Floppy tail: sidechain mutation during calculation

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    • #2160


        Recently, I am trying to predict flexible tail region of protein by using Floppy tail.

        First I tried to use Floppy tail with test data (4tailstestdata.pdb).

        I have run Floppy tail as below command

        mpiexec -np 4 FloppyTail.mpi.linuxgccrelease -in:file:s 4tailstestdata.pdb -in:file:movemap mapmover -nstruct 4

        RESIDUE 90 117 BBCHI
        RESIDUE 207 233 BBCHI
        RESIDUE 324 351 BBCHI
        RESIDUE 441 468 BBCHI

        and I got 4 pdb files those file and each model has different amino acid sequence.

        I couldn’t figure out why sidechains mutated during calculation.

        Can I disable the sidechain mutation?

      • #10866

          FloppyTail original forbade mutation. Some users wanted the ability to design, so I put that in. An unfortunate consequence of Rosetta’s underpinnings is that if it CAN design, it WILL design by default.

          The solution is to add -packing:repack_only to your command line.

          I assume this is a test command line for debugging purposes? You do not have nearly enough nstruct or cycles for real modeling.

        • #10867

            Hello smlewis

            Thank you for giving me good advice.

            I should have pay more attention when I read the documentation’s General options.

            Now, I am running FloppyTail by below command and generating structure with expected sequences without design.

            mpiexec -np 4
            -in:file:s inputstructure.pdb
            -in:file:movemap mapmover
            -FloppyTail::perturb_temp 0.8
            -FloppyTail::perturb_cycles 1000
            -FloppyTail::refine_temp 0.8
            -FloppyTail::refine_cycles 1000
            -FloppyTail::refine_repack_cycles 30
            -packing::repack_only 1
            -nstruct 300

            (Relatively few perturbation and structures compare with nstruct=30000 described in Documentation for FloppyTail)
            In my case, tail regions were not seen in crystal structure. So, I think I don’t need to generate many structures to find a unique solution.

            Your application and advice helped me a lot. Thank you!

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