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.
Best,
John
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 atoms1 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