ADL: Problem with the dpf files generated by Raccoon

Davide Mercadante dmer018 at aucklanduni.ac.nz
Sun Oct 16 13:47:50 PDT 2011


Dear Autodock users,

I have successfully carried out a virtual screening on my target using
compounds library downloaded from the ZINC database.

I have used Racoon to prepare the docking and I have run Autodock 4.2.3
which successfully terminated.

However, I have questions on how to analyze my results now. The run produced
hundred of folders where in each one is placed a .dlg file (in each dlg 50
conformations have been sampled).

I have seen on the Autodock website that Fox is a tool to analyze virtual
screening results. So I have downloaded and launched it as describes...it
seemed to work but when I try to prepare my results for filtering or
visualization it asks me to re-cluster and when I launch the clustering the
program seems to be hanging. It happens not only with the great number of
folders but also with just one dlg file as a test..

I know that Fox is still in its alpha release but do you know any way to
solve the problem and analyze the results in an automated way? Can I use a
different version of Fox if it exists or can you please suggest any other
way or tools to analyze virtual screening results?

Any help would be very much appreciated.

Thank you very much in advance..

Regards,
Davide

2011/10/14 Davide Mercadante <dmer018 at aucklanduni.ac.nz>

> 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
>
>
>
>


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


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