ADL: Which step flexible residue files used in calculation

snoze pa snoze.pa at gmail.com
Thu Oct 11 16:34:14 PDT 2007


Dear Dockers,

 I am doing a flexible residue docking using new version of autodock and
autodock tools. I am able to create the
flexible residue file and both dpf and gpf files. I am wondering which step
autodock uses the flexible residues
file in calculations. I used following trick mentiond in autodock website
but still no information about the flexible residue
is included neither in gpf not in dpf files.

Here is the expert from autodock website:
Known problems 1. The *AutoGrid* calculation must use the file containing
only the *rigid *portion of the receptor.
2. If the flexible residues have any atom types not present in the ligand,
these types must be included in the *ligand_types* list in the *grid
parameter file*.
3. The *docking parameter file* must include the keyword *flexres* followed
by the name of the file
containing the flexible residues. For example, *flexres hsg1_flex.pdbqt*


To get a closer look, I downloaded the docking tutorial from autodock
website, and open the gpf and dpf file in hsg1 example which
describe the flexible residue docking. But still I am unable to locate the
flexible residue information in these two  files.  How do autodock
know the information about these files if they are not included in the gpf
or dpf files? Is there any information/tutorial given in the
autodock website to deal with this situation?


How ever there is another program in autodock tools, prepare_flexdocking4.py
but it is also not working and have no option like "flexres"

I highly appreciate your help.

Thanks in advance
s

Here is the gpf file and dpf files in examples.

gpf file:


npts 60 60 66                        # num.grid points in xyz
gridfld hsg1_rigid.maps.fld          # grid_data_file
spacing 0.375                        # spacing(A)
receptor_types A C HD N OA SA        # receptor atom types
ligand_types C HD N A NA OA          # ligand atom types
receptor hsg1_rigid.pdbqt            # macromolecule
gridcenter 2.5 6.5 -7.5              # xyz-coordinates or auto
smooth 0.5                           # store minimum energy w/in rad(A)
map hsg1_rigid.C.map                 # atom-specific affinity map
map hsg1_rigid.HD.map                # atom-specific affinity map
map hsg1_rigid.N.map                 # atom-specific affinity map
map hsg1_rigid.A.map                 # atom-specific affinity map
map hsg1_rigid.NA.map                # atom-specific affinity map
map hsg1_rigid.OA.map                # atom-specific affinity map
elecmap hsg1_rigid.e.map             # electrostatic potential map
dsolvmap hsg1_rigid.d.map              # desolvation potential map
dielectric -0.1465                   # <0, AD4 distance-dep.diel;>0,
constant



and dpf file:

outlev 1                             # diagnostic output level
intelec                              # calculate internal electrostatics
seed pid time                        # seeds for random generator
ligand_types A C HD N NA OA          # atoms types in ligand
fld hsg1_rigid.maps.fld              # grid_data_file
map hsg1_rigid.A.map                 # atom-specific affinity map
map hsg1_rigid.C.map                 # atom-specific affinity map
map hsg1_rigid.HD.map                # atom-specific affinity map
map hsg1_rigid.N.map                 # atom-specific affinity map
map hsg1_rigid.NA.map                # atom-specific affinity map
map hsg1_rigid.OA.map                # atom-specific affinity map
elecmap hsg1_rigid.e.map             # electrostatics map
desolvmap hsg1_rigid.d.map           # desolvation map
move ind.pdbqt                       # small molecule
about 0.3689 -0.2148 -4.9865         # small molecule center
tran0 random                         # initial coordinates/A or random
quat0 random                         # initial quaternion
ndihe 6                              # number of active torsions
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 14 0.274000                   # torsional degrees of freedom and
coefficient
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_sw1                              # set the above Solis & Wets parameters
compute_unbound_extended             # compute extended ligand energy
ga_run 10                            # do this many hybrid GA-LS runs
analysis                             # perform a ranked cluster analysis


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