ComputeLigandRDF

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ComputeLigandRDF

<ComputeLigandRDF name="(string)" ligand_chain="(string)" mode="(string)">
    <(string)/>
</ComputeLigandRDF>

ComputeLigandRDF computes Radial Distribution Functions using pairs of protein-protein or protein-ligand atoms. The conceptual and theoretical basis of Rosettas RDF implementation is described in the ADRIANA.Code Documentation . A 100 bin RDF with a bin spacing of 0.1 Å is calculated.

all RDFs are inserted into the job as a string,string pair. The key is the name of the computed RDF, the value is a space separated list of floats

The outer tag requires the following options:

ligand_chain: The PDB ID of the ligand chain to be used for RDF computation.
mode: The type of RDF to compute. valid options are "interface" in which the RDF is computed using all ligand atoms and all protein atoms within 10 Å of the ligand, and "pocket" in which the RDF is computed using all protein atoms within 10 Å of the ligand.

The ComptueLigandRDF mover requires that one or more RDFs be specified as RDF subtags. Descriptions of the currently existing RDFs are below:

RDFEtableFunction

RDFEtableFunction computes 3 RDFs using the Analytic Etables used to compute fa_atr, fa_rep and fa_solv energy functions.

RDFEtableFunction requires that a score function be specified using the scorefxn option in its subtag.

RDFElecFunction

RDFElecFunction computes 1 RDF based on the fa_elec electrostatic energy function.

RDFElecFunction requires that a score function be specified using the scorefxn option in its subtag.

RDFHbondFunction

RDFHbondFunction computes 1 RDF based on the hydrogen bonding energy function.

RDFBinaryHbondFunction

RDFBinaryHbondFunction computes 1 RDF in which an atom pair has a score of 1 if one atom is a donor and the other is an acceptor, and a 0 otherwise, regardless of whether these atoms are engaged in a hydrogen bonding interaction.

ComputeLigandRDF