No RMS and IRMS values in protein/nucleic acid docking

Hello,

I am docking a small protein / nucleic acid structure to generate dockings. The scoring contains only -nan for rms and 0.000 for Irms. Why doesn’t the docking result in valid rms/irms values? Fnat and I_sc as well as total_score seem ok. What do I have to change in order to receive rms and irms values?

XML Rosetta Script (prot2.xml):

<ROSETTASCRIPTS>

    <SCOREFXNS />

        <TASKOPERATIONS />

        <FILTERS>

        <IRmsd name=”irmds” confidence=0/>

        </FILTERS>

    <LIGAND_AREAS>

                <inhibitor_dock_sc  chain=”C” cutoff=”6.0″ add_nbr_radius=”true” all_atom_mode=”true”/>

                <inhibitor_final_sc chain=”C” cutoff=”6.0″ add_nbr_radius=”true” all_atom_mode=”true”/>

        </LIGAND_AREAS>

        <INTERFACE_BUILDERS>

                <side_chain_for_docking ligand_areas=”inhibitor_dock_sc”/>

                <side_chain_for_final ligand_areas=”inhibitor_final_sc”/>

        </INTERFACE_BUILDERS>

        <MOVEMAP_BUILDERS>

                <docking sc_interface=”side_chain_for_docking” minimize_water=”false”/>

                <final sc_interface=”side_chain_for_final”  minimize_water=”false”/>

        </MOVEMAP_BUILDERS>

        <MOVERS>

        <RigidBodyTransMover name=”fix” jump=”1″ distance=”15″ x=”0″ y=”0″ z=”0″ />

        <Translate name=”trans” chain=”C” distribution=”uniform” angstroms=”5.0″ cycles=”1000″/>

        <Rotate name=”rotate” chain=”C” distribution=”uniform” degrees=”360″ cycles=”1000″/>

        <SlideTogether name=”together” chains=”C”/>

        <HighResDocker name=”highdock” scorefxn=”score_docking” cycles=”9″ repack_every_Nth=”3″ movemap_builder=”docking” />    

         <FinalMinimizer name=”mimimize” scorefxn=”score_docking” movemap_builder=”final”/>     

        <ParsedProtocol name=”low_res_dock”>

                   <!–<Add mover_name=”fix”/>–>

                   <Add mover_name=”trans”/>

                   <Add mover_name=”rotate”/>

                   <Add mover_name=”together”/>

        </ParsedProtocol>

        <ParsedProtocol name=”high_res_dock”>

                   <Add mover_name=”highdock”/>

                   <Add mover_name=”mimimize”/>

        </ParsedProtocol>

        <InterfaceAnalyzerMover name=”iface_analyzer” packstat=0 pack_input=0 pack_separated=1 fixedchains=A tracer=0/>

        <Docking name=”dock_high” score_high=”score_docking” fullatom=1 local_refine=1  optimize_fold_tree=1 conserve_foldtree=0 design=0 jumps=1/>    

        <DockingProtocol name=”dockp_high” docking_local_refine=”true” dock_min=”false” partners=”C_A” />    

    </MOVERS>

        <APPLY_TO_POSE />

        <PROTOCOLS>

                <Add mover_name=”low_res_dock”/>

                <Add mover_name=”high_res_dock”/>

                <Add mover_name=”dockp_high”/>

               <!– <Add filter_name=”irmds”/>–>

                <!–<Add mover_name=”iface_analyzer”/>–>

                <!–<Add mover_name=”add_scores”/>–>

        </PROTOCOLS>

</ROSETTASCRIPTS>

 

Command line:

DIR/rosetta_scripts.RELEASE -native FILENAME -s FILENAME -use_input_sc -nstruct 10 -ex1 -ex2aro -parser:protocol prot2.xml  -overwrite

Scores.sc output:

SEQUENCE: 

SCORE: total_score         rms        Fnat        I_sc        Irms   …

SCORE:     -91.285        -nan       0.833      -1.473       0.000      …

SCORE:     -99.662        -nan       0.778      -0.859       0.000   …

SCORE:    -105.361        -nan       1.000      -1.271       0.000    …

SCORE:     -79.505        -nan       1.000      -0.333       0.000    …

SCORE:    -106.792        -nan       0.667      -0.158       0.000    …

…