dope_loopmodel reference
Keywords: manual

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`dope_loopmodel` reference

The `dope_loopmodel` class is derived from `loopmodel`, and is very similar in operation, except that a newer DOPE-based loop modeling protocol is used (see selection.assess_dope()). The main differences are:

- DOPE (see selection.assess_dope()) potential used in combination with GB/SA implicit solvent interaction (see energy_data.dynamic_gbsa).

- Lennard-Jones potential used rather than soft-sphere.

- Improved handling of ligand-loop interactions.

To use, simply use '`dope_loopmodel`' rather than '`loopmodel`' in your Python scripts (see Section 2.3 for examples). Note that it will be significantly slower than the regular loop modeling procedure, primarily due to the GB/SA interaction.

Subsections

- dope_loopmodel() -- prepare to build models with DOPE loop refinement