Received this error from protein-protein docking:
There was an error in the simulated annealing stage of the docking.The partial run can be downloaded as a gzipped tar file here For more information, check the following CNS output files for error messages: complex_run1_it1_refine_1.out
I have no clue what i should be looking out for from the file and what the error is.
Would appreciate if anyone can teach me how to troubleshoot this as I’m totally new.
I tried looking through existing threads but am still clueless what i should do.
Went to search for ‘err’ term for errors in file and narrowed down to this.
CALLING flex_segment.cns FOR RIGID BODY SA
NO FLEXIBLE SEGMENTS for all molecule at this stage
NO FULLY FLEXIBLE SEGMENTS for molecule 1
NO FULLY FLEXIBLE SEGMENTS for molecule 2
FLEXIBILITY STATISTIC FOR MOLECULE 1 : Nres=1288 Nrigid=1288 Nflex=0
FLEXIBILITY STATISTIC FOR MOLECULE 2 : Nres=1288 Nrigid=1288 Nflex=0
%XRDECODE-ERR: Illegal argument(s).:
evaluate ($resid2=encode(decode($resid1)+1))
^
%EVALUATE-ERR: EVALUATE assignment aborted.:
evaluate ($resid2=encode(decode($resid1)+1))
^
%XRDECODE-ERR: Illegal argument(s).:
evaluate ($resid2=encode(decode($resid1)+1))
^
%EVALUATE-ERR: EVALUATE assignment aborted.:
evaluate ($resid2=encode(decode($resid1)+1))
^
%XRDECODE-ERR: Illegal argument(s).:
evaluate ($resid2=encode(decode($resid1)+1))
^
%EVALUATE-ERR: EVALUATE assignment aborted.:
evaluate ($resid2=encode(decode($resid1)+1))
^
%XRDECODE-ERR: Illegal argument(s).:
evaluate ($resid2=encode(decode($resid1)+1))
^
%EVALUATE-ERR: EVALUATE assignment aborted.:
evaluate ($resid2=encode(decode($resid1)+1))
This is not the cause of your run failure.
It1 failures are often coming from bad internal geometries (clashes) in the starting structures.
Where do you input PDB files come from?
i must have missed the minimization step! Had mutated residues but there were probably some angles that were too extreme and causes atom clashes.
let me run a minimization first and try this again. thanks for the reminder!
Hello amjjbonvin,
I had the same problem during protein-protein docking with a local version HADDOCK 2.4.
One of my PDB files was obtained by homologous modeling with rosetta software, and it may indeed have some internal geometry conflicts.
My questions are as follows:
1, where is the conflict in this PDB file(I upload it to box netdisk because I have no upload permission now，My PDB file), can I see it directly?
2, Is there any software or method to try to exclude these conflicts by calculation, or to get the model directly after resolving the conflicts?
You could try to run your model (single protein, i.e. not the complex) through the refinement server of HADDOCK (it can indeed be used for single molecule refinement) and then take the refined models as input for the docking.