NWChem comes with all the standard amino acid residue fragments and nucleotides, which covers many biological systems. I suspect that there is something wrong with your .nwchemrc file which specifies the location of these fragments and parameter files. Here is an example of my .nwchemrc file (your paths would be different if course)
nwchem_basis_library /Users/marat/opt/codes/nwchem-new/src/basis/libraries/
ffield amber
amber_1 /Users/marat/opt/codes/nwchem-new/src/data/amber_s/
amber_2 /Users/marat/opt/codes/nwchem-new/src/data/amber_q/
amber_3 /Users/marat/opt/codes/nwchem-new/src/data/amber_x/
amber_4 /Users/marat/opt/codes/nwchem-new/src/data/amber_u/
spce /Users/marat/opt/codes/nwchem-new/src/data/solvents/spce.rst
thfs /Users/marat/opt/codes/nwchem-new/src/data/solvents/thfs.rst
charmm_s /Users/marat/opt/codes/nwchem-new/src/data/charmm_s/
charmm_x /Users/marat/opt/codes/nwchem-new/src/data//charmm_x/
Marat
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