Use of mk_prepare_receptor.py instead of prepare_receptor in Vina basic docking

[xavgit]

Hi,
it is possible to use mk_prepare_receptor.py instead of prepare_receptor
that is described in Vina basic docking?
The result is valid for the next steps?
If it is possible, which is the equivalent of the command
prepare_receptor -r 1iep_receptorH.pdb -o 1iep_receptor?

Thanks.

Saverio

[rwxayheee]

Yes, if you only want a receptor PDBQT file you can do:

mk_prepare_receptor.py --pdb 1iep_receptorH.pdb -o 1iep_receptorH.pdbqt --skip_gpf

To see the help messages for other supported functions, just run:

mk_prepare_receptor.py

You can also generate the Vina box dimension with mk_prepare_receptor.py and use it as a config file for Vina. The following Colab example is a rewrite of the basic docking tutorial for PDB ID 1IEP:
https://colab.research.google.com/drive/1cHSl78lBPUc_J1IZxLgN4GwD_ADmohVU?usp=sharing#scrollTo=MwrwfQylp80i
The Meeko package used in the Colab is installed from develop branch of this repository. The usage of some options may be different from the released version