RosettaCommons - Non-Canonical Peptides

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PyRosetta - General

Any general way to generate .params file for beta and gamma NCAA?

wwwmrzkwww — Wed, 26 Apr 2023 19:35:50 +0000

Hi, I wonder if there is a general way to generate the correct params file of new beta and gamma NCAA ? I am trying to parameterize a customized gamma amino acid residue for GenKIC application. I used the molfile_to_params_polymer.py to generate .params file from the .mol file attached below:

4CG.pdb

OpenBabel04262311383D

29 28 0 0 1 0 0 0 0 0999 V2000

-5.3100 -4.8280 2.6840 N 0 0 0 0 0 0 0 0 0 0 0 0

-6.1510 -4.0380 3.5820 C 0 0 0 0 0 0 0 0 0 0 0 0

-4.6510 -4.3310 2.0960 H 0 0 0 0 0 0 0 0 0 0 0 0

-5.9440 -2.9740 3.4550 H 0 0 0 0 0 0 0 0 0 0 0 0

-5.9530 -4.3120 4.6210 H 0 0 0 0 0 0 0 0 0 0 0 0

-7.2060 -4.2180 3.3650 H 0 0 0 0 0 0 0 0 0 0 0 0

-5.3490 -6.1570 2.5880 C 0 0 0 0 0 0 0 0 0 0 0 0

-6.1220 -6.8300 3.2710 O 0 0 0 0 0 0 0 0 0 0 0 0

-3.9150 -10.3980 0.3570 N 0 0 0 0 0 0 0 0 0 0 0 0

-4.3800 -6.7990 1.5900 C 0 0 0 0 0 0 0 0 0 0 0 0

-4.4810 -8.3380 1.5130 C 0 0 0 0 0 0 0 0 0 0 0 0

-3.5680 -8.9740 0.4470 C 0 0 1 0 0 0 0 0 0 0 0 0

-2.0580 -8.7540 0.7560 C 0 0 0 0 0 0 0 0 0 0 0 0

-1.4320 -9.5120 1.5060 O 0 0 0 0 0 0 0 0 0 0 0 0

-1.4470 -7.7040 0.2120 N 0 0 0 0 0 0 0 0 0 0 0 0

-3.4240 -11.0310 0.9730 H 0 0 0 0 0 0 0 0 0 0 0 0

-3.3710 -6.5110 1.8830 H 0 0 0 0 0 0 0 0 0 0 0 0

-4.5840 -6.3770 0.6050 H 0 0 0 0 0 0 0 0 0 0 0 0

-4.2370 -8.7640 2.4890 H 0 0 0 0 0 0 0 0 0 0 0 0

-5.5140 -8.6000 1.2780 H 0 0 0 0 0 0 0 0 0 0 0 0

-3.7760 -8.4940 -0.5110 H 0 0 0 0 0 0 0 0 0 0 0 0

-1.9510 -7.0790 -0.3990 H 0 0 0 0 0 0 0 0 0 0 0 0

-0.4720 -7.5460 0.4120 H 0 0 0 0 0 0 0 0 0 0 0 0

-4.9810 -12.4060 -0.4250 C 0 0 0 0 0 0 0 0 0 0 0 0

-4.7960 -10.9110 -0.4860 C 0 0 0 0 0 0 0 0 0 0 0 0

-5.4360 -10.2300 -1.2810 O 0 0 0 0 0 0 0 0 0 0 0 0

-5.3130 -12.6860 0.5740 H 0 0 0 0 0 0 0 0 0 0 0 0

-4.0320 -12.8940 -0.6430 H 0 0 0 0 0 0 0 0 0 0 0 0

-5.7260 -12.7140 -1.1570 H 0 0 0 0 0 0 0 0 0 0 0 0

1 3 1 0 0 0 0

1 2 1 0 0 0 0

1 7 1 0 0 0 0

2 4 1 0 0 0 0

2 5 1 0 0 0 0

2 6 1 0 0 0 0

7 8 2 0 0 0 0

7 10 1 0 0 0 0

9 16 1 0 0 0 0

9 12 1 0 0 0 0

9 25 1 0 0 0 0

10 17 1 0 0 0 0

10 18 1 0 0 0 0

10 11 1 0 0 0 0

11 19 1 0 0 0 0

11 20 1 0 0 0 0

11 12 1 0 0 0 0

12 21 1 6 0 0 0

12 13 1 0 0 0 0

13 14 2 0 0 0 0

13 15 1 0 0 0 0

15 22 1 0 0 0 0

15 23 1 0 0 0 0

24 25 1 0 0 0 0

24 27 1 0 0 0 0

24 28 1 0 0 0 0

24 29 1 0 0 0 0

25 26 2 0 0 0 0

M ROOT 7

M POLY_N_BB 7

M POLY_CA_BB 10

M POLY_C_BB 7

M POLY_O_BB 8

M POLY_IGNORE 2 4 5 6 3 24 27 28 29 26

M POLY_UPPER 1

M POLY_LOWER 25

M POLY_CHG 0

M POLY_PROPERTIES PROTEIN GAMMA_AA POLAR

M END

But molfile_to_params_polymer.py gives me polymer type .params file with duplicated HA and connections as below:

NAME 4CG

IO_STRING 4CG X

TYPE POLYMER

AA UNK

ATOM N Nbb C 0.61

ATOM CA CAbb CT2 -0.19

ATOM O OCbb O -0.56

ATOM CB CH2 CT2 -0.19

ATOM CG CH1 CT1 -0.10

ATOM ND1 Ntrp NH1 -0.62

ATOM CD2 COO C 0.61

ATOM OE1 ONH2 O -0.56

ATOM NE2 NH2O NH2 -0.48

ATOM HA Hapo HB 0.08

ATOM 1HB Hapo HA 0.08

ATOM 2HB Hapo HA 0.08

ATOM 1HG Hapo HA 0.08

ATOM 1HD1 Hpol H 0.42

ATOM 1HE2 Hpol H 0.42

ATOM 2HE2 Hpol H 0.42

BOND N O

BOND N CA

BOND ND1 1HD1

BOND ND1 CG

BOND CA HA

BOND CA CB

BOND CB 1HB

BOND CB 2HB

BOND CB CG

BOND CG 1HG

BOND CG CD2

BOND CD2 OE1

BOND CD2 NE2

BOND NE2 1HE2

BOND NE2 2HE2

LOWER_CONNECT N

UPPER_CONNECT C

CHI 1 N CA CB CG

CHI 2 CA CB CG ND1

CHI 3 CB CG CD2 OE1

NBR_ATOM CB

NBR_RADIUS 6.964028

FIRST_SIDECHAIN_ATOM CB

PROPERTIES PROTEIN GAMMA_AA POLAR

ICOOR_INTERNAL N 0.000000 180.000000 1.532034 CA N N

ICOOR_INTERNAL CA 0.000000 180.000000 1.532034 N CA N

ICOOR_INTERNAL N 0.000000 180.000000 1.532034 CA N N

ICOOR_INTERNAL UPPER 0.000000 63.500431 1.333033 N CA N

ICOOR_INTERNAL O 0.000000 58.046918 1.231644 N CA N

ICOOR_INTERNAL CB -179.427009 65.873986 1.544232 CA N UPPER

ICOOR_INTERNAL CG 176.413274 65.978102 1.540916 CB CA N

ICOOR_INTERNAL ND1 -171.852472 72.383720 1.468429 CG CB CA

ICOOR_INTERNAL LOWER 0.000000 139.796380 5.688216 N CA N

ICOOR_INTERNAL 1HD1 178.457578 62.918331 1.010557 ND1 CG LOWER

ICOOR_INTERNAL CD2 -123.991199 67.726508 1.556914 CG CB ND1

ICOOR_INTERNAL OE1 85.228323 58.347236 1.236503 CD2 CG CB

ICOOR_INTERNAL NE2 -178.670448 61.604839 1.331074 CD2 CG OE1

ICOOR_INTERNAL 1HE2 -1.133616 59.545604 1.008941 NE2 CD2 CG

ICOOR_INTERNAL 2HE2 -179.466397 60.877973 1.007764 NE2 CD2 1HE2

ICOOR_INTERNAL 1HG -118.204384 71.774443 1.091526 CG CB CD2

ICOOR_INTERNAL 1HB 122.146199 70.764445 1.092515 CB CA CG

ICOOR_INTERNAL 2HB 117.406752 71.825478 1.091310 CB CA 1HB

ICOOR_INTERNAL HA -121.892522 72.553396 1.089437 CA N CB

ICOOR_INTERNAL HA -116.575863 72.072047 1.090837 CA N HA

Best Regards

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how to generate _prepro.rama file for a customized beta-amino acid residues?

wwwmrzkwww — Sun, 23 Apr 2023 21:25:17 +0000

how to generate _prepro.rama file for a customized beta-amino acid residues? I wish to generate a customized beta-amino acid residue for design applications.

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Error with xml script

almeida85 — Tue, 28 Mar 2023 08:53:40 +0000

Hello,

I am using an xml script to design macrocycle peptides similar to https://www.pnas.org/doi/abs/10.1073/pnas.2012800118.

The script runs well in my HPC machine until it crashes unexpectedly. Attached is the output with the backtrace of the error. I am using Rosetta version rosetta.source.release-314 r314 2022.11+release.512e589 512e58946eaed9de20d65cdeea465e7690dc9e9a.

I am using the same script with a different peptide sequence and it runs well, until now.

Any insight will be appreciated.

-Yasser

Attachment	Size
slurm-14037.log	80.54 KB

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Chemically Modified Residues

N-Terminal Galactose

SebastianBB — Mon, 21 Nov 2022 16:33:59 +0000

Hi,

I want to modell the HbA1c (Hb with Galactose bound to the N-Terminal Val) N-Terminal residues.

I can't find a matching paramterset for the Galactose in the database. The to6-*-*-Galp.param is very close except that instead of the O6 atom, the C6 is bound to the N of the Val.

What is the best way to add the right parameters as a new residue type? Copy the to6-*-*-Galp.param files and modify just the atoms bound to the N or start from scratch?

How would the new *.param file look like?

Thanks a lot in advance,

Best regards,

Basti

Attachment	Size
GalVal.pdb	1.43 KB
GalVal.png	200.2 KB

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Setting pivots points for GenKIC

almeida85 — Tue, 25 Oct 2022 09:32:15 +0000

Hi all,

I want to use GenKIC to generate macrocycles of a peptide bound to a receptor with the anchor design approach. Previously, I used simple_cycpep_predict, from the command line, to generate the candidates, but not bound to the receptor.

I was able to generate and relax a starting structure with the macrocycle bound to the receptor, and now I want to do a GenKIC and conformational exploration of the closed loop. As depicted in the attached picture, the cyclization is done between the Orn324 side chain and Pro328 C-terminal (Orn324@NE-Pro328@C bond, arrow). I have tried several atoms as pivots, but it hasn't worked. It only runs (kinda) if I do not include residue 325 in the loop, during the GenKIC setup, and use CA atoms of either residues 326, 327, and/or 328, but for every solution tried (up to 10000) says:

protocols.jd2.JobDistributor: [ WARNING ] solution_0010 reported failure 1 times and will no longer retry (permanent failure)

The XML code for the movers is the following:

<ROSETTASCRIPTS>
    <SCOREFXNS>
        [...]
    </SCOREFXNS>
	
    <RESIDUE_SELECTORS>
	[...]    
    </RESIDUE_SELECTORS>
	
    <TASKOPERATIONS>
        [...]
    </TASKOPERATIONS>
			
    <MOVERS>
        # Extending the stub. Adding residues to the anchor.
        <PeptideStubMover name="extend" >
            <Append resname="XXX" />
            <Append resname="XXX" />
            <Append resname="XXX" />
            <Append resname="PRO" />
        </PeptideStubMover>
        
        # Add variant of the ORN side chain conjugation to make an amide bond with the C-terminal backbone
        <ModifyVariantType name="modify_ORN_to_cycle" add_type="SIDECHAIN_CONJUGATION"
            residue_selector="peptide_branch_selection" />
            
        # Removing C-terminal variant of PRO-328 to conjugate it with the side NE atom of ORN-324
        <ModifyVariantType name="modify_PRO_to_cycle" remove_type="UPPER_TERMINUS_VARIANT"
            residue_selector="peptide_end_selection" />
     
        # This SetTorsion mover is used to initialize the torsions for the dihedral angles.
        <SetTorsion name="initialize_tors">
	    <Torsion residue="324" torsion_name="omega" angle="180.0" />
            <Torsion residue="325" torsion_name="omega" angle="180.0" />
            <Torsion residue="326" torsion_name="omega" angle="180.0" />
            <Torsion residue="327" torsion_name="omega" angle="180.0" />
            <Torsion residue="328" torsion_name="phi"   angle="180.0" />
        </SetTorsion>
        
        # This mover adds bond, angle, and torsion constraints between the ORN_324 and the PRO_328 for the closure of the peptide.
        <PeptideCyclizeMover name="connect_branch_and_termini" residue_selector="peptide_selection" >
	    <Bond res1="324" res2="328" atom1="NE" atom2="C" add_termini="false" />
	    <Distance res1="324" res2="328" atom1="NE" atom2="C" cst_func="HARMONIC 1.32865 0.01" />
	    <Angle res1="324" atom1="CD" res_center="324" atom_center="NE" res2="328" atom2="C" cst_func="HARMONIC 2.14675498 0.01" />
	    <Angle res1="324" atom1="NE" res_center="328" atom_center="C" res2="328" atom2="CA" cst_func="HARMONIC 2.14675498 0.01" />
	    <Torsion res1="324" res2="324" res3="328" res4="328" atom1="CD" atom2="NE" atom3="C" atom4="CA" cst_func="CIRCULARHARMONIC 3.141592654 0.005" />
	</PeptideCyclizeMover>
		
	# This mover adds a chemical bond between the ORN-NE and the PRO-C atoms closing the peptide.
        <DeclareBond name="update_connect" atom1="NE" res1="324" atom2="C" res2="328" add_termini="false"/>
        
        <PackRotamersMover name="repack" scorefxn="r15_soft"         task_operations="repack_peptide_loop,repack_receptor_interface,repack_peptide_and_interface,no_repack_far_from_interface" />
        
        <MinMover name="peptide_loop_bb_minimization" scorefxn="r15_cst" type="dfpmin" tolerance="0.001" bb="0" chi="0" >
            <MoveMap name="min1_mm">
		<ResidueSelector selector="loop_selection" chi="0" bb="1" />
            </MoveMap>
        </MinMover>

        <MinMover name="peptide_and_interface_minimization" scorefxn="r15_cst" type="dfpmin" tolerance="0.0001" bb="0" chi="0" max_iter="1000" >
            <MoveMap name="min4_mm">
		<ResidueSelector selector="peptide_and_interface" chi="1" bb="1" />
            </MoveMap>
        </MinMover>
        
        <FastRelax name="relax_interface" scorefxn="score_cst" ramp_down_constraints="false" repeats="1" 
			task_operations="use_input_rotamer,no_repack_far_from_interface">
	    <MoveMap name="relax_int">
                <ResidueSelector selector="peptide_and_interface" chi="1" bb="1" />
            </MoveMap>
        </FastRelax>
        
        <ParsedProtocol name="pre-genkic_steps">
            <Add mover="extend" />
	    <Add mover="modify_ORN_to_cycle" />
            <Add mover="modify_PRO_to_cycle" />
            <Add mover="initialize_tors" />
            <Add mover="connect_branch_and_termini" />
            <Add mover="peptide_loop_bb_minimization" />
            <Add mover="connect_branch_and_termini" />
            <Add mover="peptide_and_interface_minimization" />
            <Add mover="connect_branch_and_termini" />
            <Add mover="relax_interface" />
            <Add mover="update_connect" />
        </ParsedProtocol>
        
        <GeneralizedKIC name="genkic" closure_attempts="100" pre_selection_mover="pre-genkic_steps" stop_when_n_solutions_found="1" selector="lowest_energy_selector" selector_scorefunction="r15_highhbond_cst" >
            <AddResidue res_index="324"/>
	    <AddResidue res_index="328"/>
            <AddResidue res_index="327"/>
            <AddResidue res_index="326"/>
            <!--AddResidue res_index="325"/-->
            <SetPivots res1="324" res2="327" res3="326" atom1="CG" atom2="CA" atom3="CA"/>
            <CloseBond res1="324" atom1="NE" res2="328" atom2="C" bondlength="1.32" angle1="114" angle2="123" torsion="180"/>
            <AddPerturber effect="randomize_alpha_backbone_by_rama" >
                <AddResidue index="324"/>
		<!--AddResidue index="325"/-->
		<AddResidue index="326"/>
		<AddResidue index="327"/>
		<AddResidue index="328"/>
            </AddPerturber>
        </GeneralizedKIC>
        
    </MOVERS>
	
    <PROTOCOLS>
	<Add mover="pre-genkic_steps" />
	<Add mover="genkic" />
    </PROTOCOLS>
    <OUTPUT />
</ROSETTASCRIPTS>

I would really appreciate it if you help me to understand how to set the pivots in this particular case.

Best regards,

--Yasser

Attachment	Size
cycle.png	274.7 KB

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Macrocycle from a C-terminal amidated peptide

almeida85 — Thu, 18 Aug 2022 14:53:53 +0000

Hello,

I want to generate a macrocycle of a 10 residues peptide, that has an amidated C-terminal residue.

For this, I am playing with simple_cycpep_predict with the -cyclic_peptide:cyclization_type sidechain_isopeptide flag to get crosslinked sidechains between positions 5 and 10, i.e, LYS5 ... ASP10 (ASP10 is amidated). I have a lineal peptide pdb of the same sequence that I would use as native). My command line and flags are:

mpirun -n 8 simple_cycpep_predict.mpi.linuxgccrelease -database $ROSETTA_DB \
                      -cyclic_peptide:sequence_file $sequence \
                      -in:file:native $native \
                      -cyclic_peptide:cyclization_type sidechain_isopeptide \
                      -cyclic_peptide:sidechain_isopeptide_indices 5 10 \
                      -cyclic_peptide:disulf_cutoff_prerelax 100 \
                      -cyclic_peptide:disulf_cutoff_postrelax 1 \
                      -cyclic_peptide:genkic_closure_attempts 1000 \
                      -cyclic_peptide:genkic_min_solution_count 100 \
                      -cyclic_peptide:min_genkic_hbonds 0 \
                      -cyclic_peptide:MPI_auto_2level_distribution \
                      -cyclic_peptide:MPI_batchsize_by_level 10 \
                      -cyclic_peptide:MPI_sort_by energy \
                      -score:symmetric_gly_tables true \
                      -extra_patch_fa $PATCH_PATH/Cterm_amidation.txt \
                      -mute all -unmute protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_summary \
                      -out:nstruct 1000 \
                      -out:file:silent output_$filename.silent

... but I get the following error:

[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2022.11+release.512e589
[COMMIT_DATE]: 2022-03-14T17:54:23.772418
[APPLICATION]: simple_cycpep_predict.mpi.linuxgccrelease
[MODE]: Release
[EXTRAS]: mpi (OpenMPI 1.10.2)
[OS]: GNU/Linux
[COMPILER]: GCC version "5.4.0 20160609"
[STDLIB]: libstdc++ version 20160609
[START_OPTIONS]
 -in:path:database=/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/database/ -in:file:native=10mers_Ct_amidated_0001_relax.pdb -in:file:extra_patch_fa=/mnt/data/yalmeida/Softwares/Rosetta/3.13/rosetta_src_2021.16.61629_bundle/main/database/chemical/residue_type_sets/fa_standard/patches/Cterm_amidation.txt -out:nstruct=1000 -out:mute=all -out:unmute=protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_summary -out:file:silent=output_JM21_10mers_NH2.silent -score:symmetric_gly_tables -cyclic_peptide:cyclization_type=sidechain_isopeptide -cyclic_peptide:sequence_file=JM21_10mers_NH2.res -cyclic_peptide:genkic_closure_attempts=1000 -cyclic_peptide:genkic_min_solution_count=100 -cyclic_peptide:min_genkic_hbonds=0 -cyclic_peptide:disulf_cutoff_prerelax=100 -cyclic_peptide:disulf_cutoff_postrelax=1 -cyclic_peptide:sidechain_isopeptide_indices=5 10 -cyclic_peptide:MPI_auto_2level_distribution -cyclic_peptide:MPI_batchsize_by_level=10 -cyclic_peptide:MPI_sort_by=energy

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/mpi/libutility.so(utility::save_crash_report(char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x33) [0x14e4d0cf7c33]
/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/mpi/libutility.so(utility::terminate_handler()+0x184) [0x14e4d0cf8084]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8d6b6) [0x14e4d05746b6]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8d701) [0x14e4d0574701]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8d919) [0x14e4d0574919]
/usr/lib/x86_64-linux-gnu/libstdc++.so.6(std::__throw_out_of_range(char const*)+0x3f) [0x14e4d059d2cf]
/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/mpi/libprotocols.7.so(protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::align_and_calculate_rmsd(core::pose::Pose&, core::pose::Pose const&, bool) const+0xba4) [0x14e4d5556a14]
/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/mpi/libprotocols.7.so(protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::run() const+0x17a1) [0x14e4d5570d91]
/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/mpi/libprotocols.7.so(protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication_MPI::derived_worker_carry_out_n_jobs(unsigned long, utility::vector1<std::shared_ptr<protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary>, std::allocator<std::shared_ptr<protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary> > >&, utility::vector1<std::shared_ptr<core::io::silent::SilentStruct>, std::allocator<std::shared_ptr<core::io::silent::SilentStruct> > >&, std::shared_ptr<core::scoring::ScoreFunction>, std::shared_ptr<core::pose::Pose const>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const+0x24c) [0x14e4d557f25c]
/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/mpi/libprotocols.7.so(protocols::cyclic_peptide_predict::HierarchicalHybridJDApplication::worker_carry_out_njobs(unsigned long&, utility::vector1<std::shared_ptr<protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary>, std::allocator<std::shared_ptr<protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary> > >&, utility::vector1<std::shared_ptr<core::io::silent::SilentStruct>, std::allocator<std::shared_ptr<core::io::silent::SilentStruct> > >&) const+0xbb) [0x14e4d5519a3b]
/mnt/data/yalmeida/Softwares/Rosetta/v2022.11/rosetta.source.release-314/main/source/build/src/release/linux/4.15/64/x86/gcc/5.4/mpi/libprotocols.7.so(protocols::cyclic_peptide_predict::HierarchicalHybridJDApplication::run_worker() const+0xbe) [0x14e4d552ab2e]
simple_cycpep_predict.mpi.linuxgccrelease() [0x40310b]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x14e4cff27840]
simple_cycpep_predict.mpi.linuxgccrelease() [0x4038c9]

[END_BACKTRACE]

[FILE]: St12out_of_range
[LINE]: 0
[START_MESSAGE]
map::at

[END_MESSAGE]
[END_CRASH_REPORT]

Any idea what is going wrong?

Thanks in advance

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Post Situation:

Problems with ICOOR when generating polymer params file

liuwenxi — Tue, 09 Aug 2022 15:33:53 +0000

Hello,

We're trying to incorporate a nonanonical amino acid (3, 5-Difluorotyrosine) in my enzyme design protocol. We've been using the molfile_to_params_polymer.py script provided in the demos folder; however, the params file isn't generating correctly (the file is attached below as DFT.params). When running enzyme design protocol, we get the following error:

"Only the third ICOOR atom in a topology file should list itself as its own dihedral atom"

We suspect that it is because the CB (on the 4th line of the params file) is referencing itself during creation; however, we don't know how to change the file so that this does not happen. We ran the example files provided in the /main/demos/protocol_capture/using_ncaas_protein_peptide_interface_design/HowToMakeResidueTypeParamFiles/ path, and the script seemed to run correctly and generated the params file expected in the output. Does anyone know what is causing our particular structure to generate incorreclty, and how does one resolve this issue? (The molfile is also attached, in case that is where the issue is arising)

Attachment	Size
DFTMol.txt	2.9 KB
DFTParams.txt	2.84 KB
DFTKin.txt	11.52 KB

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Unknown Element "SE" when generating NCAA params file containing selenium

liuwenxi — Thu, 04 Aug 2022 23:24:11 +0000

Hello,

I've been trying to incorporate a noncanonical selenium-containing residue into my protein sequence, however, when running molefile_to_params_polymer.py I keep getting an error saying "unknown element SE." I've tried looking at the code where the error occurs, and it seems there are a series of elif statements that specify some atoms that are allowed. That being said, I swapped selenium out for xenon (not listed in the code) in the sdf file and the function ran to completion. I've attached a screenshot of my SDF.

Thank you in advance for your help!

Here is the error message:

Traceback (most recent call last):
File "./molfile_to_params_polymer.py", line 1995, in <module>
sys.exit(main(sys.argv[1:]))
File "./molfile_to_params_polymer.py", line 1932, in main
assign_rosetta_types(m.atoms)
File "./molfile_to_params_polymer.py", line 255, in assign_rosetta_types
else: raise ValueError("Unknown element '%s'" % a.elem)
ValueError: Unknown element 'SE'

Attachment	Size
image_2022-08-04_191906409.png	22.67 KB

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shape complementarity

holdenj — Fri, 15 Jul 2022 20:24:32 +0000

I am using the shape complementarity filter to evaluate noncanonical amino acids. For several noncanonicals that contain Chlorine and Fluorine atoms the sc value is -1. I suspect this is due to the code for sc not being compatible with atom types that are not C,N,O,S,and P. Does anyone have a solution or suggestion on how to get sc updated to work with all NCAA's?

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