ADL: Running Racoon1.1 encounters a python exception.

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ADL: Running Racoon1.1 encounters a python exception.

Anthony Nash
Dear Autodock users,

I'm a bit of a novice using Autodock and I'm experiencing a problem I hope you can help with.

I am using ADT 1.5.7 along with the recent and corresponding versions of autogrid4 and autoligand. I also have a copy of Raccoon1.2 (not 2) as I have a Windows 10 workstation that I'm using to perform a small virtual screen.

Firstly, I've performed several ligand binding site predictions by first preparing my receptor with AutoDockTools and AutoGrid4 then the binding site predictions using autoliagnd via the command line. Works fine, I have some sites to explore further.

I then move onto the actual VS. I download my library from ZINC15 and I fire up Raccoon. I load up the directly of mol2 files which are processed. Two structures are not fit for purpose, so they are automatically removed. I specify the receptor by selecting the same pdbqt as the one used during the site prediction. The only difference is that I need to load ADT and add additional map files. Initially, it would great files .A.map.. C, HD, N, NA, OA, SA, e.map, d.map. With only those files Raccoon throws an error when I specify that I already have the maps. So, I now add atom types F, I, BR, P, S and Cl. Now Raccoon1.1 is happy with these maps. I then set up the docking parameters by selecting the default. Incidentally, I noticed that some default values point to files that don't exist, e.g., receptor.e.map, so I change such entries to e.g., MMP1aSyn03.e.map.

At this point, with receptor, ligands, maps, configurations, and output directory setup Raccoon is happy and ready to "G E N E R A T E". I click said button and I instantly get the following error to the background console window:

Error: 1
<type 'exceptions.NotImplementedError'> Exception in Tk callback
  Function: <function TheFunction at 0x03FF9470> (type: <type 'function'>)
  Args: ()
Traceback (innermost last):
  File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\Pmw\Pmw_1_3\lib\PmwBase.py", line 1747, in __call__
    return apply(self.func, args)
  File "C:\Program Files (x86)\MGLTools-1.5.7\raccoon.py", line 4573, in TheFunction
    prepareDPF(dpf_file, receptor, ligand, flex_res)
  File "C:\Program Files (x86)\MGLTools-1.5.7\raccoon.py", line 4022, in prepareDPF
    dm.write_dpf(dpf_filename, parameter_list, pop_seed)
  File "C:\Program Files (x86)\MGLTools-1.5.7\raccoon.py", line 3761, in write_dpf
    self.dpo.write42(dpf_filename, parm_list)
  File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\DockingParameters.py", line 1556, in write42
    dpf_ptr.write( self.make_param_string('autodock_parameter_version'))
  File "C:\Program Files (x86)\MGLTools-1.5.7\lib\site-packages\AutoDockTools\DockingParameters.py", line 1236, in make_param_string
    raise NotImplementedError, "type (%s) of parameter %s unsupported" % (vt.__name__, param)
<type 'exceptions.NotImplementedError'>: type (unicode) of parameter autodock_parameter_version unsupported

The generation is stuck on the first ligand. I've checked that Raccoon launches with the packaged python2.exe that comes with AutodockTools, therefore I suspect that isn't the problem. I know that all the map files are being loaded in as earlier efforts which threw up such concerns are no longer happening. I just can't get this job to execute!

This is the raccoon parameter configurations:
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 HD OA                   # atoms types in ligand
fld MMP1aSyn03.maps.fld                # grid_data_file   <-------- I changed this by hand....
map MMP1aSyn03.HD.map                  # atom-specific affinity map
map MMP1aSyn03.OA.map                  # atom-specific affinity map
elecmap MMP1aSyn03.e.map               # electrostatics map
desolvmap MMP1aSyn03.d.map             # desolvation map
move ligand.pdbqt                    # small molecule
about 0.378 0.6623 0.648             # 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 0                            # 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 bound                  # state of unbound ligand
ga_run 10                            # do this many hybrid GA-LS runs
analysis                             # perform a ranked cluster analysis


This is my first post, I'm not sure if attachments are welcomed thus here's a link to several screenshots. Autodock Raccoon -why is it throwing a python error? (researchgate.net)<https://www.researchgate.net/post/Autodock_Raccoon-why_is_it_throwing_a_python_error>


Any suggestions are appreciated.



Kind regards
Dr Anthony Nash PhD MRSC

Senior Research Scientist
Nuffield Department of Clinical Neurosciences
RMCR Kellogg College
University of Oxford
http://www.kellogg.ox.ac.uk/

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