missing atom number 5 atom name CB

[Anonymous]

I am contacting you because I am getting an error in results with Rosetta. Successfully finished protein-protein docking. I can see in the output that following lines complaining about missing atoms. I have prepared protein in ICM, Molsoft. I checked the input file those I have given as input.pdb, there were no missing any CB atoms in all amino acid. Docking finished successfully and generated score value. Do you think this missing atom will make any impact in score value? Let me know how can solve this problem. 

>>>

core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 5 atom name CB

core.pack.pack_missing_sidechains: packing residue number 2 because of missing atom number 5 atom name CB

core.pack.pack_missing_sidechains: packing residue number 3 because of missing atom number 5 atom name CB

core.pack.pack_missing_sidechains: packing residue number 4 because of missing atom number 5 atom name CB

core.pack.pack_missing_sidechains: packing residue number 5 because of missing atom number 5 atom name CB

core.pack.pack_missing_sidechains: packing residue number 6 because of missing atom number 5 atom name CB

>>>>> 

Thanks in advance for your answer.

[Anonymous]

My first guess would be to check is the occupancy column. If that’s 0.000 for some reason, Rosetta will ignore those atoms. (I don’t know if ICM outputs zero occupancy sidechains.) This can be corrected by adding the option “-ignore_zero_occupancy false” to the command line.

 

The other thing is there might be a spacing issue with the location of the CB atom name in the input files. Compare the CB line of your input PDB with those of a PDB downloaded from the RCSB, paying particular attention to spacing and alignment.

 

Regarding it being an issue, that depends on how interested you are in the input sidechain conformations. These messages are telling you that Rosetta is ignoring the input sidechain conformations and rebuilding them based on the lowest energy ones for that backbone. — That could be perfectly fine. But if you have reason to want the input sidechain conformations to be preserve, rather than Rosetta repacking the entire protein, then its something to look into fixing.

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