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AbinitioRelax with restraints/constraints

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AbinitioRelax with restraints/constraints

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.


Post Situation: 
Mon, 2011-07-11 07:07

Try using all four constraint flags:

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

Mon, 2011-07-11 08:05

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

Tue, 2011-07-12 05:30