Structure prediction

I am trying to run a very simple threading scenario (comparative modeling - but as basic as it gets).

I am executing the command:

partial_thread.static.linuxgccrelease -database $ROSETTA_DATABASE -in:file:fasta /inputs/2yhd_model.fasta -in:file:alignment /inputs/2yhd_model.grishin.txt -in:file:template_pdb /inputs/2yhd.pdb 

But an getting the error: 

I am attempting to use the Fetures Reporter InterfaceFeatures on MacOS with Rosetta 3.8, but I get an error back. If I comment out InterfaceFeatures, the script runs fine. The PDB file is clean, just two proteins (attached). Do I have some misunderstanding about the nature of the InterfaceFeatures reporter?

My script is

<ROSETTASCRIPTS>

    <SCOREFXNS>

        <ScoreFunction name="t14" weights="talaris2014" />

    </SCOREFXNS>

    <RESIDUE_SELECTORS>

Dear Rosetta experts,

I am trying to combine some silent file representing proteins that have disulfide bonds (combine_silent.linuxgccrelease from rosetta/2015.25.57927).  The silent files were created by running minirosetta for structure determination.  I am running into the following error message:

[ERROR] EXCN_utility_exit has been thrown from: src/core/chemical/ResidueType.cc line: 2975
ERROR: unknown atom_name: CYS  SG

Can anyone please tell me how to get around this error?

Thanks,

Holly Freedman

Dear all,

I have recently started learning Rosetta. Now I am working on antibody modelling. I have prepared my inputs, have blast and Pro-Fit working.  When I am running the antibody.py with the default preprocessing options