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Docking-RMS value nan

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Docking-RMS value nan


I am new to Rosetta3 and jsut trying to dock some generated ligands into a protein PDB. Based on the generated structures it appears the docking program is working well however, when I look at the file the rms vlaues for all the generated structures is nan. I do not really understand if I should be expecting rms values. I am docking a ligand into an unbound protein substrate. Any information would be helpful.


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Wed, 2020-08-12 07:03

The rms calculation for small molecule docking needs a reference structure with the same ligand (atom-for-atom) that it's being compared to. If you're using an apo structure as the native, or are using a reference structure which contains a ligand different from your experimental ligand structure, then any rms value you get (assuming the program doesn't exit with an error) is nonsense.

The rms values are really only useful for benchmarking purposes, anyway. If you're doing a docking run with a new ligand with an unknown binding pose, you can just ignore the value (or omit the -in:file:native, which should turn off that calculation.)

Wed, 2020-08-12 07:20

Perfect. This is what I suspected. Thnak you for the quick help.

Wed, 2020-08-12 07:27