Protein solvation

The protein solvation workflow provides a guided procedure for system setup, solvation and equilibration.

The workflow consists of the following high level sequence of steps, starting from an initial PDB system:

  1. Run PDB2PQR to assign missing hydrogens and estimate titration states

  2. Solvate the system using a pre-prepared solvent background

  3. Generate a CHARMM/NAMD protein structure file (PSF) using PSFGEN

  4. Neutralise the system by adding an appropriate number of counterions

  5. Minimise and run an initial NVT-ensemble MD with solute fixed

  6. Minimise and run an NPT-ensemble MD with backbone constraints

  7. Run a final “production” NPT-ensemble MD run to equilibrate the system

General options

solute

Fragment object containing intiial structure

pdb2pqr

(default: True) Can be set to a string containing the path to PDB2PQR

Solvation options

shape

(default: 'cube') Shape of solvent background environment. Currently, cube is the only supported option.

solvent

(default: 'TIP3P') Forecfield model used in pre-prepared solvent background environment. Currently, only TIP3P is supported.

padding

(default: 28.3459) Padding size for solvent box (default = 15.0 Angstrom)

boundary

(default: 4.53534) Distance between the solute and solvent (default = 2.4 Angstrom)

unit

(default: 'a.u.') Unit for distance measurements

Neutralisation options

neutralise

(default: True) Flag to neutralise the system before MD runs

neutralise_cation

(default: 'Na') Cation species for neutralisation

neutralise_anion

(default: 'Cl') Anion species for neutralisation

General MD options

driver

A driver to run molecular dynamics. Must be a NAMD() instance.

dryrun

(default: False) If True, generate input files but do not run MD

restart_from_md

(default: 0) Specify a restart from a previous MD stage (default is to start from the beginning)

1st MD run (NVT) options

length_nvt

(default: 2000000) Length of 1st NVT MD run in fs (default = 2 ns)

minimisation_nvt

(default: 50000) Steps of minimisation before 1st NVT MD run

relax_residues_nvt

(default: ['solvents','ions']) Specify what to relax in the 1st MD run

2nd MD run (NPT) options

length_npt

(default: 5000000) Length of 2nd NPT MD run in fs (default = 5 ns)

minimisation_npt

(default: 50000) Steps of minimisation before 2nd NPT MD run

relax_residues_npt

(default: ['amino_acids','solvents','ions']) Specify what to relax in the 2nd MD run

Production MD run (NPT) options

length_production

(default: 20000000) Length of production MD run in fs (default = 20 ns)