ADL: command-line or programmatic method for detailing ligand:protein contacts?

Oleg Trott trott at scripps.edu
Thu Nov 7 15:28:23 PST 2013


Hi

I think AutoDock Raccoon 2 does that. Alternatively, you could
manually remove everything from the receptor except the residues in
question, run
  "vina --score_only ..."
on the docking results, which is essentially instant, and select the
results that still give you good "energy".

On Thu, Nov 7, 2013 at 10:13 AM, Dennis N Bromley <dbromley at uw.edu> wrote:
> Hi all,
>
> Thank you for your help recently.  I now have a pile of thousands of docked
> ligands and proteins and I need to analyze them for specific contacts e.g.
> how many of these 10,000 vina files show ligand hydrogen bonds to L123 and
> electrostatic contacts with G201?
>
> Can anyone recommend a good tool for doing this?  I don't mind parsing up
> thousands of log files if there is a tool that will create those.  I just
> can't sit there for months using a GUI and doing it all by eye.
>
> thanks!
> -denny-
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-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com


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