Rosetta 3.1 Release Manual

Score With Fullatom Energy In Condor Environment

To score with full-atom energy within condor environment, you also need to relax the structure. For example, you can use the following command line and flags to run 250 jobs in parallel.

Command line

AbinitioRelax.linuxgccrelease -in:file:silent <PATH TO SILENT FILE> -jdist_rerun -process::condor -process::nproc 250 -proc_id $(Process) -out:file:silent <PATH & NAME TO OUTPUT FILE>

Options

regular_f Regular Flags
-database  ~/rosetta_database
-frag3    ~/aacs_fgf2_03_05.200_v1_3.gz
-frag9     ~/aacs_fgf2_09_05.200_v1_3.gz
-in:file:fasta ~/cs_fgf2.fasta
-in:file:native ~/yournative.pdb

Select Favorite Score Funtion

-score::weights score13_env_hb

Relax Flags

-abinitio:fastrelax
-fastrelax_repeats 8
#-fastrelax_rampcycles              (Optional)
#-fastrelax_start_weight_low        (Optional)
#-fastrelax_start_weight_hi         (Optional)

When you need to close the loops

-close_loops
-loop:short_frag_cycles 0.5
-loop:scored_frag_cycles 0.5
-loop:non_ideal_loop_closing

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