AbinitioRelax with restraints/constraints

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    • July 11, 2011 at 2:07 pm #970
      pbradley
      Participant

        Hi all,

        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
        -in:file:frag3 aat000_03_05.200_v1_3
        -in:file:frag9 aat000_09_05.200_v1_3
        -abinitio:relax -relax:fast
        -abinitio::increase_cycles 10 -abinitio::rg_reweight 0.5 -abinitio::rsd_wt_helix 0.5 -abinitio::rsd_wt_loop 0.5
        -use_filters true
        -psipred_ss2 t000_.psipred_ss2
        -out:file:silent beta1_zn_preds.out
        -nstruct 10
        -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.

        thanks!

      • July 11, 2011 at 3:05 pm #5840
        Anonymous

          Try using all four constraint flags:
          cst_file
          cst_fa_file
          cst_weight
          cst_fa_weight

          Pass the same constraint file to both and the same weight to both.

        • July 12, 2011 at 12:30 pm #5846
          pbradley
          Participant

            ah ha. Thanks for this. This fixes the problem!

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