Hello All, 

Does the rrt sample module support DNA? It seems to not be dividing the molecule into rigid bodies like it does for proteins. I assume I just need to tell it that it's DNA and not protein, but I can't figure out how... 

Thank you in advance.


My attempt:
rrt_sample Test_DNA.pdb Linker.txt

Result:

Starting reading pdb file Test_DNA.pdb
WARNING  Could not determine CHARMM atom type for atom "O2'" in residue #2 "DG"
WARNING  Could not determine CHARMM atom type for atom "O2'" in residue #3 "DT"
WARNING  Could not determine CHARMM atom type for atom "O2'" in residue #5 "DC"
2 residues 0 bonds were read from file Linker.txt
# atoms 83 # bonds 87 # angles 131 # dihedrals 172
4 bonds were added
# atoms 83 # bonds 91 # angles 131 # dihedrals 172
begin ForceFieldParameters0::get_force_field_atom_type:
  WARNING  Atom #9 "O2'" (O) does not have a known CHARMM type
end ForceFieldParameters0::get_force_field_atom_type
Rb 0 created with 83 atoms
1 rigid bodies were created
rb order 0 --> 0 parent 0
0 joints were constructed
ProteinKinematics done
Init  RRT
Start RRT run
ERROR: No degrees of freedom to sample!

DNA Molecule Example:
ATOM      1  P    DG    2     120.209 118.900 144.134  1.00210.77      A    P
ATOM      2  C5'  DG    2     117.681 119.487 143.764  1.00210.77      A    C  
...

Linker.txt:
3
4