modified Serine: FoldTree::reorder( 1 ) failed, new/old edge_list_ size mismatch error

[Anonymous]

 

 Hello.

 I am parametrizing a new residue, the SER, which would be chemically linked to a ligand 4′-PHOSPHOPANTETHEINE (PNS). The connection invovlves SER (here renamed to SEX) CB and O23 of the ligand. 

I had no problem with parametrizing the ligand. However, I am not able to properly parametrize the SER residue.  The error I get is:

core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue TYR:CtermProteinFull 85

core.conformation.Conformation: Connecting residues: 42 ( SEX ) and 86 ( PNS ) at atoms  CB  and  O23

core.conformation.Conformation:  with mutual distances: 1.37215 and 1.82638

core.kinematics.FoldTree: FoldTree::reorder( 1 ) failed, new/old edge_list_ size mismatch

core.kinematics.FoldTree: old_edge_list.size() 4  new_edge_list.size()3

core.kinematics.FoldTree: FOLD_TREE  EDGE 42 86 -2  CB   O23  EDGE 1 52 -1  EDGE 52 85 -1  EDGE 52 87 1 

core.kinematics.FoldTree: FoldTree::reorder( 87 ) failed, new/old edge_list_ size mismatch

core.kinematics.FoldTree: old_edge_list.size() 4  new_edge_list.size()3

core.kinematics.FoldTree: FOLD_TREE  EDGE 42 86 -2  CB   O23  EDGE 1 52 -1  EDGE 52 85 -1  EDGE 52 87 1 

Segmentation fault

 

As you could see, the connection between CB and O23 of the ligand seems to work fine. However, the problem relies (I think) in the ICOOR_INTERNAL lines of the SEX. If you can look at the parameter file of the SEX residue (see attachment)  and suggest me a solution, I would be very gratefull.

 

To be clear, I have been following these instructions https://www.rosettacommons.org/demos/latest/public/relax_around_chemically_bound_ligand/README. I have also found these files in the current Rosetta distribution and I did everything what was suggested there. I have tried many different options.

 

thanks in advance

karl  

 

 

[Anonymous]

Without directly addressing your question yet, also see https://www.rosettacommons.org/docs/latest/application_documentation/docking/ubq-conjugated and the CYX and LYX residues types used there.  There’s code in those executables that shows how to set up connections through a sidechain.

 

Also without answering your question: consider just making one residue that’s serine and the sidechain together as one large residue.

[Anonymous]

Hi,

thanks. I was thinking about option number 2 as well.

Neverthless, if somebody on this fourm knows what does this error mean, I would be gratefull.  I am close and I would prefer to not define a new polymer residue from the scratch.

cheers,

karl

[Anonymous]

Well, the error just means that the FoldTree is garbage, which is clear from the printout (OK, clear if you’ve spent years learning to think about FoldTrees):

core.kinematics.FoldTree: FOLD_TREE  EDGE 42 86 -2  CB   O23  EDGE 1 52 -1  EDGE 52 85 -1  EDGE 52 87 1 

If you actually draw this tree, you’ll see peptide (that’s what -1 means) from 1-85 (ok), a jump from 52 to 87 (also OK), and a chemical edge (-2) from 42 to 86 (bad).  Neither 42 nor 86 are otherwise legal nodes in this tree.  I can definitely construct the tree you need (or even provide code for it), but since you haven’t said what executable you’re running, I can’t tell if the busted FoldTree or the SEX residue type is the real problem.  

[Anonymous]

Hey,

Thanks a lot for your comments.

I am doing cryo-em. The whole script looks like:

/cluster/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/source/bin/relax.linuxgccrelease

 -database ~/rosetta_bin_linux_2016.02.58402_bundle_serial/main/database/

 -extra_res_fa ~/rosetta_bin_linux_2016.02.58402_bundle_serial/main/database/chemical/residue_type_sets/fa_standard/residue_types/sidechain_conjugation/SEX.params

 -in::file: XXX.pdb

 -score:weights talaris2013_cart

 -cst_fa_file chemical_bond.cst

 -relax:fast  

 -relax::default_repeats 4

 -relax:jump_move true

 -edensity:mapfile MAP.mrc

 -edensity:mapreso 4.0

 -edensity::whole_structure_allatom_wt 0.1

 -out::nstruct 1

 -default_max_cycles 200

 -edensity::cryoem_scatterers

 -crystal_refine

 -out:overwrite

 -out::suffix _rnd2

I will try to play with CONN3 record . If I don’t manage, I will ask you for a help with the FoldTree.

thanks a lot

karl

[Anonymous]

OK. I tried to apply your comments.  

1.) You were right: V1 does nothing. At least, it looks like. Once I commented out all V1 lines and uncommented OG, I managed to move a step further. Neverthless, in the end I got this error:

core.io.pdb.file_data: Adding undetected upper terminus type to residue 85

core.conformation.Conformation: [ WARNING ] missing heavyatom:  OG  on residue SEX 42

core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue TYR:CtermProteinFull 85

core.conformation.Conformation: Connecting residues: 42 ( SEX ) and 86 ( PNS ) at atoms  CB  and  O23

core.conformation.Conformation:  with mutual distances: 1.37215 and 3.02339

core.pack.pack_missing_sidechains: packing residue number 42 because of missing atom number 6 atom name  OG 

core.pack.task: Packer task: initialize from command line() 

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013_cart

core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (86)

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CA,N,H to DB with theta0 = 2.07956 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: N,CA,C to DB with theta0 = 1.94081 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: N,CA,CB to DB with theta0 = 1.92225 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: N,CA,HA to DB with theta0 = 1.89368 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: C,CA,CB to DB with theta0 = 1.91703 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: C,CA,HA to DB with theta0 = 1.89009 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CB,CA,HA to DB with theta0 = 1.89908 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CA,C,O to DB with theta0 = 2.10836 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CA,CB,OG to DB with theta0 = 1.93732 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CA,CB,1HB to DB with theta0 = 1.91114 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CA,CB,2HB to DB with theta0 = 1.91114 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: OG,CB,1HB to DB with theta0 = 1.91373 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: OG,CB,2HB to DB with theta0 = 1.91373 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: 1HB,CB,2HB to DB with theta0 = 1.87575 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined length SEX: N,CA, to DB with d0 = 1.458 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length SEX: N,H, to DB with d0 = 1.01 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length SEX: CA,C, to DB with d0 = 1.52326 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length SEX: CA,CB, to DB with d0 = 1.51626 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length SEX: CA,HA, to DB with d0 = 1.09092 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length SEX: C,O, to DB with d0 = 1.23102 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length SEX: CB,OG, to DB with d0 = 1.40119 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length SEX: CB,1HB, to DB with d0 = 1.08969 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length SEX: CB,2HB, to DB with d0 = 1.08918 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: C,N,CA to DB with theta0 = 2.12407 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CB,CA,C to DB with theta0 = 1.91703 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CA,C,N to DB with theta0 = 2.02807 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: O,C,N to DB with theta0 = 2.14675 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: CA,N,C to DB with theta0 = 2.12407 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle SEX: H,N,C to DB with theta0 = 2.07956 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C34,N36,H36 to DB with theta0 = 2.08557 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C34,N36,C37 to DB with theta0 = 2.11494 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H36,N36,C37 to DB with theta0 = 2.08267 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C32,C34,O35 to DB with theta0 = 2.10899 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C32,C34,N36 to DB with theta0 = 2.02736 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O35,C34,N36 to DB with theta0 = 2.14683 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C29,C32,H32 to DB with theta0 = 1.9158 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C29,C32,O33 to DB with theta0 = 1.88963 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C29,C32,C34 to DB with theta0 = 1.92679 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H32,C32,O33 to DB with theta0 = 1.91542 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H32,C32,C34 to DB with theta0 = 1.90376 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O33,C32,C34 to DB with theta0 = 1.91243 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C28,C29,C30 to DB with theta0 = 1.91855 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C28,C29,C32 to DB with theta0 = 1.91864 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C28,C29,C31 to DB with theta0 = 1.90089 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C30,C29,C32 to DB with theta0 = 1.88486 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C30,C29,C31 to DB with theta0 = 1.92196 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C32,C29,C31 to DB with theta0 = 1.91899 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O27,C28,H282 to DB with theta0 = 1.90487 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O27,C28,H281 to DB with theta0 = 1.91919 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O27,C28,C29 to DB with theta0 = 1.90602 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H282,C28,H281 to DB with theta0 = 1.90887 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H282,C28,C29 to DB with theta0 = 1.91566 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H281,C28,C29 to DB with theta0 = 1.90921 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: P24,O27,C28 to DB with theta0 = 2.10502 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O26,P24,O23 to DB with theta0 = 1.88887 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O26,P24,O27 to DB with theta0 = 1.89061 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O26,P24,O25 to DB with theta0 = 2.09144 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O23,P24,O27 to DB with theta0 = 1.79062 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O23,P24,O25 to DB with theta0 = 1.88774 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O27,P24,O25 to DB with theta0 = 1.89121 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H301,C30,H303 to DB with theta0 = 1.91237 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H301,C30,H302 to DB with theta0 = 1.9074 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H301,C30,C29 to DB with theta0 = 1.90913 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H303,C30,H302 to DB with theta0 = 1.91147 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H303,C30,C29 to DB with theta0 = 1.91176 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H302,C30,C29 to DB with theta0 = 1.91166 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C29,C31,H313 to DB with theta0 = 1.90895 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C29,C31,H312 to DB with theta0 = 1.91038 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C29,C31,H311 to DB with theta0 = 1.91072 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H313,C31,H312 to DB with theta0 = 1.91199 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H313,C31,H311 to DB with theta0 = 1.9122 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H312,C31,H311 to DB with theta0 = 1.90957 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C32,O33,H33 to DB with theta0 = 1.88424 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: N36,C37,H372 to DB with theta0 = 1.90449 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: N36,C37,C38 to DB with theta0 = 1.92449 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: N36,C37,H371 to DB with theta0 = 1.91011 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H372,C37,C38 to DB with theta0 = 1.90839 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H372,C37,H371 to DB with theta0 = 1.90854 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C38,C37,H371 to DB with theta0 = 1.90772 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H381,C38,C37 to DB with theta0 = 1.90974 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H381,C38,C39 to DB with theta0 = 1.90818 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H381,C38,H382 to DB with theta0 = 1.90976 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C37,C38,C39 to DB with theta0 = 1.91952 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C37,C38,H382 to DB with theta0 = 1.90769 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C39,C38,H382 to DB with theta0 = 1.90889 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C38,C39,O40 to DB with theta0 = 2.10888 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C38,C39,N41 to DB with theta0 = 2.02768 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: O40,C39,N41 to DB with theta0 = 2.14663 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C39,N41,H41 to DB with theta0 = 2.08431 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C39,N41,C42 to DB with theta0 = 2.1162 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H41,N41,C42 to DB with theta0 = 2.08268 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C43,C42,N41 to DB with theta0 = 1.92289 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C43,C42,H421 to DB with theta0 = 1.90896 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: C43,C42,H422 to DB with theta0 = 1.90984 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: N41,C42,H421 to DB with theta0 = 1.9108 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: N41,C42,H422 to DB with theta0 = 1.90505 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H421,C42,H422 to DB with theta0 = 1.90619 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H432,C43,S44 to DB with theta0 = 1.91021 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H432,C43,H431 to DB with theta0 = 1.91139 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H432,C43,C42 to DB with theta0 = 1.91059 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: S44,C43,H431 to DB with theta0 = 1.91099 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: S44,C43,C42 to DB with theta0 = 1.9081 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined angle PNS: H431,C43,C42 to DB with theta0 = 1.91251 , Ktheta = 80

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: N36,C34, to DB with d0 = 1.32739 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: N36,H36, to DB with d0 = 0.979364 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: N36,C37, to DB with d0 = 1.45975 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C34,C32, to DB with d0 = 1.5267 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C34,O35, to DB with d0 = 1.23152 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C32,C29, to DB with d0 = 1.52473 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C32,H32, to DB with d0 = 1.08363 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C32,O33, to DB with d0 = 1.41703 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C29,C28, to DB with d0 = 1.53292 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C29,C30, to DB with d0 = 1.52641 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C29,C31, to DB with d0 = 1.53512 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C28,O27, to DB with d0 = 1.42255 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C28,H282, to DB with d0 = 1.07648 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C28,H281, to DB with d0 = 1.0815 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: O27,P24, to DB with d0 = 1.60917 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: P24,O26, to DB with d0 = 1.47933 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: P24,O23, to DB with d0 = 1.61056 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: P24,O25, to DB with d0 = 1.47973 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C30,H301, to DB with d0 = 1.07956 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C30,H303, to DB with d0 = 1.07934 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C30,H302, to DB with d0 = 1.08164 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C31,H313, to DB with d0 = 1.07941 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C31,H312, to DB with d0 = 1.08019 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C31,H311, to DB with d0 = 1.07966 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: O33,H33, to DB with d0 = 0.960084 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C37,H372, to DB with d0 = 1.07927 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C37,C38, to DB with d0 = 1.53065 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C37,H371, to DB with d0 = 1.07894 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C38,H381, to DB with d0 = 1.079 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C38,C39, to DB with d0 = 1.52507 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C38,H382, to DB with d0 = 1.0808 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C39,O40, to DB with d0 = 1.23013 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C39,N41, to DB with d0 = 1.32889 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: N41,H41, to DB with d0 = 0.981105 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: N41,C42, to DB with d0 = 1.458 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C42,C43, to DB with d0 = 1.53163 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C42,H421, to DB with d0 = 1.08041 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C42,H422, to DB with d0 = 1.07858 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C43,H432, to DB with d0 = 1.07923 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C43,S44, to DB with d0 = 1.78816 , Kd = 300

core.scoring.CartesianBondedEnergy: Adding undefined length PNS: C43,H431, to DB with d0 = 1.08024 , Kd = 300

core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file ‘/cluster/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/database/rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin’.

core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.22986 seconds to load from binary

Segmentation fault

2.) If possible, please provide me a code for constructing a proper FoldTree or alternatively, I can send you all input files at your email address, so that you can inspect situtatin closer by your own.

thank you once again

Best regards,

Karl

[Anonymous]

core.conformation.Conformation: [ WARNING ] missing heavyatom:  OG  on residue SEX 42

OG is in your params file but not your PDB, perhaps?  This is just a warning but it’s going to screw up your ligand.  If OG is in serine, that atom needs to NOT be in the ligand.  You can use -repack_missing_residues false to prevent this repacking, but it’s still going to duplicate the atom and screw up scoring.  I don’t think this is causing the later dunbrack crash.  

 

Foldtree: you don’t need a new one now (that isn’t where it’s failing, anyway).

 

 

[Anonymous]

Also: try preventing repacking globally with “-packing::prevent_repacking”.  This will ruin relax scientifically but it will be instructive vs. crashing.  We may want to use a resfile to prevent repacking of just your modified residue (unless that’s your actual goal, of course).

[Anonymous]

Two more ideas:

 

A) re-post the params file for your new residue type (the other Rosetta guy looking at this wants to see it)

re-run your experiment with the PDB file changed to the existing and functional CYX residue type to see if it works (in other words, is it that SEX is wrong, or just that relax can’t handle it).

 

[Anonymous]

A comment on the params file specifically:  “Yeah, since if the CHI lines are still commented out that’s definitely the problem. The canonical amino acids (e.g. AA SER

ROTAMER_AA SER) are hard-coded to have a particular number of chis, and if it tries applying the SER rotamers to a residue with zero chis, it will get dreadfully confused.”

[Anonymous]

Hi,

I went point by point, trying different options:

1.) I have deleted Dunbrack10.lib.bin and I run the script. I got error. For details, please see

error_message: error_deletedLibFile.txt

2.) I have deleted Dunbrack10.lib.bin again and I tried with the flag: -repack_missing_residues false.

    However, looks like this command is not available anymore: /run.sh 

ERROR: Option matching -repack_missing_residues not found in command line top-level context

caught exception ERROR: Option matching -repack_missing_residues not found in command line top-level context

3.) I have deleted Dunbrack10.lib.bin again and I tried with the flag: -packing::prevent_repacking

    It crashed. For details, please see the error_message:error_deletedLibFile_AND_preventRepackingOn.txt 

4.) I have tried again with the flag -packing::prevent_repacking, using a newly regenerated Dunbrack10.lib.bin and I got the error, 

    which I have seen at the very beginning. For details, please see the error_message: error_LibFileRegenerated_AND_preventRepackingOn.txt

5.) I have also tried with with the PDB file changed to the existing and functional CYX residue type. It crashed as well. Not sure is it about my ligand or CYX. I assume that CYX

    is OK, so it has to be the ligand, but I am not sure. For details of the error message please this file: error_CYX_Instead_SEX.txt

thank you,

Karl

p.s. Both, SEX and PNS params. files are attached.

[Anonymous]

Another three attachments:

 

 

[Anonymous]

Hey,

Did you have time to inspect the log files I have sent you?

Your help will be very much appreciated.

thank you

karl

[Anonymous]

Hey,

I tried with these options some time ago. These did not work. However, to be 100% sure, I repeated these steps now and these did not work as well.

Would be possible to obtain that code? I am dealing with this problem more than 2 weeks and the things are becoming urgent.

thank you for your understanding

Karl

p.s. Error with CHI lines commented out below (Input: PDB containing SEX wth OG present, SEX.params with commented out CHI-related/proton ines and V1 lines).

core.io.pdb.file_data: Adding undetected upper terminus type to residue 85

core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue TYR:CtermProteinFull 85

core.conformation.Conformation: Connecting residues: 42 ( SEX ) and 86 ( PNS ) at atoms  CB  and  O23

core.conformation.Conformation:  with mutual distances: 1.33109 and 3.21964

core.kinematics.FoldTree: FoldTree::reorder( 1 ) failed, new/old edge_list_ size mismatch

core.kinematics.FoldTree: old_edge_list.size() 4  new_edge_list.size()3

core.kinematics.FoldTree: FOLD_TREE  EDGE 42 86 -2  CB   O23  EDGE 1 52 -1  EDGE 52 85 -1  EDGE 52 87 1 

core.kinematics.FoldTree: FoldTree::reorder( 87 ) failed, new/old edge_list_ size mismatch

core.kinematics.FoldTree: old_edge_list.size() 4  new_edge_list.size()3

core.kinematics.FoldTree: FOLD_TREE  EDGE 42 86 -2  CB   O23  EDGE 1 52 -1  EDGE 52 85 -1  EDGE 52 87 1 

Segmentation fault

p.s.2 CYX has not been modified.

[Anonymous]

Comparing your SEX residue to CYX is less illuminating than i’d hoped, because you got rid of OG.  I guess it’s possible that  it’s wrong for your CONN3 to depend on VIRT, it should depend on CB-CA-N instead.  CONN3 represents where the “next atom” when connected is, which in your case should be where OG used to be.  I don’t know what it means to have it depend on the virtual atom.  (I don’t know what the virtual atom is doing, either, it’s newer than my use of CYX). 

 

It may also work better to define SEX as having OG and define your ligand as not having that atom.

[Anonymous]

Right, it’s probably trying to apply serine in the Dunbrack library to your modified residue and hitting a snag.  I know who to ask about that (I think).  

 

In the meantime, do try manually deleting the file “/cluster/home/kkaszuba/rosetta_bin_linux_2016.02.58402_bundle_serial/main/database/rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin” – Rosetta will regenerate the file for you if needed (it’s the fast-loading binary version of a human-readable text table) but on the off chance it’s corrupted or misformatted by being moved from another OS let’s try a quick fix.

[Anonymous]

For the SEX residue type: try commenting the CHI lines back in at some point – that is probably going to cause a problem in packing.

 

For the CYX test: “ERROR: In ICOOR atom line in topology file:reference atoms must be specified in earlier line.  Missing SG or CB or CA” would seem to indicate that it’s having a problem with CYX as well.  Has CYX been modified on your system (perhaps by accident when creating SEX)?

[Anonymous]

“core.conformation.Conformation: Connecting residues: 42 ( SEX ) and 86 ( PNS ) at atoms  CB  and  O23″  This suggests that your SEX residue’s CONN3 is being built off CB not OG (which is probably wrong).  Addtionally, if O23 is the same atom as OG, it will appear twice.

What is the order of residues in your file – in particular what are residues 85, 86, and 87?  (Note those numbers are in Rosetta numbering (indexed from 1), not PDB numbering).  The warnings about undetected terminus on 85, when your EDGE list goes to 87, suggests you have TWO ligands in the system?

“That code”: I can offer you a snippet of code to produce the correct fold tree, but I’m no longer convinced the offer is relevant.  I didn’t realize you were running stock relax, which should be able to handle this fine.  The FoldTree is likely a symptom not a cause, so giving you a correct FoldTree probably won’t fix it.  That said, if you want a FoldTree snippet, I need to know (in Rosetta numbering) the locations of any residue that isn’t just a regular peptide, including all termini, all cutpoints, the SEX residue, and the ligand residue.  I guess I could also just make those numbers up and give you a sample fold tree for the numbers I made up for you to fix with the real numbers.  The immediate following issue of “where to put the code to let it run” is not one I know how to address: at the time that the offer was made, I thought you were running something custom, if you’re running stock relax, we’d probably have to put this somewhere in the middle of the regular pdb reader and that will break everything.

[Author]

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