ADL: Problem with the dpf files generated by Raccoon

Davide Mercadante dmer018 at aucklanduni.ac.nz
Wed Oct 12 23:40:56 PDT 2011


Dear Autodock users,

I am writing in order to report a problem that I have been experiencing
using Raccoon. I have run Raccoon on a library of compounds (for virtual
screening) without apparent problems..I have input in the program template
.gpf and .dpf files as required.
Raccoon does its job and creates the .gpf and .dpf input files in separate
folders as expected. However, when I run the Run.sh script to launch each
docking autogrid runs well but autodock aborts abnormally showing the
following error.

*autodock4: ERROR: autodock4:  ERROR:  You must use "set_ga" to
allocate both Global Optimization object AND Local Optimization object

autodock4: Aborting...

autodock4: Unsuccessful Completion.

*

I have seen that there is something "wrong" in the .dpf files generated by
Raccoon for each molecule.
The output files generated show the parameter "set_sw1" at the bottom of the
file. This seems to be the problem because if I modify the .dpf file
inverting the order of the lines and placing the "set_sw1" parameter above
"set_ga" parameter autodock runs without problems.
If in the template file I omit the set_sw1 parameter Raccoon generates
working files inserting the default parameter "set_psw1" above the "set_ga"
parameter and autodock runs well without any errors.

I am copying the template file used to run Raccoon, an example of .dpf file
generated by Raccoon that is not working and a .dpf file generated by
Raccoon which is working fine after I modified the order of the last lines.
The lines interested are underlined in red.

Can you please advice me on why this is happening and how I can fix the
problem?

Any help will very be much appreciated...
Thank you.

Regards,
Davide Mercadante
*
Template file used to run Raccon

*outlev 1                             # diagnostic output level
intelec                              # calculate internal electrostatics
seed pid time                        # seeds for random generator
ligand_types C HD OA N               # atoms types in ligand
fld Atg5_final_model.maps.fld        # grid_data_file
map Atg5_final_model.C.map           # atom-specific affinity map
map Atg5_final_model.HD.map          # atom-specific affinity map
map Atg5_final_model.OA.map          # atom-specific affinity map
map Atg5_final_model.N.map           # atom-specific affinity map
elecmap Atg5_final_model.e.map       # electrostatics map
desolvmap Atg5_final_model.d.map     # desolvation map
move ZINC00001234.pdbqt              # small molecule
about 0.1148 1.5798 0.0168           # small molecule center
tran0 random                         # initial coordinates/A or random
quat0 random                         # initial quaternion
ndihe 2                              # 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 2 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
ga_run 10                            # do this many hybrid GA-LS runs
analysis                             # perform a ranked cluster analysis*
**
Example of working file*

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 HD N OA               # atoms types in ligand
fld Atg5_final_model.maps.fld        # grid_data_file
map Atg5_final_model.C.map           # atom-specific affinity map
map Atg5_final_model.HD.map          # atom-specific affinity map
map Atg5_final_model.N.map           # atom-specific affinity map
map Atg5_final_model.OA.map          # atom-specific affinity map
elecmap Atg5_final_model.e.map       # electrostatics map
desolvmap Atg5_final_model.d.map     # desolvation map
move ZINC00001234.pdbqt              # small molecule
about 0.1148 1.5798 0.0168           # 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 2                            # 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
#
unbound_model bound                  # state of unbound ligand
set_sw1                              # set the above Solis & Wets parameters
ga_run 10                            # do this many hybrid GA-LS runs
analysis                             # perform a ranked cluster analysis

*Example of non-working file (normally generated by Raccoon).
*
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 Cl HD N OA          # atoms types in ligand
fld Atg5_final_model.maps.fld        # grid_data_file
map Atg5_final_model.A.map           # atom-specific affinity map
map Atg5_final_model.C.map           # atom-specific affinity map
map Atg5_final_model.Cl.map          # atom-specific affinity map
map Atg5_final_model.HD.map          # atom-specific affinity map
map Atg5_final_model.N.map           # atom-specific affinity map
map Atg5_final_model.OA.map          # atom-specific affinity map
elecmap Atg5_final_model.e.map       # electrostatics map
desolvmap Atg5_final_model.d.map     # desolvation map
move ZINC00001281.pdbqt              # small molecule
about 1.6667 -2.1296 -0.5198         # 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 4                            # 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
#
unbound_model bound                  # state of unbound ligand
ga_run 10                            # do this many hybrid GA-LS runs
analysis                             # perform a ranked cluster analysis
set_sw1                              # set the above Solis & Wets parameters
*
*--
Davide Mercadante - PhD student -
School of Chemical Sciences
The University of Auckland
1142 Auckland, New Zealand


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