Template/Input length mismatch error during RosettaCM

[Anonymous]

Hi,

I’m trying to generate homology models for metalloproteins.  I’m working with a test case right now to keep things as simple as possible, and  I’m getting this error which I cannot figure out:

protocols.hybridization.FoldTreeHybridize: [ ERROR ] Template 2 has a residue with PDB number 262 but the input protein only has 261 residues.

If I remove the Zn atom from the input PDB and the template PDB files, I do not see any errors so I think it has something to do with the metal.  I’ve been looking at this post for ideas: https://www.rosettacommons.org/node/9777.  I’ve verified that there are centroid parameters for Zn in the Rosetta database.  I’ve attached the ROSETTA CRASH log, the input pdb, and the second template file.  I have not tried adding constraints between the Zn and the protein yet, since I cannot get past this simple step.  Any suggestions welcome!

Thanks,

Kristen

 

My XML file:

<ROSETTASCRIPTS>

    <TASKOPERATIONS>

    </TASKOPERATIONS>

    <SCOREFXNS>

        <ScoreFunction name=”stage1″ weights=”score3″ symmetric=”0″>

            <Reweight scoretype=”atom_pair_constraint” weight=”0.1″/>

        </ScoreFunction>

        <ScoreFunction name=”stage2″ weights=”score4_smooth_cart” symmetric=”0″>

            <Reweight scoretype=”atom_pair_constraint” weight=”0.1″/>

        </ScoreFunction>

        <ScoreFunction name=”fullatom” weights=”ref2015_cart” symmetric=”0″>

            <Reweight scoretype=”atom_pair_constraint” weight=”0.1″/>

        </ScoreFunction>

    </SCOREFXNS>

    <FILTERS>

    </FILTERS>

    <MOVERS>

        <Hybridize name=”hybridize” stage1_scorefxn=”stage1″ stage2_scorefxn=”stage2″ fa_scorefxn=”fullatom” batch=”1″ stage1_increase_cycles=”1.0″ stage2_increase_cycles=”1.0″ > 

            <Fragments three_mers=”frags.200.3mers” nine_mers=”frags.200.9mers”/>

            <Template pdb=”ca2_3fe4.pdb” cst_file=”AUTO” weight=”1.000″ />

            <Template pdb=”ca2_6hwz.pdb” cst_file=”AUTO” weight=”1.000″ />

        </Hybridize>

    </MOVERS>

    <APPLY_TO_POSE>

    </APPLY_TO_POSE>

    <PROTOCOLS>

        <Add mover=”hybridize”/>

    </PROTOCOLS>

</ROSETTASCRIPTS>

[Anonymous]

Hey Kristen,

Did you see the section called ‘How can I model with ligands/nucleic acids?’ on this page (https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM)?

I see that `use_hetatm=1` is not set in your `Hybridize` mover. As well, you need the ligand to be present in all templates with a non-zero weight. I suspect this is why you’re seeing the length mismatch. Try changing the weight of the template without the ligand to 0. It will still be used in the hydrization just never as the starting model.

And, also try everything that jadoblfr suggests. I’m not 100% positive this documentation on ligands applies to metals like you two are working with.

[Anonymous]

I am literally going through this today for MN and had the exact same crash.

While ZN is in the database, it’s not actually in the residue_types.txt file that lists all the residue types for rosetta to search in.  (database/chemical/residue_type_sets/centroid) So, you can either add add it to this file (see the metals section).  OR you can copy the ZN centroid params and add via -extra_res_cen

You should also make sure that the ZN atoms are in ALL of your templates, that the chain of the ZN is X – or something NOT in your templates, that the HETATMs are literally at the BOTTOM of your PDBs, and that -ignore_unrecognized_res is set to false.  

[Anonymous]

@nannemdp – adding use_hetatm=1 did the trick.  thanks!

@jadolfbr – luckily ZN is one of the three metals in the residue_types.txt (others are CA and MG).  I’m not sure why the parameters for other residues like MN have parameters, but aren’t in the residue_types.txt file.

Thanks for your quick responses!

[Anonymous]

I’ve managed to get RosettaCM working with metals but when I look at the output structures, there are two metal atoms when there should only be one.  The second copy of the ZN is very far from where it should be.  Has anyone else seen this?  I used the CstInfoMover to determine the constraints on the metals.  

My rosetta.options file: 

# i/o

-in:file:s 3ks3_all.pdb

-parser:protocol rosetta_cm.xml

-nstruct 10

-out:pdb

-constraints:cst_fa_file mycon.cst



# relax options

-relax:dualspace #use dualspace relax protocol

-relax:minimize_bond_angles #dualspace relax protocol setting

-relax:jump_move true

-relax:min_type lbfgs_armijo_nonmonotone

-default_max_cycles 200

-hybridize:stage1_probability 1.0

 

My constraints file:

AtomPair ZN    261  V1   261 SCALARWEIGHTEDFUNC  1 HARMONIC 2.02702 0.1

AtomPair  V1   261  V2   261 SCALARWEIGHTEDFUNC  1 HARMONIC 3.22624 0.1

AtomPair  V1   261  V3   261 SCALARWEIGHTEDFUNC  1 HARMONIC 3.38951 0.1

AtomPair ZN    261  V2   261 SCALARWEIGHTEDFUNC  1 HARMONIC 2.03757 0.1

AtomPair  V2   261  V3   261 SCALARWEIGHTEDFUNC  1 HARMONIC 3.09916 0.1

AtomPair ZN    261  V3   261 SCALARWEIGHTEDFUNC  1 HARMONIC 2.02278 0.1

AtomPair ZN    261  V1   261 SCALARWEIGHTEDFUNC  1 HARMONIC 2.02702 0.1

AtomPair  V1   261  V2   261 SCALARWEIGHTEDFUNC  1 HARMONIC 3.22624 0.1

AtomPair  V1   261  V3   261 SCALARWEIGHTEDFUNC  1 HARMONIC 3.38951 0.1

AtomPair ZN    261  V2   261 SCALARWEIGHTEDFUNC  1 HARMONIC 2.03757 0.1

AtomPair  V2   261  V3   261 SCALARWEIGHTEDFUNC  1 HARMONIC 3.09916 0.1

AtomPair ZN    261  V3   261 SCALARWEIGHTEDFUNC  1 HARMONIC 2.02278 0.1

AtomPair  V1   261  NE2   94 SCALARWEIGHTEDFUNC  1 HARMONIC 0 0.1

Angle ZN    261  NE2   94  CE1   94 SCALARWEIGHTEDFUNC  1 CIRCULARHARMONIC 2.25112 0.05

AtomPair  V1   261  NE2   94 SCALARWEIGHTEDFUNC  1 HARMONIC 0 0.1

Angle ZN    261  NE2   94  CE1   94 SCALARWEIGHTEDFUNC  1 CIRCULARHARMONIC 2.25112 0.05

AtomPair  V2   261  NE2   96 SCALARWEIGHTEDFUNC  1 HARMONIC 0 0.1

Angle ZN    261  NE2   96  CE1   96 SCALARWEIGHTEDFUNC  1 CIRCULARHARMONIC 2.24543 0.05

AtomPair  V2   261  NE2   96 SCALARWEIGHTEDFUNC  1 HARMONIC 0 0.1

Angle ZN    261  NE2   96  CE1   96 SCALARWEIGHTEDFUNC  1 CIRCULARHARMONIC 2.24543 0.05

AtomPair  V3   261  ND1  119 SCALARWEIGHTEDFUNC  1 HARMONIC 0 0.1

Angle ZN    261  ND1  119  CG   119 SCALARWEIGHTEDFUNC  1 CIRCULARHARMONIC 2.30215 0.05

AtomPair  V3   261  ND1  119 SCALARWEIGHTEDFUNC  1 HARMONIC 0 0.1

Angle ZN    261  ND1  119  CG   119 SCALARWEIGHTEDFUNC  1 CIRCULARHARMONIC 2.30215 0.05

 

My XML file

<ROSETTASCRIPTS>

<TASKOPERATIONS>

</TASKOPERATIONS>

<SCOREFXNS>

<ScoreFunction name="stage1" weights="score3" symmetric="0">

<Reweight scoretype="atom_pair_constraint" weight="1.0"/>

<Reweight scoretype="angle_constraint" weight="1.0"/>

<Reweight scoretype="metalbinding_constraint" weight="1.0" />

</ScoreFunction>

<ScoreFunction name="stage2" weights="score4_smooth_cart" symmetric="0">

<Reweight scoretype="atom_pair_constraint" weight="1.0"/>

<Reweight scoretype="angle_constraint" weight="1.0"/>

<Reweight scoretype="metalbinding_constraint" weight="1.0" />

</ScoreFunction>

<ScoreFunction name="fullatom" weights="ref2015_cart" symmetric="0">

<Reweight scoretype="atom_pair_constraint" weight="1.0"/>

<Reweight scoretype="angle_constraint" weight="1.0"/>

<Reweight scoretype="metalbinding_constraint" weight="1.0" />

</ScoreFunction>

</SCOREFXNS>

<FILTERS>

</FILTERS>

<MOVERS>

<Hybridize name="hybridize" stage1_scorefxn="stage1" stage2_scorefxn="stage2" fa_scorefxn="fullatom" batch="1" stage1_increase_cycles="1.0" stage2_increase_cycles="1.0" add_hetatm="1">

<Fragments three_mers="frags.200.3mers" nine_mers="frags.200.9mers"/>

<Template pdb="ca2_3fe4.pdb"  weight="1.000" />

<Template pdb="ca2_6hwz.pdb"  weight="1.000" />

</Hybridize>

</MOVERS>

<APPLY_TO_POSE>

</APPLY_TO_POSE>

<PROTOCOLS>

<Add mover="hybridize"/>

</PROTOCOLS>

<OUTPUT scorefxn="fullatom"/>

</ROSETTASCRIPTS>

 

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