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Computes the binding energy for the complex and if it is below the threshold returns true. o/w false. Useful for identifying complexes that have poor binding energy and killing their trajectory.
<Ddg name="(&string;)" threshold="(-15 ℜ)" threshold_min="(-999999 ℜ)" jump="(1 &positive_integer;)" repeats="(1 &positive_integer;)" repack="(1 &bool;)" symmetry="(&string;)" repack_bound="(true &bool;)" repack_unbound="(true &bool;)" relax_bound="(false &bool;)" relax_unbound="(true &bool;)" translate_by="(100 ℜ)" relax_mover="(&string;)" filter="(&string;)" chain_num="(&string;)" extreme_value_removal="(false &bool;)" dump_pdbs="(false &bool;)" task_operations="(&task_operation_comma_separated_list;)" packer_palette="(&named_packer_palette;)" scorefxn="(&string;)" confidence="(1.0 ℜ)" />
This filter 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. Because Ddg uses all-atom centroids to determine the separation vector when jump is used, it is highly recommended to use the chain_num option instead to specify the movable chains, to avoid invalidating the unbound cache when there are slight changes to atom positions.
The script below shows how to enable PB with ddg filter. 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"/> ... </MOVERS> <FILTERS> <Ddg name="ddg" scorefxn="sc12_w_pb" chain_num="2"/> ... </FILTERS> <PROTOCOLS> <Add mover_name="setup_pb"/> Initialize PB <Add mover_name="..."/> some mover <Add filter_name="ddg"/> use PB-enabled ddg <Add filter_name="..."/> more filtering </PROTOCOLS>
BUG: Always leave
repack="1" and control repacking using
repack_unbound. If not ddG may return 0 and debug pdbs are not written. If
repack=="0" a different code path is used that does not use the ddG mover and may not handle symmetry correctly (and also does not output debug_pdbs).
If a disulfide present across the interface in question the filter silently fails and the ddG column is not added to the score file. A work around (that ignores the energy contribution of the disulfide) is to provide the ddG filter a scorefunction with dslf_fa13 reweighed to zero.