7.3 Surface Calculation | ![]() |
VEGA OpenGL can calculate and display some types of
molecular surface trough its 3D engine. It's possible to display some local molecular
properties like hydropathicity, lypophilicity, volume, molecular charges, etc.
The method used by VEGA to generate a surface consists in some steps: a
sphere of 1 Å radius is generated at the (0, 0, 0) coordinates using the dot
density specified by the user. For each atom (Ai), this sphere
is scaled multiplying the dot coordinates by the correspondent Van Der Waals
radius (Ri) and translated to the atom coordinates (Xi,
Yi, Zi). The dots overlapped to near atoms
are discarded. This procedure is performed measuring the distance between the
surface dots of the Ai atom and all atomic coordinates for all
n atoms: if it's less than the An Van
der Waals radius, the dot is overlapped and it's discarded. The properties are
calculated for each valid dot with the appropriate algorithm. It's possible find
more computational details in the VEGA source code.
The Molecular Electrostatic Potential (MEP) surface is calculated projecting the atomic charge on the
surface. The value of each i surface dot is calculated with the following
equation:
Where: | ||
Vi | = | projected value on the i surface dot. |
Qj | = | partial charge of the j atom. |
dij | = | distance between the i dot and j atom. |
The ILM method is based on the principle that at equilibrium the solvent molecules will be more probably found near the hydrophilic regions of the solute, while they will be repelled by the more hydrophobic moieties. The method allows the calculation of a global hydropathicity index (ILM) and this property can be also projected on the molecular surface, giving rise to a very detailed local hydropathicity mapping. The computational steps required for the ILM calculation are:
1) Solvatation of the molecule using a
water cluster (see the solvent cluster section).
2) Molecular dynamics (T= 300K, time step = 1 fs). The simulation length is in
function of the system complexity and please remember that the solvent-solute
environment will be at the equilibrium.
3) ILM calculation.
The equation used to calculate the ILM property is the following:
where: dij is the distance between the the solute atom i and the mass center of the water molecule j, na is the number of the solute atoms and ns is the number of water molecules.
The Polar Surface Area (PSA) is calculated considering polar and apolar atom surfaces. Apolar are C and H bonded to C. Polar atoms are O, S, H, P and H not bonded to C. These properties are projected on the surfaces using two color codes: blue (apolar surface) and red (polar surface).
7.3.1 Calculation parameters
To open this dialog, you must select Calculate -> Surface -> Calculate from the main menu. Select the type of the surface to calculate, enter the probe radius and the dot density, but remember that not all of these parameters are requested by all surface types, see the following table:
Type | Description | Probe Rad. | Density |
VdW | Van der Waals Surface accessible to solvent |
Yes | Yes |
MEP | Molecular Electrostatic Potential | No | Yes |
MLP | Molecular Lypophilic Potential | No | No |
ILM | Hydropathicity profile (a water cluster is needed) |
No | Yes |
PSA | Polar Surface Area | Yes | Yes |
Checking Consider selected atoms only, it's possible calculate the surface of the visible atoms only. At the end of the surface calculation, in the console you can read the area in Ų and the range of values assigned at each dot.
This is the result of a MEP calculation. Please note that the local property isn't showed as ramp of colors. See the next section.
7.3.2 Surface coloring
To change the surface color, select from the main menu Calculate -> Surface -> Color:
With this dialog, you can select the coloring method by property, by atom and by color, choused with the slider or with the color table, pressing the Change button. Press OK to apply the selection or Cancel to close the window.
MEP surface colored by property.
MEP surface colored by atom.
MEP surface displayed with selected color.
7.3.3 Saving the surface.
To save the calculated surface, select Calculate -> Surface -> Save from the main menu. The supported formats are: CSV, Quanta, Insight/Biosym, raw binary, VRML Solid and VRML dotted.
7.3.4 Loading the surface.
To load a pre-calculated surface, select File -> Open from the main menu. The VRML files can't be loaded.
7.3.5 Removing the surface.
A surface can be deleted, using the Calculate -> Surface -> Remove or Edit -> Remove -> Surface options from the main menu.