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
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