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Tutorial 1: Molecular dynamics simulation of protein

System preparation

Let`s consider a protein comprising 500 amino acids that consists of two chains and let's assume that you have obtained its pdb structure from Protein Data Bank. First of all you should remove remarks, connectivity data and HETATM lines except crystallographic water (it's reasonable to include it in model) by some text editor. Then you should add TER card between protein chains. Optionally you could set protonation state of some histidines by editing residue name HIS to HIE, HID or HIP.

Now you're ready to launch tleap program that is a part of AmberTools package. It serves to produce files for calculation.

You can see that it tells tleap to load ff99SB force field that is appropriate for our purpose. Now you can load your protein structure into tleap creating object named mol:

This will add hydrogens to your structure. Now create 12 angstrom layer of TIP3P water around the protein:

You can check system charge:

And then you should add counterions (Na+ or Cl-) to neutralize the system:

Final step is to create prmtop and inpcrd files:

File protein.prmtop contains molecular topology, force field parameters, atom and residue names. File protein.inpcrd contains initial coordinates. You could convert prmtop and inpcrd files into pdb format by ambpdb to visualise obtained system:

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