ADL: Help with adding atomic parameter

Stefano Forli forli at scripps.edu
Mon Dec 28 11:00:00 PST 2020


Hi Rik,

unfortunately, adding new types to Vina is not as simple as it is with AutoDock4.
My recommendation is to pick the replace your atom type with the closest element (especially for the vdW radius) that is already in the force field.

Besides, if your atom is not establishing direct interactions with the receptor (i.e., it's fully substituted/coordinated by other atoms) the choice of the atom type would have a rather minimal impact on the docking outcome.

Hope this helps,

S

On 12/27/20 4:06 PM, Bhattacharyya, Rik wrote:
> Hello,
> I am looking for some help adding atomic parameters. I am pretty new to
> Vina so I apologize if I'm not familiar with every detail.
> 
> When I am running Vina, I am getting this error: Parse error on line 6234
> in file "transferrinreceptor.pdbqt": ATOM syntax incorrect: "Sm" is not a
> valid AutoDock type.
> 
>>From what I have gathered, this ATOM syntax error means that vina does not
> have the atomic parameters for samarium. I have seen some of the solutions
> to adding atomic parameters in AD4 but cannot figure out how I would do
> that in Vina.
> 
> If you could please advise with adding those parameters on Vina.
> 
> Thanks,
> Rik Bhattacharyya
> ________________________________________________
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> 

-- 

  Stefano Forli, PhD

  Assistant Professor
  Dept. of Integrative Structural
  and Computational Biology, MB-112A
  Scripps Research
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

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