ADL: [EXTERNAL] Re: Help with adding atomic parameter

Stefano Forli forli at scripps.edu
Mon Dec 28 11:17:56 PST 2020


Hi Rik,

Vina supports all the atom types in the standard AutoDock4 force field. They are defined in a text file in your AutoDockTools installation ([MGL_ROOT_DIR]/AutoDockTools/AD4_parameters.dat).

For modifying the files, there's no way to do it with the graphical interface, so open the PDBQT with any text editor and change the type manually.

S

On 12/28/20 11:13 AM, Bhattacharyya, Rik wrote:
> Hi Stefano,
> Thank you for letting me know about that. For this protein, I don't think
> this particular atom matters very much so it should be fine.
> My only other question is how would I be replacing this particular atom. Do
> I need to do this in AutoDock Tools and if so, is there any resources on
> the method for doing that?
> Also, what atoms are supported with AutoDock Vina. Once I get that
> information, I can try to figure out what to replace it with and how to do
> that.
> 
> Thanks,
> Rik
> ________________________________________________
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-- 

  Stefano Forli, PhD

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

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