Tutorial on using Qnifft

I.    What you need

II.  The Qnifft parameter file

III. Common problems

I. What you need

• First, you need to have the Qnifft program. If you need to download the program, it can be found here. This program can be run only on a UNIX machine, such as an SGI O2.

• Second, you need to have a PDB file of the structure of interest. The atoms must be labeled in Insight II style.

• Third. you need to have a Qnifft parameter file that will specify how the calculations are done.

• Fourth, you need to have parameter files for both atomic radii and partial atomic charges. Examples of these files are here. These files can be modified to any specifications that you wish.

• Fifth, you need Grasp, or a related program, so that you can view the results of the calculations.

II. The Qnifft parameter file

This section contains information on the parameters that can be altered during an electrostatics calculation run. The sample file is called prm. There are instructions on how to alter the parameters with the prm file.

• Gridsize

The largest gridsize available with this version of Qnifft is 65x65x65. Smaller gridsizes can be used but larger ones cannot (default=65).

• Scaling

You must choose one of the following to determine how the molecule fits within the grid:

• Scale: User manually inputs the dimensions for grids per angstrom (higher number gives greater resolution).

ex. sizing=scale scale=1.0

• Fill: User determines what the longest dimension of the molecule as percentage of box length will be.

ex. sizing=fill fill=50

• Border: User determines the closest distance (in angstroms) a molecule can be with respect to the boundary (default setting).

ex. sizing=border border_solvent=10

• Boundary Conditions

There are four choices for boundary conditions (I do not know what the "field" condition does). The condition must be inputted as boundary_condition=xxx

• Zero: All boundary points have zero potential. This is a rather inaccurate method but requires minimal computing. Most useful if the molecule being analyzed is very small.

• Dipolar: All boundary points have coulombic potentials as calculated from the center of positive charge and from the center of negative charge. This method is more accurate than "zero" and also requires minimal computing.

• Coulombic: All boundary points have coulombic potentials as calculated from each point charge within the system studied. This is much more accurate than "zero" or "dipolar" but requires more computing (default setting).

• Focussing: This requires two calculation runs. The first run should be done with one of the other conditions above, but at low resolution (i.e. at low grids per angstrom). The phi-map generated in the first run is then used as the basis for calculating the boundary potentials in the second "high-resolution" run.

• Solute parameters

• Dielectric: Input the value for the dielectric of the interior of the molecule (default=2).

• Spherical charge: Usually kept as false (default=f).

• Solvent parameters

• Dielectric: Input the value for the dielectric to the exterior of the molecule (default=80).

• Salt concentration: Input the value (in molar) for the concentration of a 1:1 salt to be calculated within the solvent (default=0.145, which gives a Debye-Huckel radius of 8 angstroms).

• Probe radius: Input the radius size of a sphere which will "roll" on the surface of the molecule. This determines the accessible van der Waals surface (Conolly method???) of the molecule (default=1.4).

• Ionic radius: Input the radius of a sphere which will roll on the surface of the molecule. The distance from the center of this sphere to the van der Waals surface of the molecule determines an area of solvent that is inaccessible to ions in the solvent (i.e. dielectric=80, ionic strength=0) (default=2.0).

• Algorithm parameters

• Temperature: Input the temperature (in Kelvin) for which the calculations shall be done (default=298).

• Nonlinear equation: Determines if the nonlinear Poisson-Boltzmann equation is to be used in calculating electrostatics (default=t).

• Convergence: Determines the value at which the iterations are considered to be converged (default=0.001).

• Relaxation parameter: Kept as 1.0 (default=1.0).

• Check frequency: Kept as 2 (default=2).

• Newton iterations: Determines maximum number of iterations to be performed (default=20).

• Level 0 multi-grid: Kept as 2 (default=2).
• Level 1 multi-grid: Kept as 4 (default=4).
• Level 2 multi-grid: Kept as 8 (default=8).
• Level 3 multi-grid: Kept as 16 (default=16).

• Smooth dielectric: Kept as 0 (default=0).

• Output parameters

• Concentration output: ? (default=f)

• Insight format: Determines if output pdb files will be in Insight format (default=f).

• Site potentials: Determines if a file containing site files will be output (default=f).

• Atom file output: Determines if a file containing atoms and their assigned partial charges will be output (default=f).

• Analyse map: ? (default=f)

• Title: ? (default=untitled)

• Input files

• Radius file: Specifies a file (click here for an example) that contains atomic radii.

• Charge file: Specifies a file (click here for an example) that contains partial atomic charges.

• Site charge file: ?

• PDB input file: Specifies a PDB file on which the electrostatic calculations will be performed.

• Phi input file: Specifies a phi-map to be used in calculating boundary potentials. This is used in the focussing technique.

• Site input file: Specifies a PDB file whose site potentials will be determined.

• Output files

• PDB output file: Gives a name to a file to be written that contains the PDB file used as the partial charges assigned to atoms during the calculation.

• Phi ouput file: Gives a name to a file to be written that contains the phi-map (Grasp readable) for the calculations performed.

• Dielectric map file: Gives a name to a file that shows the dielectric map.

• Site output file: Gives a name to a file to be written that contains electrostatic potentials at sites provided by the site input file.

III. Common problems

• could not find radius/charge for atom specified: probably missing an atom name; check that atoms are appropriately named to fit with the nomenclature of the radius/charge files

• parameter missing: either a necessary parameter (i.e. the PDB input file, dielectrics, etc.) or a optional parameter specifically turned is missing; see which parameter needs a value and modify the parameter file accordingly

• iterations do not converge or do not reach the convergence value: the system is probably too large; increase the salt concentration or try to decrease the size of the system; or calculations have reached the maximum iterations; increase the number of iterations

• shortest distance from molecule to boundary is a negative number: scale is too large; decrease the scale or use the fill or border scaling options

• salt points outside the grid: scale is too small; increase the scale (I have seen this during the first run of a focussing calculation. However, I'm not sure if this causes any harm for a focussing calculation.)

• If there are further problems or questions, please contact me.