it is not clear what your question is.

The synthesis of cis or trans isomer for chalcone depends in part on the synthesis method. 

it is not clear you mean by docking results cis was the best conformer. Does this mean you have found that the cis is energetically more stable? Is the phenyl of your chalcone substituted? This could cause a preference for one isomer over the other. Typically, the trans isomer should be more engergetically favourable as it is less sterically hindered.