Neutralizing a System

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Description of Neutralization


Some structures may not be neutral but instead have a positive or negative net charge. Some methods in CHARMM, such as the Ewald method for computing electrostatics, fail when there is net charge on the system so it is best to neutralize the charge by adding counter ions to the solution. 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.

However, adding charged particles close to a protein may influence its behavior. is undesirable, and therefore care must be taken to place ions far away where they will be screened by solvent.

General Neutralization Procedure

This section of the tutorial will add an ion to a system. The user must have a PSF and CRD of that structure. This tutorial will use the protein with ID 1YJP. Because the scripts are quite complex, only a brief description is given here. The files themselves are available from

As the above above output shows, 1YJP already has a charge of 0 so this tutorial will make the charge equal to 1.

After the protein and waters have been joined, the structure must searched for a location to add the ion, replacing a water molecule occupying that position. The best location is unknown a priori therefore, a Monte-Carlo like procedure has been implemented via CHARMM scripting to search for and place ions in favorable positions of a solvated structure.

In addition, it is desirable to have an ion concentration in the solution that make biological sense. For example, it is know that cellular KCL concentration is on the order of 0.15M and therefore, enough potassium and chloride ions will be added to both neutralize the system and set the correct concentration.

The logic associated with assigning charges and setting location is complicated and a but beyond the scope of the current tutorial, however, the scripts for this process are available at and the method can be applied at

The basic procedure is as follows:

  1. Read topology and parameter files
  2. Determine what ions you want to neutralize with (K+,Na+, Cs+, Mg2+,Ca2+, Cl-)
  3. Determine the concentration you want set
  4. Compute number of ions required to achieve the aforementioned concentration
  5. Read PSF and CRD files for a solvated structure
  6. Create the positive and negative ion segments in CHARMM
    1. Define the region where the ion is to be placed
    2. Delete a water molecule and add the ion
    3. Repeat until all ions required to reach the desired concentration have been added
  7. Perform short minimization
  8. Check the energy versus the previously lowest energy conformation
    1. If current energy is lower then previous then save the structure and return to step 5
    2. repeat until user is satisfied