What is the best tool to sample rotamers in side chain amino acids in a protein? More exactly, I want to sample the different rotamers only for lysine residues while keeping backbone rigid. I've tried to use the fixed backbone design application ("fixbb") in Rosetta3.4 but this program give only one (optimized?) solution. Here are my input files:
-s file.pdb -resfile RESFILE -nstruct 50 -ex1 -ex2 -database /path/to/rosetta_database
and for the RESFILE:
NATAA start 2 E NATRO 3 E NATRO 4 E NATRO 5 E NATRO [...] 212 E NATRO 213 E NATRO 214 E NATRO 215 E NATRO
The header before start
NATAA indicates that I want to only repack the input sequence and the, e.g.
2 E NATRO, command indicates to freeze the considered residue (here the second residue of chain E). For the output I obtain 50 (
nstruct) identical structures, with all the residue in the native conformation given by the
file.pdb except for the lysine residues. My question is how to obtain
nstruct different models for the lysine side chain rotamers?