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1) How many number of layers can be provided or maximum which generation can be built?

Theoretically one can give any number or can build any generation. dbtv2.pl was used to build upto G8 PAMAM and validated. Even beyond that one can try.

2) Error while doing make install after modifying top2mol2.c file

May be it is not able to detect compiler. You can again define compiler by (in amber10/src) ./configure_at gcc or icc or your_compiler. Then move to /src/antechamber and type make install.