780 -6.1620 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5240 13.4330 -4.7040 O 0 0 0 0 0 0 0 0 0 0 0 0
3.0900 12.6020 -2.7660 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 6 1 0 0 0 0
1 16 1 0 0 0 0
1 17 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
5 18 1 0 0 0 0
6 7 1 0 0 0 0
7 8 2 0 0 0 0
8 9 1 0 0 0 0
9 10 2 0 0 0 0
9 19 1 0 0 0 0
10 11 1 0 0 0 0
11 12 2 0 0 0 0
12 13 1 0 0 0 0
13 14 2 0 0 0 0
13 20 1 0 0 0 0
14 15 1 0 0 0 0
15 21 2 0 0 0 0
15 22 1 0 0 0 0
A 1
C1
A 2
C2
A 3
C3
A 4
C4
A 5
C5
A 6
C6
A 7
C7
A 8
C8
A 9
C9
A 10
C10
A 11
C11
A 12
C12
A 13
C13
A 14
C14
A 15
C15
A 16
C16
A 17
C17
A 18
C18
A 19
C19
A 20
C20
A 21
O1
A 22
O2
M END
> <InstanceId>
1CBR_REA_A_200
> <ChemCompId>
REA
> <PdbId>
1CBR
> <ChainId>
A
> <ResidueNumber>
200
> <InsertionCode>
> <Model>
1
> <AltIds>
> <MissingHeavyAtoms>
22
> <ObservedFormula>
C20 O2
> <Name>
RETINOIC ACID
> <SystematicName>
(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethyl-1-cyclohexenyl)nona-2,4,6,8-tetraenoic acid
> <Synonyms>
> <Type>
NON-POLYMER
> <Formula>
C20 H28 O2
> <MolecularWeight>
300.435
> <ModifiedDate>
2011-06-04
> <Parent>
> <OneLetterCode>
> <SubcomponentList>
> <AmbiguousFlag>
N
> <InChI>
InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+
> <InChIKey>
SHGAZHPCJJPHSC-YCNIQYBTSA-N
> <SMILES>
CC1=C(C(CCC1)(C)C)\C=C\C(=C\C=C\C(=C\C(=O)O)\C)\C
$$$$
1CBR_REA_B_200
RCSB PDB01141506563D
Coordinates from PDB:1CBR:B:200 Model:1 without hydrogens
22 22 0 0 0 0 999 V2000
7.8930 -3.6110 -18.1130 C 0 0 0 0 0 0 0 0 0 0 0 0
9.1720 -3.0570 -18.7820 C 0 0 0 0 0 0 0 0 0 0 0 0
10.3350 -3.9940 -18.8080 C 0 0 0 0 0 0 0 0 0 0 0 0
10.0230 -5.2800 -19.4960 C 0 0 0 0 0 0 0 0 0 0 0 0
8.6550 -5.8540 -19.1070 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6590 -5.0910 -18.5650 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3200 -5.5960 -18.1960 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6050 -6.5660 -18.7800 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2880 -7.0160 -18.3890 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7360 -8.0340 -19.0800 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4180 -8.5740 -18.8090 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9850 -9.6020 -19.5430 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6790 -10.1970 -19.3660 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3240 -11.2430 -20.1530 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9460 -11.9840 -20.1460 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7100 -2.7360 -18.5460 C 0 0 0 0 0 0 0 0 0 0 0 0
8.0360 -3.5610 -16.5670 C 0 0 0 0 0 0 0 0 0 0 0 0
8.5530 -7.3140 -19.5580 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5770 -6.3750 -17.1900 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2600 -9.6110 -18.2980 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3890 -12.4290 -19.0640 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.5600 -12.1530 -21.2230 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 6 1 0 0 0 0
1 16 1 0 0 0 0
1 17 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
5 18 1 0 0 0 0
6 7 1 0 0 0 0
7 8 2 0 0 0 0
8 9 1 0 0 0 0
9 10 2 0 0 0 0
9 19 1 0 0 0 0
10 11 1 0 0 0 0
11 12 2 0 0 0 0
12 13 1 0 0 0 0
13 14 2 0 0 0 0
13 20 1 0 0 0 0
14 15 1 0 0 0 0
15 21 2 0 0 0 0
15 22 1 0 0 0 0
A 1
C1
A 2
C2
A 3
C3
A 4
C4
A 5
C5
A 6
C6
A 7
C7
A 8
C8
A 9
C9
A 10
C10
A 11
C11
A 12
C12
A 13
C13
A 14
C14
A 15
C15
A 16
C16
A 17
C17
A 18
C18
A 19
C19
A 20
C20
A 21
O1
A 22
O2
M END
> <InstanceId>
1CBR_REA_B_200
> <ChemCompId>
REA
> <PdbId>
1CBR
> <ChainId>
B
> <ResidueNumber>
200
> <InsertionCode>
> <Model>
1
> <AltIds>
> <MissingHeavyAtoms>
22
> <ObservedFormula>
C20 O2
> <Name>
RETINOIC ACID
> <SystematicName>
(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethyl-1-cyclohexenyl)nona-2,4,6,8-tetraenoic acid
> <Synonyms>
> <Type>
NON-POLYMER
> <Formula>
C20 H28 O2
> <MolecularWeight>
300.435
> <ModifiedDate>
2011-06-04
> <Parent>
> <OneLetterCode>
> <SubcomponentList>
> <AmbiguousFlag>
N
> <InChI>
InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+
> <InChIKey>
SHGAZHPCJJPHSC-YCNIQYBTSA-N
> <SMILES>
CC1=C(C(CCC1)(C)C)\C=C\C(=C\C=C\C(=C\C(=O)O)\C)\C
$$$$
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autodock_parameter_version 4.2 # used by autodock to validate parameter set
outlev 1 # diagnostic output level
intelec # calculate internal electrostatics
seed pid time # seeds for random generator
ligand_types C OA # atoms types in ligand
fld 1cbr_protein.maps.fld # grid_data_file
map 1cbr_protein.C.map # atom-specific affinity map
map 1cbr_protein.OA.map # atom-specific affinity map
elecmap 1cbr_protein.e.map # electrostatics map
desolvmap 1cbr_protein.d.map # desolvation map
move 1cbr_ligand.pdbqt # small molecule
about 4.6349 6.6413 -8.2108 # small molecule center
tran0 random # initial coordinates/A or random
quaternion0 random # initial orientation
dihe0 random # initial dihedrals (relative) or random
torsdof 5 # torsional degrees of freedom
rmstol 2.0 # cluster_tolerance/A
extnrg 1000.0 # external grid energy
e0max 0.0 10000 # max initial energy; max number of retries
ga_pop_size 150 # number of individuals in population
ga_num_evals 2500000 # maximum number of energy evaluations
ga_num_generations 27000 # maximum number of generations
ga_elitism 1 # number of top individuals to survive to next generation
ga_mutation_rate 0.02 # rate of gene mutation
ga_crossover_rate 0.8 # rate of crossover
ga_window_size 10 #
ga_cauchy_alpha 0.0 # Alpha parameter of Cauchy distribution
ga_cauchy_beta 1.0 # Beta parameter Cauchy distribution
set_ga # set the above parameters for GA or LGA
sw_max_its 300 # iterations of Solis & Wets local search
sw_max_succ 4 # consecutive successes before changing rho
sw_max_fail 4 # consecutive failures before changing rho
sw_rho 1.0 # size of local search space to sample
sw_lb_rho 0.01 # lower bound on rho
ls_search_freq 0.06 # probability of performing local search on individual
set_psw1 # set the above pseudo-Solis & Wets parameters
unbound_model bound # state of unbound ligand
ga_run 10 # do this many hybrid GA-LS runs
analysis # perform a ranked cluster analysis
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npts 40 50 40 # num.grid points in xyz
gridfld 1cbr_protein.maps.fld # grid_data_file
spacing 0.375 # spacing(A)
receptor_types A C H HD N OA SA # receptor atom types
ligand_types C OA # ligand atom types
receptor 1cbr_protein.pdbqt # macromolecule
gridcenter 3.818 5.995 -7.697 # xyz-coordinates or auto
smooth 0.5 # store minimum energy w/in rad(A)
map 1cbr_protein.C.map # atom-specific affinity map
map 1cbr_protein.OA.map # atom-specific affinity map
elecmap 1cbr_protein.e.map # electrostatic potential map
dsolvmap 1cbr_protein.d.map # desolvation potential map
dielectric -0.1465 # <0, AD4 distance-dep.diel;>0, constant
HETATM 2177 C1 REA A 200 5.092 2.427 -10.794 1.00 50.77 C
HETATM 2178 C2 REA A 200 6.079 1.239 -10.879 1.00 50.77 C
HETATM 2179 C3 REA A 200 7.457 1.588 -11.340 1.00 50.77 C
HETATM 2180 C4 REA A 200 8.109 2.616 -10.479 1.00 50.77 C
HETATM 2181 C5 REA A 200 7.171 3.770 -10.104 1.00 50.77 C
HETATM 2182 C6 REA A 200 5.809 3.664 -10.159 1.00 50.77 C
HETATM 2183 C7 REA A 200 4.867 4.741 -9.787 1.00 27.93 C
HETATM 2184 C8 REA A 200 5.009 5.685 -8.849 1.00 27.93 C
HETATM 2185 C9 REA A 200 4.049 6.712 -8.512 1.00 27.93 C
HETATM 2186 C10 REA A 200 4.383 7.602 -7.555 1.00 27.93 C
HETATM 2187 C11 REA A 200 3.513 8.670 -7.105 1.00 27.93 C
HETATM 2188 C12 REA A 200 3.962 9.509 -6.167 1.00 27.93 C
HETATM 2189 C13 REA A 200 3.164 10.592 -5.637 1.00 27.93 C
HETATM 2190 C14 REA A 200 3.703 11.399 -4.689 1.00 27.93 C
HETATM 2191 C15 REA A 200 3.071 12.543 -4.016 1.00 27.93 C
HETATM 2192 C16 REA A 200 3.907 2.000 -9.919 1.00 50.77 C
HETATM 2193 C17 REA A 200 4.582 2.798 -12.213 1.00 50.77 C
HETATM 2194 C18 REA A 200 7.980 4.939 -9.536 1.00 50.77 C
HETATM 2195 C19 REA A 200 2.716 6.801 -9.266 1.00 27.93 C
HETATM 2196 C20 REA A 200 1.730 10.778 -6.162 1.00 27.93 C
HETATM 2197 O1 REA A 200 2.524 13.433 -4.704 1.00 27.93 O
HETATM 2198 O2 REA A 200 3.090 12.602 -2.766 1.00 27.93 O
HETATM 2199 C1 REA B 200 7.893 -3.611 -18.113 1.00 50.77 C
HETATM 2200 C2 REA B 200 9.172 -3.057 -18.782 1.00 50.77 C
HETATM 2201 C3 REA B 200 10.335 -3.994 -18.808 1.00 50.77 C
HETATM 2202 C4 REA B 200 10.023 -5.280 -19.496 1.00 50.77 C
HETATM 2203 C5 REA B 200 8.655 -5.854 -19.107 1.00 50.77 C
HETATM 2204 C6 REA B 200 7.659 -5.091 -18.565 1.00 50.77 C
HETATM 2205 C7 REA B 200 6.320 -5.596 -18.196 1.00 27.93 C
HETATM 2206 C8 REA B 200 5.605 -6.566 -18.780 1.00 27.93 C
HETATM 2207 C9 REA B 200 4.288 -7.016 -18.389 1.00 27.93 C
HETATM 2208 C10 REA B 200 3.736 -8.034 -19.080 1.00 27.93 C
HETATM 2209 C11 REA B 200 2.418 -8.574 -18.809 1.00 27.93 C
HETATM 2210 C12 REA B 200 1.985 -9.602 -19.543 1.00 27.93 C
HETATM 2211 C13 REA B 200 0.679 -10.197 -19.366 1.00 27.93 C
HETATM 2212 C14 REA B 200 0.324 -11.243 -20.153 1.00 27.93 C
HETATM 2213 C15 REA B 200 -0.946 -11.984 -20.146 1.00 27.93 C
HETATM 2214 C16 REA B 200 6.710 -2.736 -18.546 1.00 50.77 C
HETATM 2215 C17 REA B 200 8.036 -3.561 -16.567 1.00 50.77 C
HETATM 2216 C18 REA B 200 8.553 -7.314 -19.558 1.00 50.77 C
HETATM 2217 C19 REA B 200 3.577 -6.375 -17.190 1.00 27.93 C
HETATM 2218 C20 REA B 200 -0.260 -9.611 -18.298 1.00 27.93 C
HETATM 2219 O1 REA B 200 -1.389 -12.429 -19.064 1.00 27.93 O
HETATM 2220 O2 REA B 200 -1.560 -12.153 -21.223 1.00 27.93 O
REMARK 5 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C6_6 and C7_7
REMARK 2 A between atoms: C8_8 and C9_9
REMARK 3 A between atoms: C10_10 and C11_11
REMARK 4 A between atoms: C12_12 and C13_13
REMARK 5 A between atoms: C14_14 and C15_15
ROOT
HETATM 1 C1 REA A 200 5.092 2.427 -10.794 1.00 50.77 -0.020 C
HETATM 2 C2 REA A 200 6.079 1.239 -10.879 1.00 50.77 0.014 C
HETATM 3 C3 REA A 200 7.457 1.588 -11.340 1.00 50.77 0.005 C
HETATM 4 C4 REA A 200 8.109 2.616 -10.479 1.00 50.77 0.034 C
HETATM 5 C5 REA A 200 7.171 3.770 -10.104 1.00 50.77 -0.077 C
HETATM 6 C6 REA A 200 5.809 3.664 -10.159 1.00 50.77 -0.048 C
HETATM 7 C16 REA A 200 3.907 2.000 -9.919 1.00 50.77 0.020 C
HETATM 8 C17 REA A 200 4.582 2.798 -12.213 1.00 50.77 0.020 C
HETATM 9 C18 REA A 200 7.980 4.939 -9.536 1.00 50.77 0.044 C
ENDROOT
BRANCH 6 10
HETATM 10 C7 REA A 200 4.867 4.741 -9.787 1.00 27.93 0.009 C
HETATM 11 C8 REA A 200 5.009 5.685 -8.849 1.00 27.93 0.007 C
BRANCH 11 12
HETATM 12 C9 REA A 200 4.049 6.712 -8.512 1.00 27.93 -0.062 C
HETATM 13 C19 REA A 200 2.716 6.801 -9.266 1.00 27.93 0.048 C
HETATM 14 C10 REA A 200 4.383 7.602 -7.555 1.00 27.93 0.007 C
BRANCH 14 15
HETATM 15 C11 REA A 200 3.513 8.670 -7.105 1.00 27.93 0.001 C
HETATM 16 C12 REA A 200 3.962 9.509 -6.167 1.00 27.93 0.007 C
BRANCH 16 17
HETATM 17 C13 REA A 200 3.164 10.592 -5.637 1.00 27.93 -0.056 C
HETATM 18 C14 REA A 200 3.703 11.399 -4.689 1.00 27.93 0.091 C
HETATM 19 C20 REA A 200 1.730 10.778 -6.162 1.00 27.93 0.048 C
BRANCH 18 20
HETATM 20 C15 REA A 200 3.071 12.543 -4.016 1.00 27.93 0.199 C
HETATM 21 O1 REA A 200 2.524 13.433 -4.704 1.00 27.93 -0.644 OA
HETATM 22 O2 REA A 200 3.090 12.602 -2.766 1.00 27.93 -0.644 OA
ENDBRANCH 18 20
ENDBRANCH 16 17
ENDBRANCH 14 15
ENDBRANCH 11 12
ENDBRANCH 6 10
TORSDOF 5
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# AVS field file
#
# AutoDock Atomic Affinity and Electrostatic Grids
#
# Created by /home/wimi/lvs/ESA_Projects/bioinfo/docking_src/autodock/Run_Experiments/bin/autogrid_link.
#
#SPACING 0.375
#NELEMENTS 40 50 40
#CENTER 3.818 5.995 -7.697
#MACROMOLECULE 1cbr_protein.pdbqt
#GRID_PARAMETER_FILE ./1cbr.gpf
#
ndim=3 # number of dimensions in the field
dim1=41 # number of x-elements
dim2=51 # number of y-elements
dim3=41 # number of z-elements
nspace=3 # number of physical coordinates per point
veclen=4 # number of affinity values at each point
data=float # data type (byte, integer, float, double)
field=uniform # field type (uniform, rectilinear, irregular)
coord 1 file=1cbr_protein.maps.xyz filetype=ascii offset=0
coord 2 file=1cbr_protein.maps.xyz filetype=ascii offset=2
coord 3 file=1cbr_protein.maps.xyz filetype=ascii offset=4
label=C-affinity # component label for variable 1
label=OA-affinity # component label for variable 2
label=Electrostatics # component label for variable 2
label=Desolvation # component label for variable 3
#
# location of affinity grid files and how to read them
#
variable 1 file=1cbr_protein.C.map filetype=ascii skip=6
variable 2 file=1cbr_protein.OA.map filetype=ascii skip=6
variable 3 file=1cbr_protein.e.map filetype=ascii skip=6
variable 4 file=1cbr_protein.d.map filetype=ascii skip=6
-3.682 11.318
-3.380 15.370
-15.197 -0.197
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This ligand REA (RETINOIC ACID) contains three chains: A, B.
Inspecting visually reveals that these three chains are the same in terms
of bonds and number of atoms. Their position is different.
In adt4, chain B was removed and only chain A is kept for further analysis.
In adt4, use the dashboard to select the chains to be deleted.
The original ligand (.pdb) contains two chains, while the modified one (.pdbqt) has only one.
THE REMOVAL PROCESS WAS PERFORMED BEFORE ADDING HYDROGENS.
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