Chapter 13 Options Menu
This menu contains commands that
Printout Sets the amount of output in the file PCMOD.OUT.
Dielc Resets the dielectric constant.
DPDP Switch between dipole/dipole and electrostatic calc.
Minimizer Control which minimizer to user.
MMX_PI Options Set options for Pi calculations.
Added Constants Allows the addition of user defined constants
Standard Constants Forces the use of the default data set
Stereo Changes the direction of rotation of stereo display.
Pluto Set Pluto options
VDW Surface Set VDW display options
Dot Surface Set Dot Surface display options.
The PRINTOUT option sets the level of information written to PCMOD.OUT. The default is to write a minimal output file which lists that atomic charges, any generalized constants used and the initial and final energies for a calculation. Full printout gives a complete list of all interactions used in the calculation of the final energy. Each bend, stretch, torsion, VDW interaction and charge-charge interaction is listed with constants used, current geometry and the energy contribution from that item. A full printout can be quite long. The current option (Full or Min-imal) is indicated in the Output window.
The DIELC option sets the dielectric constant which has a default of 1.5. It is rare for increases in DIELC to reproduce the properties of molecules in higher dielectric solvents, so this should be used with great care. If a negative value for DIELC is input, then the charge-charge interaction will be calculated with a distance-dependent dielectric constant (Dielc = f(Rij )), an option that is used successfully in the AMBER program when attempting to model the effect of a polar solvent or lack of counterions. Setting Dielc to -1. will adversely effect calculations done with dipole-dipole interactions.
The DPDP options allows choice of either dipole-dipole or electrostatic calculations. The default in PCMODEL is to use electrostatic calculations with the charges being calculated from the default bond moments. This is a more general procedure and allows incorporation of charged species. However, the MM2 force field was originally developed with the dipole dipole method. The charges for the electrostatic calculations are, in most cases, derived from the bond dipoles programmed into MM2 for the bond dipole option, although heteroatom pi systems will also contribute charges. The default electrostatic calculations use the MM2 charges but also include the dielectric constant in the denominator of the energy expression. Electrostatic calculations should be used with atoms having charges (e.g., N+, C‑) and they will also allow the halogens to be considered as ions if they are not directly bonded to any other atom.
The only reason to use DP‑DP is to compare a calculation to an MM2‑like calculation.
This options controls the default actions of the minimizer. PCMODEL now includes a first derivative minimization method, BFGS, and both truncated Newton-Raphson and full Newton-Raphson second derivative minimization methods. The default behaviour is to do a first derivative minimization until the gradient falls below 1, and then a second derivative minimization until the gradient falls below 0.0001. This dialog box allows you to switch to a first derivative only minimization, second derivative only method or to the mixed method. While the mixed method appears to be the most robust method for general use, there are times when the path taken through conformational space is dependent upon the choice of minimizer.
This option allows setting a number of options for the pi calculation. The choices are:
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RHF or UHF Choose between Restricted Hartree Fock and Unrestricted HF calculation. For closed shell molecules with all the electrons paired the RHF option should be used. The UHF option is used for species with unpaired electrons (monoradicals, diradicals etc.) or for higher spin states.
Mult Set the multiplicity of the system. The default is 1 for a singlet state.
Huckel or Full SCF Set the type of the initial pi calculation. The default is to do a simple Huckel calculation which ignores the geometry of the pi system in determining the bond orders. This method is preferred when the starting geometry is poor. The Full SCF uses the geometry of the pi system in determining the bond orders and will give better bond orders if the starting geometry is close to the final geometry.
Non-Planar or Planar Pi System- This tells PCMODEL whether the entire pi system is planar or non-planar. The default is to assume a non-planar pi system and check for non-planarity. Use the Planar option only if the entire pi system is co-planar.
All of these options are reset when a structure is erased.
The Added CONSTANTS option forces allows the use of a file of user defined constants to be used in addition to or as replacements for the standard constants. The user is prompted for the name of the added constants file, which must use the same format as the standard constants file. PCMODEL checks as the added constants are read and replaces the standard constants if one exists or adds the new constant to the bottom of the parameter list if no previous constant has been defined. To return to the standard constants use the Standard Constants button below.
The STANDARD CONSTANTS option forces PCMODEL to use the default constants. All parameter arrays are set to zero and the default parameter files, mmxconst.prm is read
The Stereo option sets the direction of rotation for the stereo display. The options are to rotate the two structures inward (cross eyed display) or outward (wall eyed display, default). The selecteds option remains in effect until changed.
Choosing this option brings up the following dialog box:
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Ang1 and Ang2 - Control the position of the light source.
Shade – Controls the density of the shade lines, lower number gives more lines.
Ball_Stick or CPK – Produces a ball and stick structure or a space-filling structure.
Bond Taper – A higher number will give a greater perspective taper to bonds.
Bond Radius – Controls how wide the bonds are when drawn. A large number gives wider bonds.
Bond Lines – How many lines are drawn per bond.
The default values are given in the example dialog box.
Upon choosing this option the following dialog box appears:
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The atoms to be displayed in this manner can be all atoms, heavy atoms only or selected atoms only. In order to use the Selected-atoms option, the atoms must be SELECTed using the SELECT button from the TOOLS menu before the CPK option is chosen. The radius for the CPK model can be varied from the van der Waals radius (1.0, default) down to 0.65 (the .20 ball and stick option has been removed). The “color by” option has not been implemented. The CPK model continues as the default display until either the STICK FIGURE option is chosen, or the CPK_Surface dialog box is brought up and canceled. The CPK models can be rotated and translated. CPK models, dot surfaces and Ribbon diagrams can all be displayed at the same time.
Choosing this option brings up the following dialog box:
The dot surface is generated using the Lee and Richards algorithm and two different radii are available - the van der waals radius (default) or a water surface (van der waals + 1.4 Ĺ). The CHARGE option uses the van der waals radius and colors the surface by charge, with redder colors representing positive charge and bluer colors representing more negative charges. White is used for neutral atoms.
The atoms to be displayed in this manner can be all atoms or selected atoms only. In order to use the Selected atoms option, the atoms must be SELECTed using the SELECT button from the TOOLS menu before the DOT_SURFACE option is chosen.
The Dot Spacing option controls the number of dots displayed on the surface. A closer spacing gives more dots, but takes longer to draw and manipulate (rotate and translate).
The dot surface model continues as the default display until either the STICK_FIGURE option is selected, or the DOT_SURFACE dialog box is brought up and canceled. CPK models, dot surfaces and Ribbon diagrams can all be displayed at the same time.