I have tried to use the docking protocol of Rosetta3.2.1 for docking of well structured peptide to protein receptor. The peptide contains the D-amino acids(D-Pro, D-Arg). The corresponding "params" files are located in "residue_types/d-caa"
First I changed the related lines in "residue_types.txt", to get the params files active. The residue types seem to be recognized by Rosetta but it fails with the following error message
ERROR: unknown atom_name: DPR H
ERROR:: Exit from: src/core/chemical/ResidueType.cc line: 1454
The input PDBfile contains no hydrogen atoms. What file could be wrong or has to be changed in the rosetta database?
To check wether D-Arg will be accepted, I removed the D-Pro residue from the peptide sequence.
The program ends with segmentation fault. In the log file, the last statement was
Reading in rot lib /Users/moehle/Documents/Rosetta3.2.1/rosetta_database//ncaa_rotlibs/darg.rotlib...done!
This file is lacking in the rosetta_database. The link to get the ncaa_rotamer_libraries in the README does not work anymore.
Can anyone help me to fix these problems?
Thanks in advance.