update prepare_gpf4.py/prepare_dpf4.py for Python 3.0 >

[amir-tagh]

Hello,

I have written a script which uses biopython, obabel and pymol to loop over RNA-small molecule complexes and extracts the binding pocket and prepared the pdbqt fies for docking (Python 3.9.10). I am trying to incorporate the prepare_gpf4.py/prepare_dpf4.py into script to automate all the steps before running the docking (autodock_gpu_64wi). As the prepare*.py scripts are quite old they are not compatible with new python version, do you happen to have updated versions? if not any suggestions or workarounds?

Thanks for your help.

Best, Amir

[rwxayheee]

Hi @amir-tagh Did you get prepy_*.py from MGLTools or ADFRSuite? The scripts can be run with pythonsh, which comes with the scripts. You can locate this special python interpreter at mgltools_x86_64Linux2_1.5.7/bin or ADFRsuite-1.0/bin You can run it as a subprocess in a Python script.

Other options for receptor preparation: I think there's a Python3 (3.7?) prepare_receptor in https://ccsb.scripps.edu/adcpv11/ but I never tested it for RNA. I don't think a prepare_gpf is included. If you have a specific way of defining the grid in your mind, writing a .gpf using Python script might be easier than using the script.

There's also a receptor preparation script in Meeko. However, RNA is not currently supported (? based on the built-in residue parameters) There seems to be ongoing work and might be possible with: https://github.com/forlilab/Meeko/pull/133 Let us know what you think!

[amir-tagh]

Hi @rwxayheee

Thanks for your reply. I have used both from MGLTools or ADFRSuite but they are both incompatible with Python 3.0 (>). I have started writing a .gpf script. Meeko is a good suggestion, see if I can get it to work. Thanks for the suggestions and help, appreciated.

Best, Amir