Re: [gmx-users] RNA gro to pdbqs

I can't help you directly, because I never tried to dock nucleic acids. I also don't know, if autodock is generally able to recognize them. The best thing, you can do, is writing a script, which does the renaming of the PDB-entries in that way, autodock is able to understand them. Regards Maik

[gmx-users] RNA gro to pdbqs

Hi GMXIONS, I am trying to perform docking of em structure of RNA from gromacs using Autodock. Initially I converted the gro file to pdb formated. The force field I use for GROMACS for RNA simulation is AMBER99. Now how to convert the pdb output of RNA from gromacs to AutoDock pdbqs. I t