The AMBER 6 programs as distributed are dimensioned for a fairly large system (about 30,000 atoms), and you may want to change their dimensions to be more appropriate for the machine you are using if you are running in a tight memory environment. (Sander_classic can also be compiled the MEM_ALLOC switch set in the MACHINE file. This causes arrays to be allocated dynamically, based on the size of the molecule. If this works on your machine, it can eliminate most of the resizing effort described below.)
In src/sander/sizes.h, you will find the following parameters that might
need to be changed:
The actual memory requirements for a particular job can be determined
from the output of SANDER or GIBBS, and can be used to determine how to
change these values. Note that some sizes related to NMR refinements are
defined in nmr.h.
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