The sharedchao estimator will give you estimates for the pairing of your groups as well as an estimate for all your groups combined. This function is ram dependent, so as your number of groups grows the memory needed to do the combined group estimate grows exponentially. To avoid this problem, try comparing less groups by using the groups parameter to select the groups you would like to compare.
In version 1.7, releasing in mid November, the all parameter will be added to the [[summary.shared]] and [[collect.shared]] commands. The sharedchao and sharedsobs calculators not only give you the pairwise richness estimates for your groups, but also estimate the combined richness of all your groups. The all parameter allows you to specify whether or not you want mothur to find this combined group estimate. By default it is set to true, but if you have a large number of groups the combined estimate may cause you to run out of ram, to avoid this problem and yet still get the pairwise richness estimates set all to false.