Docking

Hi,

I'd like to rescore protein docking decoys to calculate the Irms (interface rms) against the lowest energy decoy. If I rescore using the scoring application, I can get the overall rms but not the Irms. I've tried including flags like -evaluation:Irms but can't seem to get it to work. Also, although less important, is there away to apply the same scoring as the docking application does - without specifying any scoring patches or weights or anything the overall score is completely different to the docking output score.

Cheers.

Dear all,
when I run the ab_initio Flexpepdock protocol, I got this error :src/core/fragment/ConstantLengthFragSet.cc line: 116
Can someone give me some comments?
this is my flag:
-s eq_1_0001.pdb
-database /home/tuongvy/SW/rosetta3.4/rosetta_database

-out:file:silent decoys.silent
-out:file:silent_struct_type binary

-pep_refine
-lowres_abinitio
-rep_ramp_cycles 10

-ex1
-ex2aro
-use_input_sc
-constant_seed
-jran 12456

-frag3 ../NullFragments0/output_files/frags.200.3mers

Hi Rosetta guys:)
Question about seemingly odd behaviour going from local rosetta run (rosetta_2014.16.56682_bundle) to mpi (2014.20.56383.mpi) and of course a slightly newer version of Rosetta3.5 though both are 3.5.

My normal docking scripts contains the flag
-residues:patch_selectors CENTROID_HA

this script runs smoothly.
When running on mpi I can do regular docking, but when introducing this flag (need it for SAXS runs), rosetta tells me that there is no such command on the top level.

Hi all,

I have a quick question:
i have submitted 5 antibody sequences to Rosie and for each of them got ten lowest-energy structures. I have the solved structure of a protein X. I read the paper of Snugdock, got excited by the idea of using snugdock with ensembledock together and now want to perform a docking of my protein X using the models i got from Rosie.