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Rosetta matching error

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Rosetta matching error

I am working on ligand-based protein design by rosetta. I am getting a constant error on the rosetta matching algorithm to find possible binding sites in the protein molecule for the desired ligand. The error that I receive is "Cannot normalize xyzVector of length() zero". I tried running the script on different servers and multiple times but I get the same error everytime. What could possibly be going wrong?

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Mon, 2018-03-12 02:38

Usually this means you have three colinear atoms for which the system is trying to compute a dihedral.

Look at your inputs and parameters to see if you've got three bonded colinear atoms, or bonded atoms that are defined with the same input coordinates the PDB file.  You can fuzz the coordinates a bit so they aren't perfectly colinear, and it should start working.

(Even if you are supposed to have a bunch of perfectly colinear atoms - fuzz them anyway, in the PDB and params if necessary.  A 1% error in colinearity is enough to make dihedral math work and below the resolution of the PDB file anyway).

Mon, 2018-03-12 09:57