RosettaCommons
A dihedral angle was specified that was not found in the atoms making up the loop to be closed
I have been working on GenrealizedKIC for my 10-mer peptide with 2 cysteine residues on 2 ends. The residue ID starts at 157 and ends at 166. The residues 160 and 161 are excluded from KIC as they are important and they are already in the binding site.
However, I faced this error below. File: src/protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber.cc:436 [ ERROR ] UtilityExitException ERROR: Error in GeneralizedKICperturber::apply_set_dihedral(). A dihedral angle was specified that was not found in the atoms making up the loop to be closed.
The script in xml file is below:
<GeneralizedKIC name="genkic" closure_attempts="100"
pre_selection_mover="genkic_steps" stop_when_n_solutions_found="1"
selector="lowest_energy_selector" selector_scorefunction="r15_highhbond_cst">
<AddResidue res_index="162" />
<AddResidue res_index="163" />
<AddResidue res_index="164" />
<AddResidue res_index="165" />
<AddResidue res_index="166" />
<AddResidue res_index="157" />
<AddResidue res_index="158" />
<AddResidue res_index="159" />
<SetPivots res1="162" res2="157" res3="159" atom1="CA" atom2="SG" atom3="CA" />
<CloseBond prioratom_res="166" prioratom="CB" res1="166" atom1="SG"
res2="157" atom2="SG" followingatom_res="157" followingatom="CB"
bondlength="2.05" angle1="103" angle2="103" randomize_flanking_torsions="true" />
<AddPerturber effect="randomize_alpha_backbone_by_rama">
<AddResidue index="162" />
<AddResidue index="163" />
<AddResidue index="164" />
<AddResidue index="165" />
<AddResidue index="166" />
<AddResidue index="157" />
<AddResidue index="158" />
<AddResidue index="159" />
</AddPerturber>
</GeneralizedKIC>
<ParsedProtocol name="genkic_perturb_steps">
<Add mover="connect_termini" />
<Add filter="oversat" />
<Add filter="total_hbonds_2" />
</ParsedProtocol>
<GeneralizedKIC name="genkic_perturb" closure_attempts="5"
pre_selection_mover="genkic_perturb_steps" stop_when_n_solutions_found="1"
selector="lowest_rmsd_selector" selector_scorefunction="r15_highhbond_cst">
<AddResidue res_index="162" />
<AddResidue res_index="163" />
<AddResidue res_index="164" />
<AddResidue res_index="165" />
<AddResidue res_index="166" />
<AddResidue res_index="157" />
<AddResidue res_index="158" />
<AddResidue res_index="159" />
<SetPivots res1="162" res2="157" res3="159" atom1="CA" atom2="SG" atom3="CA" />
<CloseBond prioratom_res="166" prioratom="CB" res1="166" atom1="SG"
res2="157" atom2="SG" followingatom_res="157" followingatom="CB"
bondlength="2.05" angle1="103" angle2="103" randomize_flanking_torsions="true" />
<AddPerturber effect="perturb_dihedral" >
<AddAtoms res1="162" atom1="N" res2="162" atom2="CA" />
<AddAtoms res1="162" atom1="CA" res2="162" atom2="C" />
<AddAtoms res1="163" atom1="N" res2="163" atom2="CA" />
<AddAtoms res1="163" atom1="CA" res2="163" atom2="C" />
<AddAtoms res1="164" atom1="N" res2="164" atom2="CA" />
<AddAtoms res1="164" atom1="CA" res2="164" atom2="C" />
<AddAtoms res1="165" atom1="N" res2="165" atom2="CA" />
<AddAtoms res1="165" atom1="CA" res2="165" atom2="C" />
<AddAtoms res1="166" atom1="N" res2="166" atom2="CA" />
<AddAtoms res1="166" atom1="CA" res2="166" atom2="C" />
<AddAtoms res1="157" atom1="N" res2="157" atom2="CA" />
<AddAtoms res1="157" atom1="CA" res2="157" atom2="C" />
<AddAtoms res1="158" atom1="N" res2="158" atom2="CA" />
<AddAtoms res1="158" atom1="CA" res2="158" atom2="C" />
<AddAtoms res1="159" atom1="N" res2="159" atom2="CA" />
<AddAtoms res1="159" atom1="CA" res2="159" atom2="C" />
<AddValue value="2.5" />
</AddPerturber>
</GeneralizedKIC>
I am not sure what happened. Can you give me a suggestion of how to solve this? I suspect the problem is in <AddPerturber effect="perturb_dihedral" >
Thank you for your help. I really appreciate it.
One thing that could cause this would be if the disulfide bond has not been declared between residues 166 and 157. Note that GenKIC only moves geometry, and doesn't alter covalent connectivity.
On Tue, May 6, 2025, 7:34 PM Hoang-Son Lai Le @.***> wrote:
lelaihoangson created an issue (RosettaCommons/rosetta#405) https://github.com/RosettaCommons/rosetta/issues/405
I have been working on GenrealizedKIC for my 10-mer peptide with 2 cysteine residues on 2 ends. The residue ID starts at 157 and ends at 166. The residues 160 and 161 are excluded from KIC as they are important and they are already in the binding site.
However, I faced this error below. File: src/protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber.cc:436 [ ERROR ] UtilityExitException ERROR: Error in GeneralizedKICperturber::apply_set_dihedral(). A dihedral angle was specified that was not found in the atoms making up the loop to be closed.
The script in xml file is below:
<GeneralizedKIC name="genkic" closure_attempts="100" pre_selection_mover="genkic_steps" stop_when_n_solutions_found="1" selector="lowest_energy_selector" selector_scorefunction="r15_highhbond_cst"> <AddResidue res_index="162" /> <AddResidue res_index="163" /> <AddResidue res_index="164" /> <AddResidue res_index="165" /> <AddResidue res_index="166" /> <AddResidue res_index="157" /> <AddResidue res_index="158" /> <AddResidue res_index="159" /> <SetPivots res1="162" res2="157" res3="159" atom1="CA" atom2="SG" atom3="CA" /> <CloseBond prioratom_res="166" prioratom="CB" res1="166" atom1="SG" res2="157" atom2="SG" followingatom_res="157" followingatom="CB" bondlength="2.05" angle1="103" angle2="103" randomize_flanking_torsions="true" /> <AddPerturber effect="randomize_alpha_backbone_by_rama"> <AddResidue index="162" /> <AddResidue index="163" /> <AddResidue index="164" /> <AddResidue index="165" /> <AddResidue index="166" /> <AddResidue index="157" /> <AddResidue index="158" /> <AddResidue index="159" /> </AddPerturber> </GeneralizedKIC> <ParsedProtocol name="genkic_perturb_steps"> <Add mover="connect_termini" /> <Add filter="oversat" /> <Add filter="total_hbonds_2" /> </ParsedProtocol> <GeneralizedKIC name="genkic_perturb" closure_attempts="5" pre_selection_mover="genkic_perturb_steps" stop_when_n_solutions_found="1" selector="lowest_rmsd_selector" selector_scorefunction="r15_highhbond_cst"> <AddResidue res_index="162" /> <AddResidue res_index="163" /> <AddResidue res_index="164" /> <AddResidue res_index="165" /> <AddResidue res_index="166" /> <AddResidue res_index="157" /> <AddResidue res_index="158" /> <AddResidue res_index="159" /> <SetPivots res1="162" res2="157" res3="159" atom1="CA" atom2="SG" atom3="CA" /> <CloseBond prioratom_res="166" prioratom="CB" res1="166" atom1="SG" res2="157" atom2="SG" followingatom_res="157" followingatom="CB" bondlength="2.05" angle1="103" angle2="103" randomize_flanking_torsions="true" /> <AddPerturber effect="perturb_dihedral" > <AddAtoms res1="162" atom1="N" res2="162" atom2="CA" /> <AddAtoms res1="162" atom1="CA" res2="162" atom2="C" /> <AddAtoms res1="163" atom1="N" res2="163" atom2="CA" /> <AddAtoms res1="163" atom1="CA" res2="163" atom2="C" /> <AddAtoms res1="164" atom1="N" res2="164" atom2="CA" /> <AddAtoms res1="164" atom1="CA" res2="164" atom2="C" /> <AddAtoms res1="165" atom1="N" res2="165" atom2="CA" /> <AddAtoms res1="165" atom1="CA" res2="165" atom2="C" /> <AddAtoms res1="166" atom1="N" res2="166" atom2="CA" /> <AddAtoms res1="166" atom1="CA" res2="166" atom2="C" /> <AddAtoms res1="157" atom1="N" res2="157" atom2="CA" /> <AddAtoms res1="157" atom1="CA" res2="157" atom2="C" /> <AddAtoms res1="158" atom1="N" res2="158" atom2="CA" /> <AddAtoms res1="158" atom1="CA" res2="158" atom2="C" /> <AddAtoms res1="159" atom1="N" res2="159" atom2="CA" /> <AddAtoms res1="159" atom1="CA" res2="159" atom2="C" /> <AddValue value="2.5" /> </AddPerturber> </GeneralizedKIC>I am not sure what happened. Can you give me a suggestion of how to solve this? I suspect the problem is in <AddPerturber effect="perturb_dihedral"
Thank you for your help. I really appreciate it.
— Reply to this email directly, view it on GitHub https://github.com/RosettaCommons/rosetta/issues/405, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABACZUHFYSPWDZYTIJBRAE325FWKVAVCNFSM6AAAAAB4SU6JCCVHI2DSMVQWIX3LMV43ASLTON2WKOZTGA2DINBZGYZDKNQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Thanks Dr. Mulligan. I actually did declare the disulfide bond in the previous part according to the instruction here: https://docs.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/composite_protocols/generalized_kic/GeneralizedKIC
<MOVERS>
<PeptideStubMover name="extend" >
<Append anchor_rsd="164" resname="CYD" />
<Prepend anchor_rsd="157" resname="CYD" />
</PeptideStubMover>
<DeclareBond name="connect_termini" res1="166" atom1="SG" res2="157" atom2="SG" add_termini="true"/>
Let me double-check again whether I have to declare elsewhere. Do you have any other suggestion that could cause this problem? Thank you so much
Oh, I see the problem. Psi of residue 166 and phi of residue 157 are not part of the loop to be closed, since you're closing through a disulfide. Just remove those two perturbations and it should work.
On Wed, May 7, 2025, 1:15 PM Hoang-Son Lai Le @.***> wrote:
lelaihoangson left a comment (RosettaCommons/rosetta#405) https://github.com/RosettaCommons/rosetta/issues/405#issuecomment-2859412279
Thanks Dr. Mulligan. I actually did declare the disulfide bond in the previous part according to the instruction here: https://docs.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/composite_protocols/generalized_kic/GeneralizedKIC
<MOVERS> <PeptideStubMover name="extend" > <Append anchor_rsd="165" resname="CYD" /> <Prepend anchor_rsd="157" resname="CYD" /> </PeptideStubMover> <DeclareBond name="connect_termini" res1="166" atom1="SG" res2="157" atom2="SG" add_termini="true"/>Let me double-check again whether I have to declare elsewhere. Do you have any other suggestion that could cause this problem? Thank you so much
— Reply to this email directly, view it on GitHub https://github.com/RosettaCommons/rosetta/issues/405#issuecomment-2859412279, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABACZUFPTTBUE2MYYHDWT5D25I5TBAVCNFSM6AAAAAB4SU6JCCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDQNJZGQYTEMRXHE . You are receiving this because you commented.Message ID: @.***>
Oh I see, you're right. I think it will work if I either delete them or change them to CA CB and CB SG instead. Let me try them all and see which one will work. Thank you for your help. I really appreciate it.