ADL: PDB preparation best practices for Vina?

Francois Berenger mlists at ligand.eu
Wed Dec 16 17:09:46 PST 2020


Hello,

I think chimera has a nice docking tutorial:

https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html

http://dock.compbio.ucsf.edu/DOCK_6/tutorials/struct_prep/prepping_molecules.htm

Maybe there is the same thing for Vina somewhere.

Regards,
F.

On 15/12/2020 20:13, Rick Sheridan wrote:
> Hello -
> 
> Does anyone know of a preferred go-to reference checklist for preparing 
> a
> protein from the PDB for docking in Vina?  For example it might include
> steps like 'remove any ligands the model is already in complex with' or
> 'determine if any solvent molecules are part of the protein's 
> structure' or
> managing polar vs non-polar hydrogens.
> 
> Best,
> Rick
> 
> --




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