Conformation Perturbation Block in Pele++ control file

This block configures the Conformation Perturbation in a peleSimulation command. In a peleSimulation, this phase will be active depending whether the ConformationPerturbation block is present and whether a conformation library for the ligand is present. If defined, an extra perturbation step focused on changing the conformation of the ligand will be performed after the ligand perturbation. This applies a translation to each atom with respect to the root atom (the first atom in the template) as specified in the conformation library to adopt one of the conformations defined there. Afterwards, the PELE step will proceed as specified in the control file. If no conformation can be applied due to clashes, the step will be rejected on account of that, and the reason will be specified in the log file.

Note that the frequency with which this algorithm is performed in a Pele simulation can be set in the PeleParameters section of the control file. See more information about this parameter at conformationPerturbationFrequency.

Conformation libraries

Conformation libraries used during conformation perturbation are located in the Data/ directory.

If you use non-standard molecules and residues not included in the data directories, then you should create and add the conformation library definition file in your DataLocal/ directory (at <DataLocal>/Conformations).

More information about create conformation libraries files in Conformation library files.

Example

The ConformationPerturbation block can be defined inside the pele simulation command block section. In this case, a perturbation with an overlapFactor of 0.65 is defined. At each Pele step, it will reproduce one of the conformations specified in the conformation library until one without clashes is found.

{
    "ConformationPerturbation":
    {
        "parameters":
        {
            "overlapFactor": 0.65
        }
    }
}

Parameters

All the possible parameters that can be specified in this section are the following ones:

{
    "parameters":
    {
            "overlapFactor": 0.65
    }
}

overlapFactor

The overlap factor that is used when looking for steric clashes of the resulting conformation. When this factor gets lower, a higher steric overlap is accepted. See Overlap factor for more information about this parameter.

  • Parameter: overlapFactor

  • Type: float

  • Default: 0.65

  • Units: dimensionless

  • Range: [0, 1]