ADL: Problem with the dpf files generated by Raccoon

Davide Mercadante dmer018 at aucklanduni.ac.nz
Thu Oct 13 15:44:23 PDT 2011


Hi Stefano,

thank you very much for your reply.
Solved.!

Cheers,
Davide

2011/10/14 Stefano Forli <forli at scripps.edu>

> Hi Davide,
>
> this is an bug with the old AutoDock 4.0 local search keyword ('set_sw1')
> that has now been substituted with 'set_psw1' (pseudo Solis-Wet).
>
> The issue has been fixed, so try to update your ADT to the latest stable
> version (1.5.4) and see if it works.
>
> Although, my suggestion is to change your template file to have the
> 'set_psw1' (and use the latest AutoDock version 4.2), because the
> performances with the pseudo Solis-Wet local search have been reported to be
> significantly better.
>
> Hope this helps,
>
>
> Stefano
>
>
>
> On 10/12/2011 11:40 PM, Davide Mercadante wrote:
>
>> 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
>> ______________________________**__________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/**mailing_list<http://autodock.scripps.edu/mailing_list>---
>>
>
>
> --
>  Stefano Forli, PhD
>
>  Research Associate
>  Olson Molecular Graphics Laboratory
>  Dept. Molecular Biology,  MB-112
>  The Scripps Research Institute
>  10550  North Torrey Pines Road
>  La Jolla,  CA 92037-1000,  USA.
>
>    tel: (858) 784-2055
>    fax: (858) 784-2860
>    email: forli at scripps.edu
>    http://www.scripps.edu/~forli/
>
> ______________________________**__________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/**mailing_list<http://autodock.scripps.edu/mailing_list>---
>



-- 
Davide Mercadante - PhD student -
School of Chemical Sciences
The University of Auckland
1142 Auckland, New Zealand


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