Hello bb users,

I had posted a VOIDOO question a while ago, I have since re-done VOIDOO. Thanks to everyone who replied.

So, the verdict:


(i) increase number of refinement cycles to 30 (or more)
(ii) drop convergence criterion from 0.1 (both A and %) to a lower value e.g. 0.02
(ii) repeat a couple of times on randomly oriented copies.
(iv) if you know where the cavity is give xyz coords for center and search for this cavity
(v) average the converged volumes for 10 different orientations (if you want to strictly follow the manual) or just 2-3 orientations with very strict convergence criteria (I found that between 20 and 25 cycles, the volume varies only about <5 A^3, or ~1-2% for me). Also, in the latter case, on the 25th cycle, there is <0.5 A^3 difference between different orientations. So, there is little point really in calculating cavity volumes for more than 2-3 orientations.

Voila!

I pilfered most of this from email exchanges with Dr. Mark Mayer. Thanks, Dr. Mayer. The resultant numbers, however, are mine.