ADL: problem while generating parameter file for autodock4

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ADL: problem while generating parameter file for autodock4

preetichoudhary
Hello,
While using prepare_dpf4.py for generating my autodock .dlg parameter file
I am using the following command:
pythonsh Utilities24/prepare_dpf4.py -l trans_cys_2d32_rot.pdbqt -r
f61d_1va6.pdbqt -p ga_num_evals=2500000 -p ga_run=2000 -p
ligand_types='C,SA,OA,HD,N' -o autodock.dpf

Now .dpf file generates but the ligand types are comma seperaated not
space seperated and also it doesn't take map files in
acconut.Thus,Autodock doesn't run.


Please help me in troubleshooting this issue


file generated:
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,SA,OA,HD,N            # atoms types in ligand
fld f61d_1va6.maps.fld               # grid_data_file
map f61d_1va6.C,SA,OA,HD,N.map       # atom-specific affinity map
elecmap f61d_1va6.e.map              # electrostatics map
desolvmap f61d_1va6.d.map            # desolvation map
move trans_cys_2d32_rot.pdbqt        # small molecule
about 65.0344 -12.6564 30.8085       # small molecule center
tran0 random                         # initial coordinates/A or random
quaternion0 random                   # initial orientation
dihe0 random                         # initial dihedrals (relative) or random
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
set_psw1                             # set the above pseudo-Solis & Wets
parameters
unbound_model extended               # state of unbound ligand
ga_run 10                            # do this many hybrid GA-LS runs
analysis                             # perform a ranked cluster analysis

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Re: ADL: problem while generating parameter file for autodock4

Ruth Huey
Hi,
________________________________________
From: [hidden email] [[hidden email]] On Behalf Of [hidden email] [[hidden email]]
Sent: Sunday, September 01, 2013 5:48 AM
To: [hidden email]
Subject: ADL: problem while generating parameter file for autodock4

Hello,
While using prepare_dpf4.py for generating my autodock .dlg parameter file
I am using the following command:
pythonsh Utilities24/prepare_dpf4.py -l trans_cys_2d32_rot.pdbqt -r
f61d_1va6.pdbqt -p ga_num_evals=2500000 -p ga_run=2000 -p
ligand_types='C,SA,OA,HD,N' -o autodock.dpf

When using  'prepare_dpf4.py', you must specify the file(s) containing the moving atoms:
   the ligand filename and (possibly) a flexres filename (if there is one)...
This sets the  'ligand_types' value and generates the correct map filenames in the dpf.
There may be a case where you would need to specify the ligand_types + the individual maps
directly but at the moment I cannot imagine what it would be...

       Best wishes,
             Ruth

=========================================================

Now .dpf file generates but the ligand types are comma seperaated not
space seperated and also it doesn't take map files in
acconut.Thus,Autodock doesn't run.


Please help me in troubleshooting this issue


file generated:
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,SA,OA,HD,N            # atoms types in ligand
fld f61d_1va6.maps.fld               # grid_data_file
map f61d_1va6.C,SA,OA,HD,N.map       # atom-specific affinity map
elecmap f61d_1va6.e.map              # electrostatics map
desolvmap f61d_1va6.d.map            # desolvation map
move trans_cys_2d32_rot.pdbqt        # small molecule
about 65.0344 -12.6564 30.8085       # small molecule center
tran0 random                         # initial coordinates/A or random
quaternion0 random                   # initial orientation
dihe0 random                         # initial dihedrals (relative) or random
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
set_psw1                             # set the above pseudo-Solis & Wets
parameters
unbound_model extended               # state of unbound ligand
ga_run 10                            # do this many hybrid GA-LS runs
analysis                             # perform a ranked cluster analysis

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---