This menu contains the following options:
Minimize: Minimize the current structure(s).
Single Point Calculate the energy of the current structure(s).
Normal Vibrational Modes: Compute normal vibrational modes
Conformational Search: Search the rotatable bonds and flexible rings of the current structure.
Batch Optimization: Process a file of structures.
Dihedral Driver: Rotate about specific dihedral angle and optimize the structure at each step while holding the specific dihedral angle fixes.
Full Energy Printout: Run a single point calculation and write all the energy terms and parameters to the log file.
Use GBSA Solvation Model: Apply GBSA solvation model during geometry optimization.
Mopac2012: Run the semi-empirical quantum program Mopac
Gaussian: Run the quantum chemistry program Gaussian
Batch Submit to QM: Batch conversion of conformational search structures to input files for Mopac, Gaussian or Gamess.
This option optimizes the geometry of the current molecular system using the currently selected force field. The current molecular structure is analyzed for atom types, bonds, angles and dihedral angles and the appropriate constants are extracted from the database of parameters. These parameters are found in the text files mmxconst.prm, mm3.prm, mmff94.prm, oplsaa.prm or oplsua.prm. The energy of the molecular system is evaluated and written to the screen in the Output Window, and then the minimizer is called. The default action of the minimizer is to first do a first derivative minimization until the gradient falls below 1, then a second derivative minimization until the gradient falls below 0.0001. The minimizer attempts to lower the energy of the system by moving the atoms. Every 5 iterations during the first derivative minimization, and then ever 2 iterations during the second derivative minimization the Molecule window is updated with the current geometry and the Output Window is updated with the iteration number, the atomic movement (in 10-5 Å units) and the energy (in kcal/mol). If the energy goes up, or if the energy difference between two calculations falls within the convergence criterion the calculation is stopped, the final energy and its components, the heat of formation (for MMX and MM3 force fields) and the SE (strain energy) are written to the Output Window, and the Structure window is updated. In general, the energy minimum found will be a local energy minimum. A calculation may be stopped at any time by clicking the Stop Calculation button in the Output Window.
The results, in abbreviated form, are written to the log file. This file is a record of all the minimizations done during the current session and can get quite large. The log file can be saved upon exiting Pcmodel and given a specific filename
A major problem in minimizing structures drawn without a template is that hydrogens and lone pairs are often forced into inappropriate positions resulting in high energy structures. It is a good idea to do an H-delete-H-add sequence (select H-A/D in the TOOLS menu twice) then reminimize. For large structures, reminimize to be sure the structure is fully converged. Since minimization is quite time-consuming with large molecules, it is often economical to minimize the structure without added hydrogens to get the three-dimensional structure approximately right prior to H-A/D and final minimization.
In the MMX force field PCMODEL has access to a number of generalized force field parameters ( i.e., torsional potentials dependent only on the two central atoms) to which the program defaults if no standard MMX parameters are available. These parameters are not optimal and energies produced with them should be considered accordingly (however, geometries should not be too far off). The use of generalized parameters is always noted in the log file.
It is important to note that the MMX energy resulting from a minimization with a pi calculation does not contain the potential energy of the pi system. So a comparison of MMX energies for isomeric pi systems is invalid, just as a comparison of MMX energies is invalid for structural isomers. A comparison of the heats of formation, on the other hand, is appropriate. The only circumstance where MMX energies may be compared directly is with conformers or diastereomers.
SINGLE POINT does a single calculation of the energy of the current structure(s). The calculation is begun just as for the MINIMIZE option, however the calculation is stopped before the minimizer is called. The heat of formation is not calculated during a single point calculation.
Since PCMODEL now has a full second derivative minimizer included the normal vibrational modes of a molecule may be computed. You will first be prompted for the name of a file to write the normal vibrational mode information, then a mass weighted hessian matrix will be generated, diagonalized and the vibrational modes will be written to the file. The vibrational modes can be displayed using the IR Spectra option from the Display Menu. MM3 and MMFF94 do a reasonable job with vibrational frequencies while MMX does not give reasonable frequencies.
This command initiates a conformational search on the current structure and up to four rings and fifty rotatable bonds can be searched at one time. There are many options available to control the search and they are discussed in the chapter on conformational searching.
The BATCH option allows the handling of multiple structure files without user intervention. There are a number of options including both calculations and file conversions. Selection of the BATCH option first brings up a file dialog box to get the name of a file containing multiple structures (see FILE OPEN for a detailed description of this dialog box). Any file format that supports multiple structures may be used. Next a FILE SAVE dialog box is presented to get the name and filetype for the results. Any type of file that supports multiple structures may be selected. Then a new dialog to select the desired options is presented. The current options include energy minimization, addition and removal of hydrogens prior to optimization, computation of the surface area, volume or conversion of file type. One or more of these options can be selected. Finally a FILE SAVE dialog is presented to prompt for the filename to use for the Summary file.
The DIHEDRAL_DRIVER option is an accurate, but more time consuming alternative to the ROT_E option. With the DIHEDRAL_DRIVER option, a particular dihedral angle is fixed at a specified value, and all the other degrees of freedom are allowed to relax. Up to two dihedral angles can be driven in one calculation.
Selecting the Dihedral Driver option brings up a dialog box with options for entering data on two angles. The SELA button from the DRAW TOOLS is used to select atoms. Using SELA select four atoms for the first dihedral of interest and then select “Get First Angle”. The atom numbers and current angle will be entered into the dialog box. You may then enter the desired starting angle, stop angle and step size. If you wish to drive a second angle then hit SELA from the DRAW TOOLS (which clears the currently selected atoms) and this pick the four atoms for the second dihedral. Select “Get Second Angle” and the atom numbers and current angle for the second angle will be updated. Enter the start, stop and step for the second angle. You may choose to start each calculation from the original structure or from the last optimized structure. You must set the filename for the output file using the “Set Save Filename” button. When all the required information has been entered, click on CALCULATE. During the calculation, the coordinates of each step, along with angle 1, angle 2 and the energy will be saved in a multiple structure file in either PCM format for later display and analysis. The one or two dihedral angles are rotated to their initial values and the energy of the structure is minimized, while holding the one or two angles fixed. When the energy of that structure is minimized, the second angle is incremented by its step size and the minimization is repeated. This procedure is repeated until the final angle of angle 2 is reached, then angle 2 is reset, angle 1 is stepped to a new angle and angle 2 is stepped through again. Choosing "last structure" (default) uses the previously minimized structure for the next calculation, while choosing "original structure" reads the original structure in, rotates the dihedrals to the specified angles, then calculates. The "last structure" option is faster if machine I/O is slow, but can have problems with very hindered structures where attached groups have a difficult time rotating past each other.
The result of all these calculations is an n by m grid of points where n is total rotation of angle 1 divided by step size for angle 1, and m is the total rotation of angle 2 divided by step size of angle 2. The results will be plotted as a dihedral map and can be plotted again using the Dihedral Plot option from the Display Menu.
This options does a single point calculation on the current structure using the selected force field and writes all the interactions to the log files. This will print all the distances, angles, dihedrals and non-bonded interactions along with all the parameters used in the calculations. This is equivalent to the Full Energy Printout in previous versions of Pcmodel. In general the best option is to start Pcmodel, import the desired structure, set the force field, do a Full Energy Printout and then exit Pcmodel and save the log file, and then exit Pcmodel again. (Two exits are required. This allows you to save the structure and save the log file if necessary).
Apply a GBSA solvation model during energy minimization. Selecting this option brings up a dialog box where you can set the dielectric constant for the solvent and an internal dielectric. The default solvent is Water and the default for the internal dielectric is 1.0.
This command attempts to execute the program Mopac2012 using as input the current structure. PCMODEL first attempts to find Mopac2012 in the default directory. If Mopac2012 is not located in the current directory and PCMODEL does not have any previous information about the location of Mopac2012 you will be prompted to provide a path to the executable file. Use the browse dialog box to locate and select the program. You should only need to do this the first time you run Mopac2012 since the path information will be saved when you exit PCMODEL. After Mopac2012 is located, you will first be prompted for a name for a Mopac2102 input file that will be generated, and then a dialog box for creating a Mopac format file will be presented. Either select from the standard options or enter the keywords you wish to use on the Keyword line. When the calculation is complete a new prompt will be displayed asking if you want to read the Mopac2101 AUX file. If you chose Yes, then filename.aux will be read. If this file does not exist then the Mopac calculation failed and you should look at the file filename.out (or FOR006) to discover the source of the problem.
PCMODEL can directly run Gaussian 09 . In the Windows version the executable program to be run is g09.exe (not g09w.exe !!!!!).The Linux version and Macintosh versions will run g09. In all versions a path to the Gaussian programs should be set before running Gaussian. (See the Windows documentation for setting the Path. In Linux read the Gaussian documentation for setting up the Gaussian environment variables) See the description for running Mopac for more details on finding the Gaussian executable and generating filenames. The dialog box for generating a Gaussian job file provides most of the standard options (see File Menu save section for more information about the dialog box), however additional options can be added by typing them on the keywords line.
This option provides a means for converting the output from a conformational search into input files for Gaussian, Gamess, TurboMole or Mopac2012. Initially you will be prompted for which quantum chemistry program you want and whether you want a single input file will conformers appended (works for Gaussian but not the the other programs) or multiple files each with one conformer. Next you will be prompted for the name of the structure file. The structure file will be read and a list of all the structures will be presented. You may submit all structures (default) or remove some by selecting the structure and then the Change Use button. When done with selections then hit OK and you will get a File Save Dialog for the name of the quantum chemistry input file. If you have previously chosen to output multiple files the files will be named “filename_cX.yyy” where X is the number in the structure sequence and yyy is the extension appropriate for the quantum chemistry program. Next you will get a dialog box appropriate for the quantum chemistry program, The options chosen will be applied to all structures. Selecting OK will then generate the input files.