System Setup

Prepare Input

Aside from the APBS calculation, Rocklin correction required several input

  • box: The size of the simulation box is the average box dimensions across the simulations. The input is a list with length 3 (e.g. [10, 10, 10]). The unit should be Å.

  • lig_netq: The charge of the ligand.

  • protein_netq: The charge of the system without the ligand.

  • temp: The temperature of the system in kelvin (e.g. 310K)

  • water: The water model used in the simulation. Currently only tip3p and tip4p water are supported. The input should be rocklinc.waters objects.

Run command

To use rocklinc, one need to create a rocklinc.RocklinCorrection object to perform the computation.

import rocklinc
rc = rocklinc.RocklinCorrection(box, lig_netq, protein_netq, temp,
                                rocklinc.waters.TIP3P)

This is followed up by APBS calculations.

Optional Water models

Different water models and related constants

class rocklinc.waters.TIP3P[source]

The TIP3P water model.

Variables

  • epsilon_S – The relative dielectric constant of TIP4P water.

  • gamma_s – quadrupole-moment trace of the solvent model.

class rocklinc.waters.TIP4P[source]

The TIP4P water model.

Variables

  • epsilon_S – The relative dielectric constant of TIP4P water.

  • gamma_s – quadrupole-moment trace of the solvent model.