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Running Rosetta CM Hybridize step errors with: Scorefunction not set up for nonideal/Cartesian scoring

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Running Rosetta CM Hybridize step errors with: Scorefunction not set up for nonideal/Cartesian scoring
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I am running the example protocol (RosettaCM multi-template comparative modeling) supplied by the Meiler lab (I think?). Only I am using a different starting protein that the one provided. I have successfull made it to the hybridize step:

rosetta_scripts.static.linuxgccrelease -database $ROSETTA_DATABASE -in:file:fasta /inputs/2yhd_model.fasta -parser:protocol /inputs/2yhd_model_threaded.xml -relax:minimize_bond_angles -relax:minimize_bond_lengths -relax:jump_move true -default_max_cycles 200 -relax:min_type lbfgs_armijo_nonmonotone -relax:jump_move true -score:weights stage3.wts -use_bicubic_interpolation -hybridize:stage1_probability 1.0 -nstruct 3

but am running into an execution error.

Two questions:

(1) Should the nstruct be increased? Most Rosetta protocols use (in a real run) use nstruct >= 1000 or so. Then if I do that, the following relax step would have nstruct >= 1000'ish also? What is the best practices for the number of structures to generate on this hybridize step?

(2) This question is more important. When running the above command, rosetta scripts errors with the error:

protocols.hybridization.CartesianHybridize: RUNNING FOR 4 MACROCYCLES
protocols.hybridization.CartesianHybridize:  total_res=249   prot_res=249
protocols.hybridization.CartesianHybridize: CYCLE 1
protocols.hybridization.CartesianHybridize:   setting bonded weight = 0
protocols.hybridization.CartesianHybridize:   setting bonded angle weight = 0
protocols.hybridization.CartesianHybridize:   setting bonded length weight = 0
protocols.hybridization.CartesianHybridize:   setting bonded torsion weight = 0
protocols.hybridization.CartesianHybridize:   setting cst    weight = 0.5
protocols.hybridization.CartesianHybridize:   setting vdw    weight = 0.02

ERROR: Scorefunction not set up for nonideal/Cartesian scoring
ERROR:: Exit from: src/core/optimization/CartesianMinimizer.cc line: 64
[0x312d151]
[0x491c7ff]
[0x2f7eff5]
[0x1284f6c]
[0x1169361]
[0x2870f98]
[0x287355b]
[0x2873e7e]
[0x2a567af]
[0x2a57fba]
[0x2b2297a]
[0x41243e]
[0x4c2a8d4]
[0x95250d]
protocols.rosetta_scripts.ParsedProtocol: Exception while processing procotol:
protocols.jd2.JobDistributor: 

 

I found another topc here that had the same error, and the recommeded answer was to include cart_bonded in the score function, so updated my rosetta script XML to:

<dock_design>
    <TASKOPERATIONS>
    </TASKOPERATIONS>
    <SCOREFXNS>
        <stage1 weights="stage1.wts" symmetric=0>
            <Reweight scoretype=cart_bonded weight=0.5/>
            <Reweight scoretype=atom_pair_constraint weight=1/>
        </stage1>
        <stage2 weights="stage2.wts" symmetric=0>
            <Reweight scoretype=cart_bonded weight=0.5/>
            <Reweight scoretype=atom_pair_constraint weight=0.5/>
        </stage2>
        <fullatom weights="stage3.wts" symmetric=0>
            <Reweight scoretype=cart_bonded weight=0.5/>
            <Reweight scoretype=atom_pair_constraint weight=0.5/>
        </fullatom>
    </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 linmin_only=1>
            <Fragments 3mers="/inputs/2yhd_model.200.3mers" 9mers="/inputs/2yhd_model.200.3mers"/>
            <Template pdb="/inputs/2yhd_model_threaded.pdb" cst_file="AUTO" weight=1.000 />
        </Hybridize>
    </MOVERS>
    <APPLY_TO_POSE>
    </APPLY_TO_POSE>
    <PROTOCOLS>
        <Add mover=hybridize/>
    </PROTOCOLS>
</dock_design>

 

Running the same command as above now yields a different error:

...
protocols.hybridization.CartesianHybridize: RUNNING FOR 4 MACROCYCLES
protocols.hybridization.CartesianHybridize:  total_res=249   prot_res=249
protocols.hybridization.CartesianHybridize: CYCLE 1
protocols.hybridization.CartesianHybridize:   setting bonded weight = 0
protocols.hybridization.CartesianHybridize:   setting bonded angle weight = 0
protocols.hybridization.CartesianHybridize:   setting bonded length weight = 0
protocols.hybridization.CartesianHybridize:   setting bonded torsion weight = 0
protocols.hybridization.CartesianHybridize:   setting cst    weight = 0.5
protocols.hybridization.CartesianHybridize:   setting vdw    weight = 0.02
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (249)

ERROR: cartfrag_overlap_>=1 && cartfrag_overlap_<=len/2
ERROR:: Exit from: src/protocols/hybridization/CartesianHybridize.cc line: 341
[0x312d151]
[0x491c7ff]
[0x128360b]
[0x1284d74]
[0x1169361]
[0x2870f98]
[0x287355b]
[0x2873e7e]
[0x2a567af]
[0x2a57fba]
[0x2b2297a]
[0x41243e]
[0x4c2a8d4]
[0x95250d]
protocols.rosetta_scripts.ParsedProtocol: Exception while processing procotol:
protocols.jd2.JobDistributor: 

 

What additional information should I post to help diagnose this issue? The weights are attacted (and relabled as .txt so I can upload).

 

AttachmentSize
stage1.wts_.txt182 bytes
stage2.wts_.txt257 bytes
stage3.wts_.txt536 bytes
Post Situation: 
Wed, 2017-03-29 13:19
brspurri

I have a same problem (2019 rosetta).

Sat, 2019-12-07 13:12
dnamkr

I have a same problem (2019 rosetta).

Sat, 2019-12-07 13:12
dnamkr

Hi,

I'm not sure if this will work for your application, but you might try adding -score:set_weights pro_close 0 cart_bonded 0.5

I run things from a command line, not a script, so I'm not sure how these flags would translate into your script.

I've been trying to do Cartesian and Dualspace Relax, and Frank DiMaio helped me get them running with this extra flag!

Here's the full Dualspace Relax command that worked for me:

$HOME/ROSETTA_2019_22/main/source/bin/relax.default.linuxgccrelease -in:file:s 16pk.cif -score:set_weights pro_close 0 cart_bonded 0.5 -default_max_cycles 200 -dualspace -nstruct 5 -out:suffix _relaxed -out:mmCIF -out:path:mmCIF Output_CIFs/16pk -out:path:score Output_Scores/16pk > Output_Logs/16pk/16pk_Relax.log

Hope it helps,

AJ Vincelli

 

Thu, 2019-12-12 07:27
AJVincelli

May I ask what is the score function you're using? Is it cart_bonded or atom_pair_constraint?

Thu, 2020-03-05 10:07
Morrian_Lynn