Comparative modeling Error: potential mismatch between sequence from alignment and sequence from PDB!

[Anonymous]

Hi!

I´m very new at Rosetta Commons and not an expert.

We wanted to predict comparative models using a standard protocol.

Then, we always got the Error:

unknown atom_name: CA  CB

 

Is this because of the Error before? :

Error: potential mismatch between sequence from alignment  and sequence from PDB! ??

 

This error is because no secondary structure is defined at 20 residues and therefore the coordinates for the atoms of these missing amino acids are missing.

 

And how can we avoid getting these error messages? Do we have to supplement these PDB files?

 

I appreciate your answers very much!

Best

 

Zsuzsi

Here I copied an excerpt of the log.

 

ols.comparative_modeling.util: Error: potential mismatch between sequence from alignment  and sequence from PDB!

protocols.comparative_modeling.util: alignment: 

protocols.comparative_modeling.util: score: 49040 identities: 412/432 gaps: 20/432

protocols.comparative_modeling.util:      3dw8B_align_seq       1 FSQVKGAVDDDVAEADIISTVEFNHSGELLATGDKGGRVVIFQQEQENKIQSHSRGEYNVYSTFQSHEPEFDYLKSLEIEEKINKIRWLPQ–AAQFLLSTNDKTIKLWKISERDKRPEGYNLKEEDGRYRDPTTVTTLRVPVFRPMDLMVEASPRRIFANAHTYHINSISINSDYETYLSADDLRINLWHLEITDRSFNIVDIKPANMEELTEVITAAEFHPNSCNTFVYSSSKGTIRLCDMRASALCDRHSKLFEEPEDPSNRSFFSEIISSISDVKFSHSGRYMMTRDYLSVKVWDLNMENRPVETYQVHEYLRSKLCSLYENDCIFDKFECCWNGSDSVVMTGSYNNFFRMFDRNTKRDITLEASRENNKPRTVLKPRKVCASGKRKKDEISVDSLDFNKKILHTAWHPKENIIAVATTNNLYIFQDK

protocols.comparative_modeling.util:        3dw8B_pdb_seq       7 FSQVKGAVDDDVAEADIISTVEFNHSGELLATGDKGGRVVIFQQEQ

---

SHSRGEYNVYSTFQSHEPEFDYLKSLEIEEKINKIRWLPQKNAAQFLLSTNDKTIKLWKISERDKRPEGYNLK

---

PTTVTTLRVPVFRPMDLMVEASPRRIFANAHTYHINSISINSDYETYLSADDLRINLWHLEITDRSFNIVDIKPANMEELTEVITAAEFHPNSCNTFVYSSSKGTIRLCDMRASALCDRHSKLFEEP

---

RSFFSEIISSISDVKFSHSGRYMMTRDYLSVKVWDLNMENRPVETYQVHEYLRSKLCSLYENDCIFDKFECCWNGSDSVVMTGSYNNFFRMFDRNTKRDITLEASRENNKPRTVLKPRKVCASGKRKKDEISVDSLDFNKKILHTAWHPKENIIAVATTNNLYIFQDK

protocols.comparative_modeling.util: 

protocols.comparative_modeling.threading: skipping atom,position 1HA ,2 because template doesn’t have atom 1HA .

protocols.comparative_modeling.threading: skipping atom,position 2HA ,2 because template doesn’t have atom 2HA .

protocols.comparative_modeling.threading: skipping atom,position  CB ,8 because template doesn’t have atom  CB .

protocols.comparative_modeling.threading: skipping atom,position  HA ,8 because template doesn’t have atom  HA .

core.chemical.ResidueType: atom name : CB not available in residue  CA

core.chemical.ResidueType: ‘CA  ‘ 0x138fb328

core.chemical.ResidueType: ‘ V1 ‘ 0x139ad398

core.chemical.ResidueType: ‘ V2 ‘ 0x139ad5c8

core.chemical.ResidueType: ‘ V3 ‘ 0x13a25788

core.chemical.ResidueType: ‘ V4 ‘ 0x13a25938

core.chemical.ResidueType: 

ERROR: unknown atom_name: CA  CB

ERROR:: Exit from: src/core/chemical/ResidueType.cc line: 3389

 

This were the last rows:

Error: Treating failure as bad input; canceling similar jobs

protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: S_3DW8B_0001

protocols.jd2.JobDistributor: no more batches to process… 

protocols.jd2.JobDistributor: 200 jobs considered, 200 jobs attempted in 1834 seconds

std::cerr: Exception was thrown: 

200 jobs failed; check output for error messages

std::cout: Exception was thrown: 

200 jobs failed; check output for error messages

[Anonymous]

“ERROR: unknown atom_name: CA  CB” 

This probably means it’s trying to map a beta carbon (CB) onto a calcium atom (CA).  Probably your alignments are off because the template has calcium atoms that occur before the protein part you wanted to model.  If the calcium atoms aren’t important, just get rid of them.  If they are important, try moving them to the end of the file.

 

[Anonymous]

Many thanks for your comment:

 

The command is

minirosetta.default.linuxgccrelease

-database /biosw/debian7-x86_64/rosetta/2016.11.58563/database

-run:protocol threading

-run:shuffle

-in:file:fasta 2ABG.fasta

-in:file:psipred_ss2 2ABG.psipass2

-in:file:template_pdb 3dw8B.pdb

-in:file:alignment 2ABG-3dw8B.aln

-out:overwrite

-out:nstruct 200

-out:shuffle_nstruct 200

-cm:aln_format general

-idealize_after_loop_close

-out:file:silent_struct_type binary

-loops:extended

-loops:build_initial

-loops:remodel quick_ccd

-loops:frag_sizes 9 3 1

-loops:frag_files aat000_09_05.200_v1_3 aat000_03_05.200_v1_3 none

-frag9 aat000_09_05.200_v1_3

-frag3 aat000_03_05.200_v1_3

-relax:fast

-relax:default_repeats 2

-random_grow_loops_by 4

-select_best_loop_from 1

-in:detect_disulf false

-fail_on_bad_hbond false

-overwrite

 

Best

Zsuzsi

[Anonymous]

Many many thanks for your reply!

I do not have any calcium atoms in the PDB, I thought it means alpha Carbon.

And I checked the pdb template file and as atom either CA or CB is defined.

 

concerning the gaps between alignment and pdb file . Is this true that Rosetta anyhow can handle such gaps?

 

I uploaded the pdb file.

 

 

 

 

[Anonymous]

What’s the exact command you’re using?  Because Rosetta is definitely thinking there’s calcium atoms in your template PDB. 

[Author]

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