Ineffective Constraints

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    • September 6, 2017 at 2:36 am #2736
      Anonymous

        Hi all,

        I am attempting to use Rosetta 3.8 (2017.29.59598) AbinitioRelax with some constraints I have defined, but I get the feeling that the constraints are not being properly implemented. In particular, I attempt to implement a single harmonic constraint using a constraint file with this line:

        AtomPair CA 1 CA 41 HARMONIC 55.0 .1

        My flags are:

        -overwrite

        -in:file:fasta /home/safa/RosettaWork/Hunt/Cterm.fasta                  

        -in:file:frag3 /home/safa/RosettaWork/Hunt/aat000_03_05.200_v1_3

        -in:file:frag9 /home/safa/RosettaWork/Hunt/aat000_09_05.200_v1_3

        -database /home/safa/Downloads/rosetta_src_2017.29.59598_bundle/main/database                                                

        -nstruct 16                                       

        -out:pdb true                                                    

        -out:path /home/safa/RosettaWork/Hunt

        -abinitio:increase_cycles 10

        -abinitio:rg_reweight 0

        -abinitio:rsd_wt_helix 0.5

        -abinitio:rsd_wt_loop 0.5

        -relax:fast

        -constraints:cst_weight 10.0

        -constraints:cst_fa_weight 10.0

        -constraints:cst_file /home/safa/RosettaWork/Hunt/constraints

        -constraints:cst_fa_file /home/safa/RosettaWork/Hunt/constraints

        -fold_cst:force_minimize

        During the run,  I see the score output always says “atom_pair_constraint        10.000       0.000       0.000”, and the final structures do not seem to be using the constraint I have given. However the final structure file does contain the energy breakdown table, and this table typically has an extremely high (>10,000) energy for the constraint. I do not understand how this constraint only seems to gain energy when the final structure is scored.

        I know I am probably just missing some key parameter but I cannot figure out what. This is very confusing because I used Rosetta 2.5 and 2.4 about 2 years ago and as best I can remember, everything I am showing now would work with them. Does anyone have any advice on how I can fix this problem?

        Thanks a lot,

        Sandy                                           

      • September 8, 2017 at 6:05 pm #13770
        Anonymous

          I don’t think this will expose a problem, but let me suggest that you make your constraint deliberately corrupted – call it an AbomPair constraint or something, with a deliberate misspelling – and let’s see when and if it rejects that?  

           

        • January 20, 2022 at 4:50 am #16107
          Anonymous

            Hello, 

            I seem to have a similar situation going on. I am trying to run the rna_denovo command to perform RNA-protein docking. I have a constraint file and a constraint flag file as per the constraint tutorial, but the program doesn’t even seem to acknowledge my constraint inputs. There are no returned errors and the terminal doesn’t show anything to do with my constraint. Can I get some help on this?

            I have already tried intentionally mispelling the constraint and no errors are returned.

            Constraint flag file:

            -constraints:cst_fa_file my_constraint.cst

            -constraints:cst_fa_weight 10

            Constraint file:

            AtomPair CA 36A CA 243C FLAT_HARMONIC 9 2 1

             

            https://new.rosettacommons.org/demos/latest/tutorials/Constraints_Tutorial/Constraints?fbclid=IwAR2PepilszJG5pccebeqPFhzTAYRhcnMJggONrq2bwE5e-alAZfjBRhZSXs

            https://www.rosettacommons.org/demos/latest/public/rnp_structure_prediction/README

            https://new.rosettacommons.org/docs/latest/application_documentation/rna/rnp-modeling

             

            EDIT:

            I realized that I was using the option “-constraints:cst_fa_file my_constraint.cst” as in the tutorial, but the rna_denovo -help command shows that the option should be “-constraints:cst_file my_constraint.cst”. 

            I did not expect these commands to be different.

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