Using Patches in Rosetta

[Anonymous]

Hello,

I’d like to work with a sulfated tyrosin, and I have noticed that there is a patch for this special problem. Unfortunately I couldn’t figure out in which modes (Abinitio …) this patch can be applied and how to apply it.

I’d appreciate any help regarding this topic!

JS

[Anonymous]

Generally speaking the patched residue types are automatically detected by the PDB reader. So, if you’ve already got a PDB, it ought to apply automatically for any structure that has one. This would work for most applications that take PDBs.

Abinitio is not my area of expertise, but I believe there’s an “extended FASTA” format brewed up for Rosetta. Here’s an example from one of the metalloprotein abrelax benchmarks:

PPGLC[CYZ]PRC[CYZ]KKGYH[HIS_D]WKSEC[CYZ]KSKFDKDGNPLPPZ[ZN]

I think if you put your SO3-Tyr in with the [syntax] it might work. I think the patched name is [TYR_p:sulfated]. If this is a terminus residue, or has anything else weird about it, that name needs to change to reflect it.

Also, make sure the patch is on by default in patches.txt (which I assume you found…)

[Anonymous]

Thank you for the fast reply, unfortunately I still couldn’t get it to work.

When I try to use the patch in Abinitio with the altered FASTA-file, the patch is not recognized because only the patches for the centroid residue-type-set are loaded, but the patch applies only to the fa-standard set. Referencing the patch in the centroid patch.txt-file only results in another error. I haven’t found any option that results in the fa-standard residue-type-set being used when the fasta-file is checked instead of the centroid one even though the generated files are full-atom structures (-return_full_atom, or -in:file:fullatom didn’t change anything).
Besides this does it matter that the sulfation is not included in the fragment libraries?

I also tried inserting the sulfation with another program in a structure generated with Abinitio. After modifying the pdb-file to match the format of the pdb-files generated by rosetta the sulfation is recognized but the program terminates with a segmentation fault.
So what does segmentation fault mean and is there any way to avoid it?

I’d welcome any further suggestions!

JS

[Anonymous]

A couple of things:

1) I failed to check that the formatting didn’t break – all the special residues are supposed to be surrounded by square brackets, which the formatting turned into underscores (perhaps you knew this?)

2) I forgot about centroid for abinitio. The sulfur won’t make any difference in centroid mode (it’s not fine grained enough), but I see why it was giving you problems. You should try creating a centroid tyrosine sulfate patch. Then maybe it will do centroid with tyrosine, and then convert it to fullatom centroid when it switches into fullatom mode. I think it would look something like this:

~~~~~~~~~~~~~~~~~~~begin~~~~~~~~~~~~~~~~~~~~~~`

NAME sulfated
TYPES SULFATION

## general requirements for this patch
## require protein, ignore anything that’s already nterm patched:

BEGIN_SELECTOR
PROPERTY PROTEIN
AA TYR
NOT VARIANT_TYPE PHOSPHORYLATION ## Just in case
NOT VARIANT_TYPE SULFATION
NOT VARIANT_TYPE PROTONATED
NOT VARIANT_TYPE DEPROTONATED
END_SELECTOR

BEGIN_CASE ### THE GENERAL CASE ##########################################

ADD_PROPERTY CHARGED ## For the sulfate group

END_CASE

~~~~~~~~~~~~~~~~~~~~~~~end~~~~~~~~~~~~~~~~~~~~“`

3) Just knowing that there’s a segfault is not enough for me to diagnose, sorry!

[Anonymous]

First of all thanks for taking the time to bother with this problems!

Using the suggested patch in Abinitio centroid mode only resulted in following segmentation fault after Abinitio:

===================================================================
Finished Abinitio

core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
core.io.database: Database file opened: /Applications/Rosetta/rosetta_database/scoring/score_functions/disulfides/fa_SS_distance_score
core.io.database: Database file opened: /Applications/Rosetta/rosetta_database/scoring/score_functions/disulfides/fa_CaCbS_angle_score
core.io.database: Database file opened: /Applications/Rosetta/rosetta_database/scoring/score_functions/disulfides/fa_CbSSCb_dihedral_score
core.scoring.dunbrack: Dunbrack library took 0.06947 seconds to load from binary
Segmentation fault

Using a modified pdb file in the relax Application, the error message comes after following lines:

protocols.jd2.PDBJobInputter: filling pose from PDB FSH_S_a_000019073.pdb
core.io.database: Database file opened: /Applications/Rosetta/rosetta_database/scoring/score_functions/disulfides/fa_SS_distance_score
core.io.database: Database file opened: /Applications/Rosetta/rosetta_database/scoring/score_functions/disulfides/fa_CaCbS_angle_score
core.io.database: Database file opened: /Applications/Rosetta/rosetta_database/scoring/score_functions/disulfides/fa_CbSSCb_dihedral_score
core.scoring.dunbrack: Dunbrack library took 0.068129 seconds to load from binary
core.pack.task: Packer task: initialize from command line()
core.pack.task: Packer task: initialize from command line()
protocols.relax.ClassicRelax:
protocols.relax.ClassicRelax:
protocols.relax.ClassicRelax:

===================================================================
protocols.relax.ClassicRelax: Stage 1
protocols.relax.ClassicRelax: Ramping repulsives with 8 outer cycles and 1 inner cycles
Segmentation fault

I assume it has something to do with the format of the pdb-file but I’m not quite sure.
Is there any other information that might be helpful!

[Anonymous]

seg-fault doesn’t mean enough to help.

You can try compiling in debug mode and re-running; that will usually give a more informative error. (Replace mode=release with mode=debug when you compile). This will take probably 10x longer to run.

I suspect the error is going to be a generic vector overrun error anyway, so I’m not sure that will be useful…

[Anonymous]

Hi,

in debug mode there’s always following assertion failure:

Assertion failed: (static_cast< size_type >( i – l_ ) < super::size()), function operator[], file src/utility/vectorL.hh, line 341. Is there any chance the sulfation patch has been successfully applied and that it’s just me using it wrong?
If not is there another program for protein-protein docking that might be able to handle the modified tyrosine?

Thank’s in advance

JS

[Author]

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