I am confused which score to choose for my docking results in Glide. Kindly also explain the significance of these two different scores and which is the best for using as docking score.
You might find this answer from the developers useful:
http://www.schrodinger.com/kb/348
Usually, the gscore (aka glide score) is used to show the estimated free energy of binding. Keep in mind however, that this score can differ depending on which docking method was used (SP, XP, peptide, HTS). SP is the default (XPscore is the gscore for XP runs). Also, be sure to account for the poorly cited +/- 2 kcal/mol error for rigid docking (See links).
From the previous answer, "The docking score and the GlideScore are the same unless you include Epik state penalties in the scoring (the recommended and default behavior). The penalties from Epik are applied only to the docking score." This means that glide attempts to account for the energy penalties of specific tautomeric states of the given compounds calculated by the program Epik and modifies the gscore accordingly (usually lowering it due to unfavorable or statistically unlikely states).
As to which one is better to use, it really depends on what you are looking for, but the docking score is usually best.
http://pubs.acs.org/doi/full/10.1021/jm0306430
http://pubs.acs.org/doi/full/10.1021/jm051256o
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