Hi Dina,

Thank you!

Best, John

On Mon, Mar 1, 2021 at 1:45 PM Dina Schneidman duhovka@gmail.com wrote:

> 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 >> > _______________________________________________ > IMP-users mailing list > IMP-users@salilab.org > https://salilab.org/mailman/listinfo/imp-users >