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.
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 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