ddG filter gives deltaG calculation number?

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  • This topic has 2 replies, 2 voices, and was last updated 11 years ago by Anonymous.
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    • #1598
      Anonymous

        Hi,

        I used attached “design2.xml” to design interface of Ag-Fab complex (see my previous thread). A “ddG” filter was used in the design script to calculate ddG of mutant.
        After the required mutants were dumped out into PDBs, I used another very simple script (attached “ddg.xml”) with just only one “ddG” filter to calculate ddG for each output PDB. When I was checking the log file, I found the ddG values calculated by two scripts are different.

        For example, for the structure decoy des5xxxx_0005,

        its ddG reported in log file of “design2.xml” is about -27:

        protocols.simple_filters.DdgFilter:


        Scores Wghtd.Score


        fa_atr -31.914
        fa_rep 2.873
        fa_sol 10.251
        fa_intra_rep -0.002
        fa_pair -1.793
        hbond_sr_bb 0.000
        hbond_lr_bb -0.021
        hbond_bb_sc -5.270
        hbond_sc -1.988
        dslf_ss_dst 0.000
        dslf_cs_ang 0.000
        dslf_ss_dih 0.000
        dslf_ca_dih 0.000
        rama 0.000
        omega 0.000
        fa_dun 0.555
        p_aa_pp 0.000
        ref 0.000


        Sum ddg: -27.3098
        protocols.rosetta_scripts.ParsedProtocol.REPORT: ddg -27.3098
        ============End report for ddG_binding==================
        protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for sasa==================
        protocols.moves.RigidBodyMover: Translate: Jump (before): RT 0.444934 -0.854746 0.267286 0.0281422 -0.284964 -0.958125 0.895121 0.433825 -0.102736 47.3926 6.81371 0.854232
        protocols.moves.RigidBodyMover: Translate: Jump (after): RT 0.444934 -0.854746 0.267286 0.0281422 -0.284964 -0.958125 0.895121 0.433825 -0.102736 904.898 477.211 -207.497
        protocols.rosetta_scripts.ParsedProtocol.REPORT: Sasa= 1514.21
        ============End report for sasa==================
        core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
        core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
        protocols.jd2.JobDistributor: des5xxxx_0005 reported success in 23756 seconds

        But it is reported as about -70 in log file of “ddg.xml”:

        protocols.simple_filters.DdgFilter:


        Scores Wghtd.Score


        fa_atr -104.726
        fa_rep 13.659
        fa_sol 45.538
        fa_intra_rep 0.015
        fa_pair -5.928
        hbond_sr_bb 0.000
        hbond_lr_bb -0.021
        hbond_bb_sc -12.158
        hbond_sc -11.771
        dslf_ss_dst 0.000
        dslf_cs_ang 0.000
        dslf_ss_dih 0.000
        dslf_ca_dih 0.000
        rama 0.000
        omega 0.000
        fa_dun 6.792
        p_aa_pp 0.000
        ref 0.000


        Sum ddg: -68.6011
        protocols.rosetta_scripts.ParsedProtocol.REPORT: ddg -70.0259
        ============End report for ddG==================
        core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
        core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
        protocols.jd2.JobDistributor: des5xxxx_0005_0001 reported success in 30 seconds

        I don’t know why there is such difference. I used application InterfaceAnalyzer to get the binding properties of this structure, “dG_separated” of this structure is about -27, similar to that reported in design log.

      • #8842
        Anonymous

          I believe the issue is the foldtree. The current default foldtree is a star-like one where each chain moves independently. The simple_ft option of AtomTree, on the other hand, gives you a pseudo-linear foldtree, where each chain is dependent on the rigid body orientation of the preceding chain (but not the backbone degrees of freedom.) For your AB_HL complex, the GreedyOpt script and the InterfaceAnalyzer are computing the energy of the AB – HL interaction, whereas the separate ddG XML is probably calculating the ABL – H interaction (as jump 2 is only controlling H and not L), giving you a higher interaction energy.

          Add the AtomTree mover to the ddG rescoring script, and you’ll probably get equivalent results.

        • #8845
          Anonymous

            Thank you!
            I added “<AtomTree name=simple_FT docking_ft=0 simple_ft=1/>” before ddG filter, it works.

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