I have reread this thread carefully because it's interesting. There is an important point to be made: If you don't take this super-easy call because you are deep, then you are afraid of flopping.
Ffs, according to posts above, you know what the opponent is holding, AA, KK. You basically have a holecard camera. Call with everything you open with in the first place (if this deep), suited connectors too.
Do you think Phil Ivey (or anyone else you would consider really good) would pass on this perfect opportunity?
The OP also indicates in one of the posts in the middle that he doesn't know what to do when getting deep. The solution is just to leave the table the very moment you get deep. Scared money don't play well.
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As far as stacking your opponent if the board comes as you want, then the "standard line" will not work. You can use the standard line 100bb deep (for which it is pretty much designed), but much deeper, then you need to be innovative.
Stacking here begins with a massive donk on the flop. If he folds - well, you missed out on a puny c-bet from him. If he calls - continue donking with large bets.
But, here is the fine point, he might very well raise with his AA/KK overpair, not enjoying being donked into by a creep. You call. Now you are in a sweet spot. You have built a big pot for the turn, bigger than a check-raise would achieve. Best of all, your opponent has the initiative... You take it from here.
To be sure, the above line doesn't have the highest EV versus every opponent, but it has the highest chance of getting it in. Some opponents will bite. The now ridiculed Super System II takes this line. It's still an interesting read, and it's primarily for very deep stack NL Hold'em, 200bb+. Another reference would be No Limit Hold'em - Theory and Practice by Sklansky and (I think) Miller. (Unfashionable too - but still correct) They handle this situation too - how to get it all in deep with the nuts, and also provide some number crunching.
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As far as not getting stacked, on an AKT board, why not just proceed cautiously? Check and call as many times you want, based on the size of your opponents bets. You simply cannot get stacked.
On an KTX board, you simply have to go further, versus a looser opponent perhaps all the way. You are supposed to sometimes lose money with the second nuts - or else you will rarely win a really big one. To get action you must give action.
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Did I mention you should consider stealing on ragged flops like 972? You know what he is holding, but he can't be to sure of your holding.
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Sorry about the rant, the advocating of the wimpy play of folding the fifth or sixth strongest hand for a few bb when 300bb deep, and when the opponents cards are face up, got me a little upset.