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Autogenerated Tag Syntax Documentation:
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;)" jump_selector="(&string;)"
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.
Example:
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_bound
and 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.