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Description of Neutralization


Some macromolecules may have an overall positive or negative charge instead of being neutral. The implementation of the Particle Mesh Ewald method (PME) for computing electrostatics that is present in CHARMM works most reliably when there is no net charge on the system. Therefore, when a molecule has a charge, it is generally thought best to cancel it out by adding counter ions to the solution. It is easy to detect when this needs to be done since when CHARMM reads in or modifies a PSF, it will output the total charge of the system as shown in the following sample output.

Output of generate

The charge can also be calculated by printing out the ?STOT variable after running the SCALar CHARge STAT command.

Even if the system is neutral overall, it is often desirable to have an ion concentration since this more realistically mimics the interior of a cell or conditions in the blood stream. For example, it is known that cellular NaCL or KCL concentration is on the order of 0.15M and therefore, enough sodium or potassium and chloride ions will be added to both neutralize the system and set the correct concentration. However, adding charged particles close to a protein may influence its behavior in undesirable ways. Therefore, unless it is known that ions are found in close proximity to the macromolecule, they should be placed at some distance from it so that they are screened by the solvent.

Points to Consider before Neutralizing

There are a few things that need to be considered before you write a script to perform neutralization.

  • How many total counter-ions will be needed? Is there enough volume to accommodate them without getting too close to the solute?
  • If you want to change the overall charge on the system (e.g. from +3 to 0) you will need different numbers of positive and negative ions (in this case, you would need 3 more negative ions than positive ones).
  • Which ions should be used? CHARMM has parameters for a number of different salts.
  • Are there any charged residues on the surface of the macromolecule that might be particularly disturbed in the presence of counter-ions?
  • Conversely, are there any charged residues that might not behave correctly without a nearby counter-ion?

The example given in this tutorial describes a general procedure for neutralizing a system, however it does not consider too carefully the points mentioned above. You will need to understand the electrostatic and physical behavior of your system to know what concentration of ions is most appropriate.

General Neutralization Procedure

The neutralization procedure implemented in CHARMMing is described below and uses a monte-carlo like method for picking a "good" configuration of ions in the solvent. The basic idea is that solvent waters are randomly replaced (with a few caveats) with ions. The system is then minimized briefly to remove bad contacts and the final energy is stored. This is repeated a certain number of times, and the minimized structure with the lowest total energy is chosen as the final neutralized system.

A more detailed outline of the procedure is as follows:

  1. User inputs the desired salt and concentration (it is assumed that the final charge will be 0) as well as the desired number of trials.
  2. Compute number of positive and negative counter-ions required to achieve the desired concentration and to make the system neutral.
  3. Create the positive and negative ion segments in CHARMM.
  4. Define all possible water molecules that could be replaced by this ion. These are all bulk waters that are not too close to the solvent or to another ion (CHARMMing uses a 5.5 Å cut-off).
  5. For each ion to be placed:
    1. Delete a water molecule at random. and add the ion in its place
    2. Repeat until all ions required to reach the desired concentration have been added
  6. Perform short minimization (100 steps of steepest descent)
  7. Check the energy versus the previous lowest energy conformation
  8. If current energy is lower then previous then save the structure and return to step 4
  9. Repeat until the desired number of trials have been run

Needless to say, some of these steps require some advanced magic with the SELEct command. A complete example of this is given later on in the tutorial.