Artur Soares To dock these compounds, you will have to transform their SMILES to .mol2 format (do not forget to optimize the geometry).

Read this https://www.researchgate.net/post/How_to_convert_macromolecule_inhibitors_from_smiles_format_to_mole2_format

Hi Artur,

The following links should help you:

https://www.ccdc.cam.ac.uk/support-and-resources/ccdcresources/GOLD_User_Guide.pdf

https://masterchemoinfo.u-strasbg.fr/Documents/DrugDesign/cours25112009.pdf

https://bio-protocol.org/prep268

First of all select the small molecules to dock for a Virtual Screening. Then choose the Choose the file database of compounds (your small compounds). Then the number of docking experiment performed by ligand (default 10). The ligands structures must be carefully prepared and you can use prepared molecules for docking.

The Genetic Algorithm settings will keep the default settings. And you can go with, Very Flexible Very slow but very accurate sampling for 1 compound. All parameters of the Genetic Algorithm can be modified according to your set protocol.

Thank You.

Tassadaq Hussain Jaffar.