ddG

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ddG

Autogenerated Tag Syntax Documentation:

This mover is useful for reporting the total or per-residue ddgs in cases where you don't want to use the ddG filter for some reason. (also, the ddg filter can't currently do per-residue ddgs). Ddg scores are reported as string-real pairs in the output scorefile. The total ddg score has the tag "ddg" and the each per residue ddg has the tag "residue_ddg_n" where n is the residue number.

<ddG name="(&string;)" scorefxn="(&string;)" jump="(1 &non_negative_integer;)"
        per_residue_ddg="(false &bool;)" repack_unbound="(false &bool;)"
        task_operations="(&task_operation_comma_separated_list;)"
        packer_palette="(&named_packer_palette;)" repack_bound="(true &bool;)"
        relax_bound="(false &bool;)" relax_unbound="(true &bool;)"
        translate_by="(1000.0 &real;)" relax_mover="(&string;)"
        filter="(&string;)" chain_num="(&string;)" chain_name="(&string;)"
        solvate="(false &bool;)" solvate_unbound="(false &bool;)"
        solvate_rbmin="(false &bool;)" min_water_jump="(true &bool;)"
        compute_rmsd="(false &bool;)" dump_pdbs="(false &bool;)" />

scorefxn: Name of score function to use
jump: XSD XRW TO DO
per_residue_ddg: XSD XRW TO DO
repack_unbound: XSD XRW TO DO
task_operations: A comma-separated list of TaskOperations to use.
packer_palette: A previously-defined PackerPalette to use, which specifies the set of residue types with which to design (to be pruned with TaskOperations).
repack_bound: XSD XRW TO DO
relax_bound: Should we relax the bound state, if a relax mover is specified? Default false.
relax_unbound: Should we relax the unbound state, if a relax mover is specified? Default true.
translate_by: Distance in Angstroms by which to separate the components of the bound state
relax_mover: XSD XRW TO DO
filter: XSD XRW TO DO
chain_num: XSD XRW TO DO
chain_name: XSD XRW TO DO
solvate: Solvate bound pose (using ExplicitWater mover)
solvate_unbound: Solvate unbound pose (using ExplicitWater mover)
solvate_rbmin: Use rigid-body minimization following solvation
min_water_jump: Include waters in rigid-body minimization following solvation and packing
compute_rmsd: Compute the rmsd both with and without superimposing -- requires in:file:native to be supplied
dump_pdbs: Dump debugging PDB files. Dumps 6 pdbs per instance: BOUND_before_repack, BOUND_after_repack, BOUND_after_relax, UNBOUND_before_repack, UNBOUND_after_repack, and UNBOUND_after_relax.

Ddg (or delta-delta-G) is an estimate of the binding energy of a complex. It is computed by taking the difference of the energy of the complex and of the separated components. Repacking or relaxation can be done on the bound and/or unbound state, in which case averaging over several attempts is recommended.

This mover is useful for reporting the total or per-residue ddgs in cases where you don't want to use the Ddg filter for some reason. (The Ddg filter can't currently do per-residue ddgs, for example). Ddg scores are reported as string-real pairs in the job. The total ddg score has the tag "ddg" and the each per residue ddg has the tag "residue_ddg_n" where n is the residue number.

The repack_bound and repack_unbound control whether global repacking is applied to the bound and unbound states, respectively. Both are true by default, though this can be expensive for large structures (and can result in irrelevant noise caused by different configurations of residues far from the binding interface). The relax_bound and relax_unbound options provide an alternative, if a configured relaxation mover is provided with the relax_mover option. This allows the user to specify, for example, a FastRelaxMover that only repacks and minimizes side-chains in the binding interface.

chain_num and chain_name allow you to specify a list of chain numbers or chain names to use to calculate the ddg, rather than a single jump. You cannot move chain 1, moving all the other chains is the same thing as moving chain 1, so do that instead. If filter is specified, the computed value of the filter will be used for the reported difference in score, rather than the given scorefunction. Use of the filter with per-residue ddG is not supported.

This mover supports the Poisson-Boltzmann energy method by setting the runtime environment to indicate the altering state, either bound or unbound. When used properly in conjunction with SetupPoissonBoltzmannPotential (mover), the energy method (see: core/scoring/methods/PoissonBoltzmannEnergy) is enabled to solve for the PDE only when the conformation in corresponding state has changed sufficiently enough. As ddG uses all-atom centroids to determine the separation vector when the movable chains are specified by jump, it is highly recommended to use chain_num/chain_name to specify the movable chains, to avoid invalidating the unbound PB cache due to small changes in atom positioning.

Example:

The script below shows how to enable PB with ddg mover. I have APBS (Adaptive Poisson-Boltzmann Solver) installed in /home/honda/apbs-1.4/ and "apbs" executable is in the bin/ subdiretory. Chain 1 is charged in this case. You can list more than one chain by comma-delimit (without extra whitespace. e.g. "1,2,3"). I use full scorefxn as the basis and add the PB term.

<SCOREFXNS>
    <ScoreFunction name="sc12_w_pb" weights="score12_full" patch="pb_elec"/>  patch PB term
</SCOREFXNS>
<MOVERS>
    <SetupPoissonBoltzmannPotential name="setup_pb" scorefxn="sc12_w_pb" charged_chains="1" apbs_path="/home/honda/apbs-1.4/bin/apbs"/>
    <ddG name="ddg" scorefxn="sc12_w_pb" chain_num="2"/>
</MOVERS>
<FILTERS>
    ...
</FILTERS>
<PROTOCOLS>
    <Add mover_name="setup_pb"/>  Initialize PB
    <Add mover_name="..."/>  some mover
    <Add mover_name="ddg"/> use PB-enabled ddg as if filter
    <Add filter_name="..."/>  more filtering
</PROTOCOLS>

ddG

ddG

See Also