ADL: PDB preparation best practices for Vina?

Mark Pohl at
Tue Dec 22 09:54:09 PST 2020

The content is there.  The email below has a typographical error in it.  The link is, not  
If you've further problems, let me know!
Mark Pohl, Esq.
Pharmaceutical Patent Attorneys, LLC   
55 Madison Avenue, 4th floorMorristown, NJ 07960-7397  USA
+1 (973) 984-6159 x304

    On Tuesday, December 22, 2020, 11:27:02 AM EST, Drasko Tomic <drasko.tomic at> wrote:  
 Dear Mark,
seems there is no content there:

The requested URL /tutorial.htmlThe was not found on this server.
Apache Server at Port 80



    On Thursday, December 17, 2020, 9:00:18 PM GMT+1, Mark Pohl < at> wrote:  
 Oleg Trott, the graduate student who wrote VINA, made a nice (albeit somewhat dated) video: same page provides a link to his test files, so you can follow along with his lecture. 
Hope this helps!
Mark Pohl, Esq.
Pharmaceutical Patent Attorneys, LLC   

    On Wednesday, December 16, 2020, 8:12:39 PM EST, Francois Berenger <mlists at> wrote:  

I think chimera has a nice docking tutorial:

Maybe there is the same thing for Vina somewhere.


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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