MBG wiki: Create the files needed

What is needed:
- A force field parameter file
- A force field topology file
- A pdb file with the initial coordinates of the system → typically obtained by Protein Data Bank
- A configuration file which contains the conditions for the simulation to be run → the files referred as heating-up script and equilibration script
- A psf file which contains structural information for the system → created for each case.

Create the psf file
- Initial pdb file → start.pdb?
- Remove water molecules1 → start-H2O.pdb?
- Change the assignment of Histidine residue from HIS to HSE?2
- Make separate pdb files for each chain
- Psfgen? package: using the separate .pdb files and the force field topology file predicts coordinates for atoms which are absent from the start-H2O.pdb i.e. flexible atoms of side chains and hydrogens → gen.pdb and gen.psf

Align the axes of inertia of the molecule and translate its center of mass to (0,0,0) [in the orthogonal (Brookhaven) frame].

Solvation-Ionization
- Solvate? the protein using periodic boundary conditions i.e. place the protein into a water box which is repeated in three dimensions.
- Ionize? the system to equilibrate the protein charge
- Measure the box dimensions and determine the coordinates of the center of the box.

Details for each project

Footnotes:

1. Note here that on some occasions in may be advantageous to keep crystallographically determined waters (or ions) belonging to the first hydration sphere.
2. This assumes that your intention is to perform a simulation corresponding to a neutral pH.