I am using rosetta scripts to build a protein into electron density.
However, I am getting some warning messages, which relate to my CYX residues. I understand the message itself, but I don't know why it appears, what it means to my structure and whether I should be worried about it. As I said, I have several CYS residues, which I mutated to CYX (CYX name in PDB file) and when I start my calculations I am getting the following warning message for all CYX residues:
core.chemical.AtomICoor: Warning from IcoorAtomID::xyz(): ICoorAtomID xyz depends on invalid residue connection, returning BOGUS coords (null vector): this_rsd= CYX 352 connid= 3 partner_seqpos= 0
core.chemical.AtomICoor: Warning from IcoorAtomID::xyz(): ICoorAtomID xyz depends on invalid residue connection, returning BOGUS coords (null vector): this_rsd= CYX 355 connid= 3 partner_seqpos= 0
... and so on
core.conformation.Conformation: Failed to find a residue connection for residue 352 with connection point 3
core.conformation.Conformation: Connecting residues: 355 ( CYX ) and 399 ( CYX ) at atoms SG and SG
... and so on
The weirdest thing is that this message appears only when I submit my job in a threaded mode. When I run it on a single core, I don't have this kind of problem.
I am using Rosetta version: rosetta_bin_linux_2016.32.58837_bundle
rosetta_scripts.linuxgccrelease \ -database database/ \ -in::file::PDB.pdb \ -parser::protocol xml.xml \ -auto_setup_metals \ -detect_disulf false \ -extra_res_fa CYX.params \ -relax:min_type lbfgs_armijo_nonmonotone \ -default_max_cycles 200 \ -relax:jump_move true \ -edensity:mapreso X \ -edensity::cryoem_scatterers \ -crystal_refine \
Any comments will be greatly appreciated