ADL: help with AutoDock4.2 covalent type docking set up

Aquillah Kanzi kanziaquillah at gmail.com
Wed Oct 31 09:15:13 PDT 2012


Hi,

I am a Bioinformatics Master Student at Rhodes University, South Africa. I
am using autodock to study protein ligand interactions and some of my
ligands are known to form covalent bonds with the receptor proteins. i have
used the autodock manual to set up the covalent map, select an atom and
labelled it as "Z" in the ligand pdbqt file. i have edited my gpf to have
the Z map and the dpf file to contain the Z ligand type as well but the
ligand isn't being positioned correctly in the binding site and the Z
labelled atom is not being tethered to the selected atom in the receptor. I
would like your assistance on this.

below are my GPF and DPF files;

*gpf*

npts 70 70 65                        # num.grid points in xyz
gridfld 2OUL.maps.fld # grid_data_file
spacing 0.375000000000               # spacing(A)
receptor_types A C HD N OA SA NA        # receptor atom types
ligand_types S Cl Br F A C NA OA N SA HD Z      # ligand atom types
receptor 2OUL.pdbqt  # macromolecule
gridcenter 130.264000 83.419000 -183.662000        # xyz-coordinates or auto
smooth 0.5                           # store minimum energy w/in rad(A)
map 2OUL.S.map       # atom-specific affinity map
map 2OUL.Cl.map       # atom-specific affinity map
map 2OUL.Br.map       # atom-specific affinity map
map 2OUL.F.map       # atom-specific affinity map
map 2OUL.A.map       # atom-specific affinity map
map 2OUL.C.map       # atom-specific affinity map
map 2OUL.NA.map      # atom-specific affinity map
map 2OUL.OA.map      # atom-specific affinity map
map 2OUL.N.map       # atom-specific affinity map
map 2OUL.SA.map      # atom-specific affinity map
map 2OUL.HD.map      # atom-specific affinity map
map 2OUL.Z.map      # atom-specific affinity map
elecmap 2OUL.e.map   # electrostatic potential map
dsolvmap 2OUL.d.map              # desolvation potential map
dielectric -0.1465                   # <0, AD4 distance-dep.diel;>0,
constant
covalentmap 5.0 1000.0 2.573000 0.342000 -0.531000


*dpf *
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 A C HD N OA S Z         # atoms types in ligand
fld 2OUL.maps.fld                    # grid_data_file
map 2OUL.A.map                       # atom-specific affinity map
map 2OUL.C.map                       # atom-specific affinity map
map 2OUL.HD.map                      # atom-specific affinity map
map 2OUL.N.map                       # atom-specific affinity map
map 2OUL.OA.map                      # atom-specific affinity map
map 2OUL.S.map                       # atom-specific affinity map
map 2OUL.Z.map                       # atom-specific affinity map
elecmap 2OUL.e.map                   # electrostatics map
desolvmap 2OUL.d.map                 # desolvation map
move peptidylvinylsulfone_cov.pdbqt  # small molecule
about -0.6083 -0.3684 -0.0805        # small molecule center
tran0 random                         # initial coordinates/A or random
axisangle0 random             # initial orientation
dihe0 random                     # initial dihedrals (relative) or random
tstep 2.0                            # translation step/A
qstep 50.0                            # quaternion step/deg
dstep 50.0                            # torsion step/deg
torsdof 15                            # 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 450000                  # 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 extended               # state of unbound ligand
ga_run 100                           # do this many hybrid GA-LS runs
analysis                             # perform a ranked cluster analysis

thank you!
-- 

Aquillah Kanzi,
Postgraduate Student,
Bioinformatics Research Group (RUBi),
Rhodes University,
Grahamstown, 6140,
South Africa.

*"More flexible life patterns could . . . nurture and renew our spirits
through opportunities to actualize personal dreams" *


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