I am using Rosetta 3.4 for docking. but, I do not know how to fix this Error:
core.io.pdb.file_data: (4) PDB reader is ignoring atom N in residue 40 P. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pdb.file_data: (4) PDB reader is ignoring atom HT1 in residue 40 P. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pdb.file_data: (4) PDB reader is ignoring atom HT2 in residue 40 P. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pdb.file_data: (4) PDB reader is ignoring atom HT3 in residue 40 P. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pdb.file_data: (4) PDB reader is ignoring atom CA in residue 40 P. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pdb.file_data: (4) PDB reader is ignoring atom HA in residue 40 P. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pdb.file_data: (4) PDB reader is ignoring atom CB in residue 40 P. Pass flag -ignore_zero_occupancy false to change this behavior
...until to the terminal atom of protein.
Please help me!
Best regard and thank you!!!
Have you tried adding "-ignore_zero_occupancy false" to your commandline?
By default Rosetta ignores atoms with zeros in the occupancy column. (A zero occupancy means that the crystallographer couldn't see experimental evidence to put the atom there, but they though that was the likely location.) You need to add the indicated option to the commandline to change this default behavior.
thank you so much rmoretti. big thank!
you replied all my questions.
I run docking successfully now :)