Prepare a Protein for Simulation

This tutorial shows how to prepare a protein for simulation. There are expensive commercial programs like Schrodinger’s Maestro, but we here focus on free methods.

Download a Model of the Protein

There are several sources:

  1. Download an experimental structure from the PDB.
  2. Create a homology model using SWISS-MODEL. You can find the sequences of many proteins using uniprot.

Build Missing Loops

Use SL2‘s SuperLoop2. Here’s the manual.

Add Hydrogen Atoms

PDB2PQR can be used to add hydrogen atoms.

  1. Be sure to pick the output naming scheme that corresponds to the MD forcefield you’ll eventually use (probably AMBER).
  2. Select the right pH. For most proteins, 7 is fine.
  3. Download the PQR file.

Waters and Ions: CHARMM-GUI

Try CHARMM-GUI Quick MD Simulator.

  1. Select the PDB format.
  2. Under “PDB Manipulation Options,” select “Terminal group patching.”
  3. For the ion concentration, 150 mM is typically good. I prefer NaCl to KCl.
  4. Keep going through the steps. It takes a long time. In the end, download the .tgz file. It should contain what you need to run the MD simulation.

Parameterize for Amber

Unfortunately, the CHARMM-GUI output isn’t quite where it needs to be for an Amber simulation. We need to parameterize the system for amber. Start with the amber/step3_charmm2amber.pdb file. You can use tleap to parameterize this file. It’s part of AmberTools. On, you can access it by typing in module purge then module load amber/14-intel-2013-cuda-5.0. Here’s a sample input file (

The above won’t work if you try tleap -f, though, because the PDB file isn’t in AMBER format. You need to change some strings. This simple bash script should do the trick:

Save that script as fix_names.bash and run bash fix_names.bash MESSED_UP_PDB.pdb > FIXED_PDB.pdb.

You still need to modify FIXED_PDB.pdb though. Find the place in the file where the HOH fields start, and add a TER before it.

Now run the tleap script above: tleap -f

Make sure the total charge of your system is 0.0! You should now have the files to use in Amber.

Run MD Simulation

If you modify the files from CHARMM-GUI (in the amber subdirectory) to read in your newly parameterized Amber files, it should run fine. The COMET supercomputer is a good choice. Here’s an example submission script: