Member Site › Forums › Rosetta 3 › Rosetta 3 – General › AbinitioRelax with restraints/constraints
Is it possible to do fragment assembly using AbinitioRelax with harmonic distance restraints.
I tried running it with this command line:
AbinitioRelax.linuxgccrelease -database ~/rosetta_database
-in:file:fasta t000_.fasta -in:file:native native.pdb
-abinitio::increase_cycles 10 -abinitio::rg_reweight 0.5 -abinitio::rsd_wt_helix 0.5 -abinitio::rsd_wt_loop 0.5
-constraints:cst_fa_file constraints.cst -constraints:cst_weight 10.0 -loopfcst::coord_cst_weight 10.0
where constraints.cst contains entries like:
AtomPair CA 3 CA 23 HARMONIC 11.165 1
AtomPair CA 3 CA 25 HARMONIC 6.95044 1
AtomPair CA 3 CA 26 HARMONIC 7.05951 1
AtomPair CA 3 CA 27 HARMONIC 6.97899 1
but this doesn’t seem to work as expected as I am not sure the constraints are being applied to the scoring functions during frag assembly.
Try using all four constraint flags:
Pass the same constraint file to both and the same weight to both.
ah ha. Thanks for this. This fixes the problem!