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

[Anonymous]

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).

 

[Anonymous]

I have a same problem (2019 rosetta).

[Anonymous]

I have a same problem (2019 rosetta).

[Anonymous]

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

 

[Anonymous]

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

[Anonymous]

Hi Morrian, I’m sorry that I just saw your comment! (I’m going to have to check my notification settings…) In case this info is helpful despite being so late: I’m just using the default score function, which is ref2015 for the version of Rosetta that I’m using. The “cart_bonded 0.5” flag turns on this score term I believe, and the “pro_close 0” turns off this score term (a weight of 0). Let me know if you want more info!

[Anonymous]

Hi Morrian, I’m sorry that I just saw your comment! (I’m going to have to check my notification settings…) In case this info is helpful despite being so late: I’m just using the default score function, which is ref2015 for the version of Rosetta that I’m using. The “cart_bonded 0.5” flag turns on this score term I believe, and the “pro_close 0” turns off this score term (a weight of 0). Let me know if you want more info!

[Anonymous]

There is a dedicated cartesian scorefunction version of the ref2015, called ref2015_cart in the database, which already has the following difference:

| name         |   pro_close |   cart_bonded |

|:

|





| ref2015      |        1.25 |           0   |

| ref2015_cart |        0    |           0.5 |

Also note that 0.8 & 0.44 for the Lenard-Jones as seen in the stage3.wts is Score12 and Talaris2013 as opposed to 1.0 & 0.55 for Talaris2014 and ref2015.

But its actually Score12 derived, as seen for solvatation and the residue specific ∆∆G fudge factors (REF). Unfortunately my code to compare scorefxns does not allow loading from outside of of the database, so I cannot load the stage3 but here are the regular scorefunctions:

	fa_atr	fa_rep	fa_sol	fa_intra_rep	pro_close	fa_pair	hbond_sr_bb	hbond_lr_bb	hbond_bb_sc	hbond_sc	dslf_ss_dst	dslf_cs_ang	dslf_ss_dih	dslf_ca_dih	rama	omega	fa_dun	p_aa_pp	ref_ALA	ref_ARG	ref_ASN	ref_ASP	ref_CYS	ref_GLN	ref_GLU	ref_GLY	ref_HIS	ref_ILE	ref_LEU	ref_LYS	ref_MET	ref_PHE	ref_PRO	ref_SER	ref_THR	ref_TRP	ref_TYR	ref_VAL	fa_elec	dslf_fa13	yhh_planarity	fa_intra_sol_xover4	lk_ball_wtd	rama_prepro
name
score12	0.8	0.44	0.6500	0.004	1.00	0.49	0.585	1.17	1.17	1.1	1.0	1.0	1.0	1.0	0.20	0.500	0.56	0.32	0.160000	-0.98000	-0.89000	-0.67000	1.700000	-0.97000	-0.81000	-0.170000	0.560000	0.240000	-0.100000	-0.650000	-0.340000	0.63000	0.020000	-0.370000	-0.27000	0.91000	0.510000	0.290000	0.000	0.00	0.000	0.0	0.0	0.00
talaris2013	0.8	0.44	0.7500	0.004	1.00	0.00	1.170	1.17	1.17	1.1	0.0	0.0	0.0	0.0	0.20	0.500	0.56	0.32	0.592942	-0.14916	-0.94198	-1.28682	0.354993	-1.17797	-1.55374	0.140526	0.357498	0.831803	0.602328	-0.287374	0.158677	0.43057	-0.219285	0.176583	0.16454	0.92933	0.131696	0.744844	0.700	1.00	0.000	0.0	0.0	0.00
talaris2014	1.0	0.55	0.9375	0.005	1.25	0.00	1.170	1.17	1.17	1.1	0.0	0.0	0.0	0.0	0.25	0.625	0.70	0.40	0.773742	-0.32436	-1.19118	-1.63002	0.443793	-1.51717	-1.96094	0.173326	0.388298	1.080600	0.761128	-0.358574	0.249477	0.61937	-0.250485	0.165383	0.20134	1.23413	0.162496	0.979644	0.875	1.25	0.625	0.0	0.0	0.00
ref2015	1.0	0.55	1.0000	0.005	1.25	0.00	1.000	1.00	1.00	1.0	0.0	0.0	0.0	0.0	0.00	0.400	0.70	0.60	1.324680	-0.09474	-1.34026	-2.14574	3.254790	-1.45095	-2.72453	0.798160	-0.300650	2.303740	1.661470	-0.714580	1.657350	1.21829	-1.643210	-0.289690	1.15175	2.26099	0.582230	2.642690	1.000	1.25	0.625	1.0	1.0	0.45

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