Check docking

[Roger Williams]

I would like to do lead optimization, starting with a compound for which I have a crystal structure of the compound bound to its receptor. I started with fragments of the compound to generate possible improvements. To get the center for the pocket, I used the centroid of all of the residues interacting with the compound in the crystal structure, and I used these interacting residues ot get sizex, sizey and sizez (using scoria).

The results at the end of autogrow4 do not look encouraging. Although all of the output sloutions are in the box, I am not sure that each compound generated the GA evolution is actually docked optimally. To check that Vina/QuickVina are actually working optimally, I wanted to start with the smi for which I already have a crystal structure and see whether autogrow4 would actually dock it correctly, without any evolution. However, I cannot see how I can set up the json file to just do docking of a single smi, evaluate it, write outputs and stop. I would appreciate it if someone could advise.

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