F.A.Q.

F.A.Q


1. During receptor preparation with AutoDock PyMOL plugin I get the following error and the program hangs:
“ValueError: Could not find atomic number for Z Z”

Even if you correct the pdb file you will get the following warning:
Sorry, there are no Gasteiger parameters available for atom protein4autodock_model1: : ZN400:ZN
In that case kill all processes running “RunScript”, open frames/preparedProtein.pdbqt file under the project subdirectory and change the Zn charge from 0.000 to 2.000 . After that you can restart docking by executing “RunScript”, e.g.
screen -S docking sh RunScript
You can find charges of other elements or chemical groups here.
Or if you prefer QM derived partial charges for some very special chemical entities look here.
However, your problems have not finished yet. Read F.A.Q. 6, too!                         
 
2. During receptor preparation with AutoDock PyMOL plugin I get the following error and the program hangs:
TypeError: unsupported operand type(s) for +: ‘type’ and ‘str’

Many things may have gone wrong, some of which are listed below:

* The “Project subdirectory” you have given does not much one already existing directory. If yes then remove it. Remember that AutoDock PyMOL plugin always appends the suffix “_client” to the name you give.

3. There are missing folders under “out/” directory although all the ligands are present in “in/” directory.

In that case look if all ligands are present in “RunScript” script:

grep vina RunScript | wc -l
Now it’s getting more complicated. Although ConsScoreTK.py can cope with single quotes in filenames, NNScore2.py cannot, so you will have to substitute all single quotes in every folder or file with something readable by UNIX, e.g. “sq” (for “single quote”). You can do that as follows:
shopt -s globstar
  for file in ./**; do 
      echo "${file%/*}/"
  done | sort | uniq > dirnames.txtfor dirname in $(cat dirnames.txt); do 
      echo mv $dirname "$(echo $dirname | perl -pi -e "s/\'/sq/g")"; # remove echo to rename directories

done
 
for file in ./**; do 
      if [[ -f "$file" ]]; then
          dirname="${file%/*}/"
          basename="${file:${#dirname}}"
          echo mv "$file" "$(echo $dirname${basename%} | perl -pi -e "s/\'/sq/g")" # remove echo to rename files
      fi
done
If you are satisfied with the new names remove the designated “echo” words. Don’t forget to modify accordingly the ligand names in you Ki/IC50/DeltaG file.

In the future ConsScorTK.py will support more relevant special characters in filenames like “^”.

4. How to run Vina on a cluster using Moab/Torque queuing system:
Enter the docking home directory and execute “create_pbs_jobs.sh” script to create the necessary submission files. Then submit the all the jobs in batch mode by executing “submit_pbs_jobs.sh” script.                                                                                                                                                                                                                                                                                                                                                     5. socket.gaierror: [Errno -2] Name or service not known
If you get the following error when executing consscore_optimization_script.py or scoringfunction_selection_script.py:
Traceback (most recent call last):
   File "/home/thomas/Documents/Commandlines_and_Hints/AutoDock_Vina/consscore_optimization_script.py", line 13, in <module>
     from scoop import futures
   File "/usr/local/lib/python2.7/site-packages/scoop/futures.py", line 28, in <module>
     from ._types import Future, NotStartedProperly, CallbackType
   File "/usr/local/lib/python2.7/site-packages/scoop/_types.py", line 23, in <module>
     from scoop._comm import ZMQCommunicator, Shutdown
   File "/usr/local/lib/python2.7/site-packages/scoop/_comm.py", line 31, in <module>
     from . import shared, encapsulation, utils
   File "/usr/local/lib/python2.7/site-packages/scoop/shared.py", line 24, in <module>
     from . import encapsulation, utils
   File "/usr/local/lib/python2.7/site-packages/scoop/utils.py", line 43, in <module>
     ip for ip in socket.gethostbyname_ex(socket.gethostname())[2]
 socket.gaierror: [Errno -2] Name or service not known
It means that scoop cannot find your host name. Find your hostname using:
hostname
And modify the first two lines of you /etc/hosts to read:
127.0.0.1  <hostname>                                                                            ::1        <hostname>
where <hostname> is the output of hostname command.                                                                                                                                                                                                                                                                                                                                                   6. Although I get evaluation results from Vina and NNscore1, for NNscore2 I get only messages like:
WARNING: there must be a problem with cluster  000001 , no docking results were detected!
In that case creation of the .pdbqt file of the full-length protein (rigid+flexible) in complex with the ligand has failed possibly due to wrong atom name syntax. Usually these issue are created by ions (have a look in this thread). A work around is to correct the error manually. For instance, if you have a Mg2+ ion do:
 

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