27.15 GEPOL Command — Set GEPOL Defaults

The GEPOL command is used to set defaults for GEPOL surface calculations¹ in the analysis facility. See Atom Properties, for more information about the GEPOL surfaces.

There is also an experimental capability to invoke the GEPOL_INCR subroutine using the RUN option.

27.15.1 Syntax

     GEPOL [NDIV int] [OFAC real] [RMIN real]
     
           [RSOL real] [RGRI real] [CAVIty real] [[NO]BULK]
     
           [RUN run-options]
     
     run-options ::= [WSURF] {INIT               } [PEER <UNIT>] [PROP <UNIT>]
                     [ASURF] {PUSH atom-selection}
                     [ESURF] {POP                }

27.15.2 Function

The options in the GEPOL command control parameters used by the GEPOL algorithm.²³⁴ They have the following interpretation:

NDIV

NDIV specifies the division level for the triangles on the surface. It may be a number between 1 and 5. The accuracy of the calculation improves as NDIV rises, but the CPU time rises a lot faster. The default for this command is 3.

OFAC

This parameter will be used only if the molecular surface is computed. In the second field goes a real number that can take values between 0.0 and 1.0. This parameter is the Overlapping FACtor. The accuracy improves as the OFAC value increases. The default value is 0.8.

RMIN

This parameter will be used only if molecular surface is computed. In the second field goes a real number that can take values larger than 0.0. This parameter is the radius of the smallest sphere that can be created. The accuracy improves as the RMIN value decreases. The default value is 0.50.

OFAC and RMIN are the parameters that control the creation of new spheres.

RSOL

This parameter will be used only if accessible or molecular surface is computed. In the second field goes a real number. It is the probe or solvent radius. The default value is 1.4 Angstroms.

RGRID

This parameter sets the dimension of the space grid used to find neighbors when GEPOL runs. The default setting of 2.5 Angstroms was optimal for running GEPOL on a large protein. A value of 0.0 will result in the dimension being set by code within $CGS/gridc.c.

CAVITY

This parameters sets the cavity energy term. If this value is non-zero, then the conformational search command, see Conformational Search, will include a energy term equal to the molecular surface area calculated by GEPOL multiplied by this cavity energy factor. The units for the parameter are kcal/mole/Angstrom**2. A good value for this parameter is 0.072.⁵

BULK

The BULK flag controls whether the BULK subroutine is invoked as part of GEPOL. BULK adds spheres in the interior of large molecules to speed up the molecular surface generation.

The RUN keyword specifies that the GEPOL_INCR subroutine is to be run. The keywords; WSURF, ASURF, and ESURF; specify van der Waals, accessible, and molecular surfaces, respectively. The keywords; INIT, PUSH, and POP; specify initialization, pushing the selected set of atoms, and popping the last set of atoms, respectively. The PEER keyword specifies a unit where all the spheres will be written as input to the peer program, see Peer. The PROP keyword specifies a unit where the atomic surfaces will be written as a property table suitable for use in the Analysis Facility, see Table I/O.