Error: in membrane docking : Cannot split pose by membrane jump! Quitting…

[Anonymous]

I’m trying to run the demo files of RosettaMP and it fails in the last docking step. We were able to prepack the files normally , but the last command throws error:

 

core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set.  Created 62 residue types

core.chemical.GlobalResidueTypeSet: Total time to initialize 0.016093 seconds.

protocols.docking.DockingProtocol: FOLD_TREE  EDGE 81 1 1  EDGE 1 40 -1  EDGE 1 61 2  EDGE 61 80 -1  EDGE 61 41 -1

protocols.docking.DockingInitialPerturbation: dock_pert: true

protocols.docking.DockingInitialPerturbation: option[ docking::dock_pert ]()8 3

protocols.docking.DockingInitialPerturbation: sliding into contact for centroid mode

protocols.docking.DockingInitialPerturbation: Adjusting slide axis for membrane proteins

protocols.docking.DockingInitialPerturbation:      slide axis before: (0, 0, 0)

 

ERROR: Cannot split pose by membrane jump! Quitting…

ERROR:: Exit from: src/protocols/membrane/util.cc line: 1770

protocols.jd2.JobDistributor: [ ERROR ] 

 

[ERROR] Exception caught by JobDistributor for job 1AFO_AB_ppk_0001

 

[ ERROR ]: Caught exception:

 

 

File: src/protocols/membrane/util.cc:1770

[ ERROR ] UtilityExitException

ERROR: Cannot split pose by membrane jump! Quitting…

 

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

 

protocols.jd2.JobDistributor: [ WARNING ] 1AFO_AB_ppk_0001 reported failure and will NOT retry

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

protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 1 seconds

 

---

[ ERROR ]: Error(s) were encountered when running jobs.

1 jobs failed;

Check the output further up for additional error messages.

---

 

I also attach the input prepacked file and the options we give to the mp_dock command.

The option flag is:

-in:file:s 1AFO_AB_ppk.pdb                  

-in:file:native 1AFO_AB.pdb                   

-score:weights mpframework_docking_fa_2015.wts    

-mp:setup:spanfiles 1afo.span                

-mp:scoring:hbond                           

-docking:partners A_B                           

-docking:dock_pert 3 8                            

-packing:pack_missing_sidechains 0            

 

Could you help us with this error? 

Thank you.

[Anonymous]

This can happen if the prepacking step has added a membrane residue. The docking step does not detect that membrane residue and therefore throws a FoldTree error. Try removing the membrane residue after prepacking. The mp_dock app will add it back in.

Disclaimer: this will only give the correct result if you’re protein is properly inserted into the default membrane as the mp_dock will add the default membrane.

 

[Anonymous]

Hi, thank you so much, this solved the issue.

We are now trying to run mp_prepack and mp_dock on our pdb file, with the corresponding spanfile and we get the following error.

This is the error that we get when running it:

 

core.conformation.membrane.MembraneInfo: Setting a new membrane jump number in MembraneInfo to 1.

core.conformation.membrane.MembraneInfo: Use with caution!

basic.io.database: Database file opened: scoring/score_functions/MembranePotential/CEN10_Menv_smooth_log.txt

protocols.membrane.geometry.Embedding: Constructing Embedding object from topology and pose

protocols.membrane.geometry.Embedding: Computing membrane embedding from TMspans: 

protocols.membrane.geometry.EmbeddingDef: Computing membrane embedding from TMspan 11 to 31

protocols.membrane.geometry.EmbeddingDef: Computing membrane embedding from TMspan 11 to 31

protocols.membrane.geometry.EmbeddingDef: Computing membrane embedding from TMspan 60 to 80

protocols.membrane.geometry.EmbeddingDef: Computing membrane embedding from TMspan 92 to 112

protocols.membrane.geometry.EmbeddingDef: [ WARNING ] If your starting PDB is already translated into the 

protocols.membrane.geometry.EmbeddingDef: [ WARNING ] membrane, then your TMspan does not span the membrane!

protocols.membrane.geometry.Embedding: Span Embedding: 

protocols.membrane.geometry.EmbeddingDef: Embedding: center: (-7.903, -2.409, -2.885), normal: (-0.143098, -0.416793, 0.897667)

protocols.membrane.geometry.EmbeddingDef: Embedding: center: (-10.998, 3.201, 8.6145), normal: (-0.783732, -0.153359, 0.601869)

protocols.membrane.geometry.EmbeddingDef: Embedding: center: (-3.056, -5.1045, -20.9745), normal: (-0.80767, -0.560262, -0.183781)

protocols.membrane.geometry.Embedding: Total Embedding: 

protocols.membrane.geometry.EmbeddingDef: Embedding: center: (-7.319, -1.4375, -5.08167), normal: (-0.707074, -0.460816, 0.536372)

 

ERROR: The SpanningTopology object in MembraneInfo is empty!

ERROR:: Exit from: src/protocols/membrane/util.cc line: 1221

protocols.jd2.JobDistributor: [ ERROR ] 

 

[ERROR] Exception caught by JobDistributor for job TOMs_MP_0003

 

[ ERROR ]: Caught exception:

 

 

File: src/protocols/membrane/util.cc:1221

[ ERROR ] UtilityExitException

ERROR: The SpanningTopology object in MembraneInfo is empty!

 

 

 

 

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.

 

 

protocols.jd2.JobDistributor: [ WARNING ] TOMs_MP_0003 reported failure and will NOT retry

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

protocols.jd2.JobDistributor: 3 jobs considered, 3 jobs attempted in 2 seconds

 

---

[ ERROR ]: Error(s) were encountered when running jobs.

3 jobs failed;

Check the output further up for additional error messages.

---

Could you kindly help us to solve the problem? 

I have also attached the pdb file, in membrane coordinates and the input spanfile. 

I copy the content of the spanfile here:

TM region prediction for TOMs.octopus predicted using OCTOPUS

3 141

antiparallel

n2c

  11    31    11    31

  60    80    60    80

  92    112      92    112

        

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