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_databaseand for the RESFILE:NATAAstart2 E NATRO3 E NATRO4 E NATRO5 E NATRO[...]212 E NATRO213 E NATRO214 E NATRO215 E NATROThe 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?
Side chain rotamers sampling in protein
software;structural biology;molecular mechanics
I've actually used BASILISK to solve my problem. I've written python functions that compute dihedral angles and python module to rotate side chains according to the distribution given by basilisk.