RosettaRemodel: ERROR: ‘Replacing’ an atom which doesn’t currently exist.

[Anonymous]

Hello!

I am trying to truncate a CDR loop using remodel. I have previously used Rosetta version 58825.2016 (Score function:talaris2014)  successful.

However I recently switched to rosetta weekly release: 

“version”: “rosetta.source.release-156”, “week”: 43,  “year”: 2017

And I am getting this error 

protocols.forge.remodel.RemodelWorkingSet: (1) normal rebuild

core.kinematics.tree.Atom_: (1) [ FATAL ] old_atom not present in atoms list! 1

ERROR: ‘Replacing’ an atom which doesn’t currently exist.

ERROR:: Exit from: src/core/kinematics/tree/Atom_.cc line: 311

here is the blueprint region where remodeling should be done

102 Y L PIKAA N

103 G L PIKAA T

104 S L PIKAA S

106 G L PIKAA G

107 L L PIKAA S

108 V L PIKAA T

my pdb file has been cleaned and relaxed with the relax application 

Could you advice on what to do to fix this problem

 

Thanks for your time 

 

Kamau

 

 

 

 

[Anonymous]

Hello !

This is an update of the above error

I have tinkered with the remodel application to see if i could fix the problem. It seems like there is a bug associated with compiling the remodel application

I did the following

I downloaded Rosetta version 58825.2016 that the remodel application worked for me before and compiled it using gcc/4.8.0 on 

 GNU/Linux release 2.6.32-642.11.1.el6.x86_64

 I now get the above error if i use these flags

remodel.mpi.linuxgccrelease -s pdb_file  -remodel:blueprint blueprint_file  -extrachi_cutoff1  -ex1 -ex2 -use_input_sc -save_top 5 -find_neighbors

and the error below if i remove -ex1 -ex2  -use_input_sc flags

protocols.forge.remodel.RemodelWorkingSet: (0) normal rebuild

core.kinematics.FoldTree: (0) [ ERROR ] FoldTree::reorder( 1 ) failed, new/old edge_list_ size mismatch

core.kinematics.FoldTree: (0) [ ERROR ] old_edge_list.size() 9  new_edge_list.size()8

core.kinematics.FoldTree: (0) [ ERROR ] FOLD_TREE  EDGE 1 112 -1  EDGE 1 113 1  EDGE 1 237 2  EDGE 237 250 -1  EDGE 113 216 -1  EDGE 222 236 -1  EDGE 216 221 -1  EDGE 222 221 -1  JEDGE 216 222 3 N C  END 

[phoenix2:14100] *** Process received signal ***

[phoenix2:14100] Signal: Segmentation fault (11)

[phoenix2:14100] Signal code: Address not mapped (1)

[phoenix2:14100] Failing at address: 0x28

Both errors occur whether using either ref2015 or talaris2014 scorefunctions.

However the remodel application works fine if compiled using clang version 9.0.0 on my MacOS High Sierra

 

Hope this helps to fix the problem as I have several jobs that would be faster to run on a cluster instead of my Mac

 

Thank you 

 

Edwin 

 

 

 

 

 

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