Docking tree issues

[Anonymous]

Hi all,

I am trying to design the interface of a peptide docked on a protein. For that, I have written a design XML considering only peptide residues to be designed. I use a docking tree mover that should define 1 jump in the sequence, but when I run the script I always get the same error:

File: src/core/pose/util.cc:1341

[ ERROR ] UtilityExitException

ERROR: Cannot compute center of mass of zero residues!

Any suggestions? This is the complete XML script that I use:

<ROSETTASCRIPTS>

    <SCOREFXNS>

        <ScoreFunction name=”beta” weights=”beta_nov16″/>

        <ScoreFunction name=”beta_cst” weights=”beta_nov16″>

            <Reweight scoretype=”coordinate_constraint” weight=”1″/>

            <Reweight scoretype=”atom_pair_constraint” weight=”1″/>

            <Reweight scoretype=”dihedral_constraint” weight=”1″/>

            <Reweight scoretype=”angle_constraint” weight=”1″/>

            <Reweight scoretype=”aa_composition” weight=”1.0″/>

        </ScoreFunction>

    </SCOREFXNS>

    <RESIDUE_SELECTORS>

        <Chain name=”peptide” chains=”B”/>

        <Chain name=”PD1″ chains=”A”/>

        <Phi name=”posPhi” select_positive_phi=”true” />

        <And name=”posPhi_pep” selectors=”peptide,posPhi”/>

        <Phi name=”negPhi” select_positive_phi=”false” />

        <And name=”negPhi_pep” selectors=”peptide,negPhi”/>

        <Neighborhood name=”interface_chA” selector=”peptide” distance=”8.0″/>

        

    <Neighborhood name=”interface_chB” selector=”PD1″ distance=”8.0″/>

        <And name=”AB_interface” selectors=”interface_chA,interface_chB”/>

    </RESIDUE_SELECTORS>

    <TASKOPERATIONS>

        <ReadResfile name=”l_res” filename=”l_res.txt” selector=”negPhi_pep”/>

        <ReadResfile name=”d_res” filename=”d_res.txt” selector=”posPhi_pep”/>

        <RestrictChainToRepacking name=”only_repack_chain” chain=”1″/>

        <DisallowIfNonnative name=”no_cys” disallow_aas=”CG”/>

        <OperateOnResidueSubset name=”no_repack_except_interface”>

            <And>

                <Chain chains=”1″/>

                <Not>

                    <Neighborhood distance=”8.0″>

                        <Chain chains=”2″/>

                    </Neighborhood>

                </Not>

            </And>

            <PreventRepackingRLT />

        </OperateOnResidueSubset>

        <LimitAromaChi2 name=”limchi2″/>

        <IncludeCurrent name=”current”/>

        <OperateOnResidueSubset name=”restrict_to_interface” selector=”AB_interface”>

            <RestrictToRepackingRLT/>

        </OperateOnResidueSubset>

        <RestrictResiduesToRepacking name=”no_design_turn” residues=”107,115,116,123″/>

        <ExtraRotamersGeneric ex1=”true” ex2=”true” name=”ex1ex2″/>

    </TASKOPERATIONS>

    <FILTERS>

        <ScoreType name=”score” scorefxn=”beta” score_type=”total_score” threshold=”-600″ confidence=”0″ />

        <ScoreType name=”score_low” scorefxn=”beta” score_type=”total_score” threshold=”0″/>

        <ShapeComplementarity name=”sc_filter” verbose=”0″ min_sc=”0.6″ write_int_area=”1″ jump=”1″ confidence=”1″/>

        <AtomicContactCount name=”interface_contactcount” task_operations=”restrict_to_interface” confidence=”0″/>

        <Ddg name=”ddg”  threshold=”-1″ jump=”1″ repeats=”5″ repack=”1″ confidence=”1″ scorefxn=”beta”/>

        <Ddg name=”ddg_norepack”  threshold=”-1″ jump=”1″ repeats=”1″ repack=”0″ confidence=”1″ scorefxn=”beta”/>

        <Sasa name=”interface_buried_sasa” confidence=”0″/>

        <Sasa name=”interface_hydrophobic_sasa” confidence=”0″ hydrophobic=”True”/>

        <Sasa name=”interface_polar_sasa” confidence=”0″ polar=”True”/>

        <BuriedUnsatHbonds name=”new_buns_sc_heavy” use_reporter_behavior=”true” report_sc_heavy_atom_unsats=”true” scorefxn=”beta” residue_surface_cutoff=”15.0″ ignore_surface_res=”true” print_out_info_to_pdb=”true” confidence=”0″ residue_selector=”AB_interface”/>

        

        <BuriedUnsatHbonds name=”new_buns_bb_heavy” use_reporter_behavior=”true” report_bb_heavy_atom_unsats=”true” scorefxn=”beta” residue_surface_cutoff=”15.0″ ignore_surface_res=”true” print_out_info_to_pdb=”true” confidence=”0″ residue_selector=”AB_interface”/>

    </FILTERS>

    <MOVERS>

        <PeptideCyclizeMover name=”cyclize” residue_selector=”peptide”/>

        <AtomTree name=”docking_tree” docking_ft=”1″/>

        <RollMover name=”roll” chain=”1″ random_roll=”true”/>

        <GenericMonteCarlo name=”roll_gmc” mover_name=”roll” filter_name=”ddg” trials=”10″/>

        <FastDesign name=”design” task_operations=”ex1ex2,l_res,d_res,only_repack_chain,no_repack_except_interface,no_design_turn,no_cys,limchi2,current” scorefxn=”beta_cst” repeats=”5″ ramp_down_constraints=”false”>

            <MoveMap name=”specifics”>

                <Jump number=”1″ setting=”0″ />

                <Chain number=”1″ chi=”0″ bb=”0″/>

            </MoveMap>

        </FastDesign>

    </MOVERS>

    <APPLY_TO_POSE>

    </APPLY_TO_POSE>

    <PROTOCOLS>

        <Add mover=”cyclize”/>

        <Add mover=”docking_tree”/>

        <Add mover=”cyclize”/>

        <Add mover=”roll_gmc”/>

        <Add mover=”design”/>

        <Add mover=”cyclize”/>

        <Add filter=”score”/>

        <Add filter=”sc_filter”/>

        <Add filter=”interface_contactcount”/>

        <Add filter=”ddg”/>

        <Add filter=”ddg_norepack”/>

        <Add filter=”interface_buried_sasa”/>

        <Add filter=”interface_hydrophobic_sasa”/>

        <Add filter=”interface_polar_sasa”/>

        <Add filter=”new_buns_sc_heavy”/>

        <Add filter=”new_buns_bb_heavy”/>

    </PROTOCOLS>

    <OUTPUT />

</ROSETTASCRIPTS>

 

[Anonymous]

It’s a bit hard to tell with just that bit of the error message, as I can’t say for sure which part of the protocol is generating the error, but if I had to guess, I’d say that one of your residue selectors is coming up with an empty set of residues, and when that’s fed to a Mover/Filter/etc., that Mover/Filter/etc. can’t work properly with an empty set of selected residues. (Its definite that something’s coming up with an empty set of residues. I’m guessing it’s probably the residue selectors, but I can’t say for certain.)

You may be able to use the AddResidueLabelMover (https://www.rosettacommons.org/docs/latest/AddResidueLabelMover) within your protocol to report on which residues the various ResidueSelectors are selecting, to help debug things.

 

[Anonymous]

The other possibility – and I just mention this to be complete – is that for some reason you’re passing a single-chain input to your docking protocol. It then goes to find the residues in the docking partner and comes up with an empty set, leading to your error message.

[Anonymous]

Many thanks rmoretti!

I have tried using the AddResidueLabel mover and all the selections are fine, they contain at least one residue. Regarding the input PDB, it has two chains specified like this, this is the cut point between both:

ATOM   1641 1HB  GLU A 106      18.228  -8.179  12.321  1.00  0.00           H

ATOM   1642 2HB  GLU A 106      18.913  -7.304  13.689  1.00  0.00           H

ATOM   1643 1HG  GLU A 106      18.294  -9.134  15.222  1.00  0.00           H

ATOM   1644 2HG  GLU A 106      17.497  -9.998  13.899  1.00  0.00           H

ATOM   1645  N   GLY B 107       7.700   4.913 -20.512  1.00  0.00           N

ATOM   1646  CA  GLY B 107       7.363   6.306 -20.174  1.00  0.00           C

ATOM   1647  C   GLY B 107       5.856   6.609 -20.090  1.00  0.00           C

ATOM   1648  O   GLY B 107       5.454   7.702 -19.690  1.00  0.00           O

ATOM   1649  H   GLY B 107       8.057   4.703 -21.433  1.00  0.00           H

 

I have also tried manually specifying a FoldTree manually, do you think this would work? It’s a peptide (107-123) docked on a protein (1-106)

FOLD_TREE EDGE 1 106 -1 EDGE 106 107 1 EDGE 107 123 -1

 

Many thanks for the input!!

[Anonymous]

Can you post the full error log — including the backtrace that should be printed?

[Anonymous]

Hi, by specifying a manual FoldTree it works now

FOLD_TREE EDGE 1 106 -1 EDGE 106 107 1 EDGE 107 123 -1

Thanks!!

[Author]

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