John,
rrt_sample is only applicable to proteins.
Dina
On Sun, Feb 28, 2021 at 12:14 AM John Stiller jstiller@brandeis.edu wrote:
> 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 > > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users >