[gmx-users] RNA gro to pdbqs

[Maik Goette]

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 Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


raja wrote:
> 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 tried to use ADT
> tool as I use it for protein , but It fails to recognize the new residue
> types of AMBER99 specific (ie., RA5,RA3, RC...etc.,) .
> 
> Experienced out there help me to fix this problem.
> 
> With thanks !
> B.Nataraj