9. Using External Applications

This chapter describes the interfaces between QUANTA and a variety of third-party computational chemistry programs. Some of these applications are bundled with core QUANTA; several are additional options. Read this chapter or portions of it to become familiar with access procedures for the following programs:

• Molecular orbital calculations - CINDO and MOPAC

• Poisson-Boltzmann electrostatics and Brownian dynamics - UHBD

As far as possible, the options available within QUANTA cover all functionality in the original versions of these external programs. In addition, the default options in the calculation setup dialog boxes have been specified so that changes are rarely necessary.

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Accessing external programs from QUANTA

External third-party programs are automatically started from QUANTA when a request is made for a calculation. While QUANTA requires a graphics workstation for its interactive graphics and molecular displays, the more computationally intensive programs run either on the local workstation or on a range of available network hosts.

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Specifying a host

For each third-party application, you may select a host from the list in the applcomm.db file, which is customized to contain site-specific information at the time QUANTA is installed.

To select a host for the CINDO, MOPAC, or UHBD applications, display the Calculate menu, select Select Host, and then select the appropriate application from the pull-right menu.

For all applications, selecting Select Host opens a dialog box with a scrolling list of network-available hosts. You can select a different host for each application.

When you select a host, the selection is retained for the duration of the QUANTA session. If no host is specified, QUANTA automatically tries to run the application on your local workstation.

When you select a host, another dialog box opens with fields containing necessary information for running the job over the network. Table 45 lists the options and describes each briefly. Although there already is default information in certain fields, you may change or add more information. This information remains in effect for the entire QUANTA session unless explicitly changed.

Table 45. Select Host dialog box 

Data Entry Field	Function
Machine	The name of the host selected from the previous scrolling list dialog box.
Pathname	The full pathname of the program executable on the selected host. Environment variables are valid only if you are running the application on the local machine.
Account	The user ID to run the program on the selected host. A valid user account must exist on the selected host to successfully launch the program.
Password	The password for the user identified in the Account field. A password typed in this field is not revealed on the screen, as all characters are represented as asterisks. By default, no password is used. Depending on site-specific system setup, the host may not require a password to run a remote job.
Working Directory	The directory from which the program is run on the selected host. If the selected host is local, the default working directory is the current QUANTA directory. If the selected host is remote, the default working directory is the login directory of the user identified in the Account field.
Number of Nodes to Use	Number of nodes needed to run the application. Default is 1.

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Performing a calculation on a remote host

QUANTA network communication requires one additional program, the remote job remote daemon (RJRD). QUANTA uses RJRD to run each third-party application. After it is started, RJRD establishes a connection back to QUANTA, then receives the path to the third-party application to run and the necessary files to start the program. After the third-party calculation is completed, RJRD sends the resulting file back to QUANTA. RJRD remains active until the calculation is completed and the resulting files are sent back to QUANTA.

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Using CINDO

The CINDO function in the QUANTA Calculate menu provides an interactive interface to the CINDO program (QCPE Program 141). Charges generated by the program are stored either in a quantum mechanical (QM) coordinate file or incorporated directly into the MSF. Once incorporated into the MSF, these charges can be used in subsequent QUANTA and CHARMm calculations or displayed using the Label Atoms function on the Draw menu.

The CINDO program has an upper limit of 200 atoms. The options available in the QUANTA interface cover virtually all functionality in the original version of the external programs. The default options in the CINDO calculation setup dialog box have been set up so that changes are rarely necessary. Information on the methods used in the CINDO calculation can be found in Citation 2 in the References section of this chapter.

The CINDO program, although started from QUANTA, can be run in the background so that other QUANTA tasks can be performed during CINDO calculation.

Since CINDO and QUANTA are separate programs, files are used to send information between them. All files associated with a particular calculation have the same user-defined base filename. Table 46 lists the file types associated with CINDO calculations

Table 46. CINDO files

File	Description
filename.cin	Input file to CINDO, automatically created by QUANTA. Contains data that describe the molecular structure and selected calculation options.
filename.out	Log file from the CINDO calculation.
filename.qmc	Quantum mechanical (QM) coordinate file containing the final calculated charges.
CINDO.in	File where CINDO specifically looks for input for running a job.

If you run CINDO in the background, results are not automatically incorporated into the MSF. The calculated atomic charges are stored in the QM coordinate file.

To read the charges stored in the QM coordinate file into the MSF, display the Calculate menu and select Read/Display Results from the pull-right menu that opens when CINDO is selected. A dialog box allows you to choose to:

• Change the current MSF

• Check output for errors

• Report results

• Read charges into the MSF

• Display the dipole moment vector

The contents of the QM coordinate file also can be incorporated into the MSF using the Import function in the File menu.

All other results to be output can be retrieved from the CINDO.out log file. This file is overwritten when another CINDO calculation is run. To save the data in the log file, change the name of the file at UNIX level.

Complete the following exercise to become familiar with the QUANTA/CINDO interface. To do the exercise, the structure cyclohexanol must be displayed in the QUANTA viewing area. This structure was built in the section Generating an Electrostatic Potential Energy Surface in Chapter 6. If you have not completed that section, do so before proceeding.

1.   Start CINDO.

Display the Calculate menu and select the CINDO function. From the pull-right menu that opens, select Calculate. A dialog box opens for selecting CINDO options. Table 47 lists these options and provides a brief description of each.

Enter the values:

Title for Calculation: CINDO Calculation on cyclohexanol
Set Charge On System: 0

Select the options:

Specify which Hamiltonian to use: CNDO
Specify Open or Closed Shell Calculation: Closed
Specify Multiplicity: Singlet

Specify the print options:

Minimum - Final energy, partial charges and dipole

Click the OK button and a File Librarian dialog box requests the name for a CINDO input file.

Enter the text:

cyclohexanol

Click the Save button and the filename extension .cin is automatically added, and a dialog box opens for selecting run options. Table 48 lists the options and provides a brief description of each.

Select the option:

Run in Background

Click the OK button and the cursor changes to a watch while the calculation is running. The message line reads:

	Submitting CINDO calculation to batch

Other QUANTA functions can be used while the CINDO calculation runs in background mode.

2.   Check the status of the CINDO calculation.

Display the Calculate menu and select Show Status A dialog box displays a list of background jobs that can be started by QUANTA.

Select the option:

CINDO

Click the OK button and the textport reports if the CINDO calculation is in progress or completed.

3.   Display the charges for the atoms.

Display the Draw menu and select Label Atoms. On the pull-right menu that opens, select Atomic Charge and the atomic charge assigned by QUANTA is displayed next to each atom.

4.   Display CINDO results.

Display the Calculate menu and select CINDO. From the pull-right menu that opens, select Read/Display Results and click the OK button. The CINDO Postprocessing Options dialog box opens.

Select the options:

Check output for errors and report results
Read charges into MSF
Display Dipole Moment Vector

Click tns, select Atomic Charge and the atomic charge is assigned by the OK button.

A File Librarian dialog box requests the name of a CINDO output file. The filename extension .out is automatically contained in the data entry field.

Select the entry:

cyclohexanol.out

Click the Open button and the calculation results are displayed in the textport. In a dialog box that offers the option of saving the structure, select the option:

Create New Generation of cyclohexane.msf

Click the OK button. The dialog box is cleared from the screen, the textport indicates that the old structure file is renamed cyclohexanol.msf,002, and the new charges are saved in cyclohexanol.msf. The atom labels are also changed to reflect the new CINDO-generated charges.

The dipole moment vector, a graphical object, is displayed in the viewing area. The Object Management Table opens, listing Dipole_1.

5.   Delete the dipole moment vector.

Select the Delete cell for Dipole_1. The text changes from no to yes, the dipole moment vector is no longer displayed, and the Object Management Table closes.

6.   Delete the labels for the structure cyclohexanol.ene.

Display the Draw menu and select Label Atoms. From the pull-right menu that opens, select Off and the labels are no longer displayed.

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Using MOPAC

MOPAC is a semi-empirical molecular orbital program that is generally used in the study of chemical reactions and molecular structure problems. The interactive interface allows you to run the MOPAC program and display some of the results within QUANTA. For example, you can process results of calculations to obtain molecular orbitals and display them as graphical objects.

Versions of MOPAC that can be used with QUANTA include MOPAC 5 and MOPAC 6. MOPAC 93 is not known to work.

The semi-empirical Hamiltonians available within MOPAC include:

• PM3

• AM1

• MNDO

• MINDO/3

Available calculations include:

• Vibrational frequencies

• Thermodynamic quantities

• Polarizability

• Isotopic substitution effects

• Geometries

In MOPAC, calculations may be performed when more than one molecular structure is selected, for example, during drug docking studies. However, do not perform MOPAC calculations on multiple molecules that are not connected by covalent bonds. If MOPAC results are to be read back into QUANTA, all selected structures must be contained in a single MSF.

MOPAC creates a series of files for each calculation. All files associated with a particular calculation have the same user-defined base filename. Table 49 lists the files and provides a brief description of each.

Table 49. MOPAC files 

File	Description
filename.ain	Input file to MOPAC.
filename.out	Log file from the MOPAC calculation.
filename.arc	Archive file containing a short summary of the calculation results (final heat of formation, dipole moment, geometry, etc.).
filename.shu	Shutdown file automatically created by the Shutdown MOPAC option. Writing anything to this file shuts down MOPAC, creating filename.den and filename.res for restarting the calculation.
filename.den	Density matrix file automatically created during normal shutdown. This file is needed for the Restart Calculation option.
filename.res	Restart file automatically created during normal shutdown. This file is needed for the Restart Calculation option.
filename.gra	Results file containing calculation results in a form suitable for processing into graphical output (for example, orbital and electron density maps).
filename.qmc	Quantum mechanical (QM) coordinate file containing the final Cartesian coordinates and calculated charges.
filename.qpt	Results file containing the dipole moment vector for the calculated structure

Complete the following exercises to learn the basics of using the QUANTA MOPAC application. The exercises use cyclohexanol.msf, which was built in the Electrostatic Potential section of Chapter 6. If you did not complete that section, do so before proceeding.

1.   Display a structure.

From the File menu, select Open. From the scrolling list in the Open MSF File Librarian, select cyclohexanol.msf.

Select the option:

Replace

Click the Open button and the structure cyclohexanol is displayed in the viewing area.

2.   Start the QUANTA/MOPAC interface.

Display the Calculate menu and select the MOPAC function. From the pull-right menu that opens, select Calculate.

3.   Run a MOPAC/AM1 calculation.

Select the option:

Set up Calculation

Select the OK button and the Setup MOPAC Calculation dialog box opens.

Fill in (or leave the default) for the title for the calculation:

MOPAC calculation on cyclohexanol

Select the options:

AM1
Z-matrix with Automatic Setup

Enter the value:

Molecular charge: 0

Click the OK button and the Geometry Optimization Options dialog box opens.

Select the option:

Full Geometry Optimization

In the File Librarian dialog box that opens, enter the text:

cyclohexanol

Click the Save button and the input file cyclohexanol.ain is saved. In the MOPAC Run Options dialog box that opens, select the option:

Run Calculation Now

Click the OK button. This sends the coordinates and element types to MOPAC and starts the MOPAC calculation. This calculation takes several minutes since a geometry optimization (energy minimization) is requested. For large molecules, run calculations of this type in the background. The textport reports the progress of the MOPAC calculation.

4.   Process MOPAC results and incorporate them into the MSF.

After the calculation finishes, the MOPAC Postprocessing Options dialog box opens.

Select the options:

Check output for errors and report results
Read coordinates into MSF
Read charges into MSF

Select the OK button. In the MSF Saving Options dialog box, select the option:

Save to New Filename

In a File Librarian dialog box that opens, enter a new filename:

cyclohexanol_mo

Select the Save button to save the MOPAC-generated structure. This ensures that the molecule on the screen has the same Cartesian coordinates as the molecule saved in the MSF file. It permits comparison between the initial cyclohexanol structure (cyclohexanol.msf) and the MOPAC-processed cyclohexanol structure (cyclohexanol_mo.msf). QUANTA automatically returns to Molecular Modeling mode.

5.   Display MOPAC AM1 results - Bond lengths.

Display the Calculate menu and select Internal Coordinates. From the pull-right menu that opens, select Bond Lengths and the Select Atoms and Selection Utilities palettes open.

From the Select Atoms palette, select Include and All Atoms.

Select Finish. The palettes close and a dialog box asks for directions about what to report when both atoms in a bond are selected.

Select the option:

Report bond length once only

Select the OK button and a list is displayed in the textport showing the bond assignments and lengths. The atom labels for defining the bonds are the same as those shown on the structure in the viewing area.

This same procedure can be used to display a list of bond angles or dihedral angles. The only difference is in the selection from the Internal Coordinates pull-right menu.

6.   Display bond lengths in the viewing area.

From the Geometry palette, select Distance and Show Distance Monitors .

Pick any two carbon atoms. The bond length between them is displayed in the viewing area in the space between the two atoms picked. The bond length is the same as that listed earlier in the textport.

Continue picking atom pairs to display other bond lengths. Use Delete Distance Monitors in the Geometry palette to remove reported bond lengths from the screen. Deselect Distance.

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Executing a single-energy AM1 calculation

AM1 (Austin Model 1) is parameterized to be especially useful for hydrocarbons and other polar structures that have appreciable hydrogen bonding interactions. For more information about this calculation, see citation 3 in the references section of this chapter.

1.   Set Up the AM1 Calculation.

Display the Calculate menu and select MOPAC. In the Select MOPAC option dialog box, select the option:

Setup Calculation

Click the OK button. In the Setup MOPAC Calculation dialog box, select the option:

AM1

Click the OK button. In the Geometry Optimization Options dialog box, select the option:

No Geometry Optimization

Click the OK button. In the File Librarian dialog box, enter the text:

cyclohexanol_single.ain

Select the Save button and the MOPAC Run Options dialog box opens.

2.   Run MOPAC.

Select the option:

Run Calculations Now

Select the OK button and the MOPAC calculation starts.

3.   Display the results.

When the calculation is complete, the MOPAC Post Processor Options dialog box opens.

Select only the option:

Create MO or Charge Density Map

Select the OK button. In the Molecular Orbital Postprocessing dialog box, enter the values:

Select the MO [HOMO]: 21
Grid points per map edge: 20
Conformation Number: 1

Select the options:

Molecular Orbital Map
Wait for Calculation to Complete

Click the OK button.

The orbitals are calculated for the coordinates of the molecule as it appears in the viewing area. When you run this calculation, the molecule should not be moved relative to the saved MSF.

When the calculation of the orbitals is completed, a default name for the graphical object, MOLORB1, is offered.

Click the OK button to accept the name, and the Object Management table is displayed with MOLORB1 listed.

In a dialog box that lists display options for the brick map, select the option:

All of the map displayed

Select the OK button and the dialog boxes for displaying the objects open. In each of the dialog boxes, accept the defaults for contour levels as well as the colors associated with them.

The brick map is displayed on the screen.

4.   Delete the brick map object.

Select the Delete cell in the Object Management Table for MOLORB1. The text changes from no to yes, the brick map is removed from the screen, and the Object Management Table closes.

5.   Repeat the calculation using a different Hamiltonian.

To obtain data to compare with AM1, rerun the MOPAC calculation, Steps 1 through 4, using the Hamiltonian PM3 instead of AM1.

Table 51. Set Up MOPAC Calculation dialog box 

Option	Description
Title for Calculation	Title for the calculation to be performed.
Specify Which Hamiltonian To Use
PM3	Performs calculation using PM3 Hamiltonian.
AM1	Performs calculation using AM1 Hamiltonian.
MINDO	Performs calculation using MINDO Hamiltonian.
MINDO/3	Performs calculation using MINDO/3 Hamiltonian.
Specify Input Format
Z-Matrix with Automatic Setup	Automatically creates a z-matrix (internal coordinate table) to specify the initial geometry. The starting chain includes nonhydrogen atoms and excludes terminating groups such as methyl.
Z-Matrix with User Specified Order	Specifies the atom ordering of the z-matrix.
Cartesian Coordinates	Indicates that the input file contains Cartesian coordinates (not z-matrix). Useful for comparing similar systems. Geometry optimization is limited to all or nothing. Symmetry constraints cannot be applied.
Setup Dummy Atoms in the Z-Matrix	Allows dummy atoms to be created and included in the z-matrix. Allows the formation of dummy bonds linking fragments. Essential for reaction coordinate studies.
Use Symmetry Constraints	Simplifies optimization by requiring bond lengths, angles, and torsion angles to equal those for reference bonds, angles, and torsions.
Molecular Charge	Specifies the net charge on the structure.
Other Options	Displays a dialog box of several advanced options.

Table 52. MOPAC Geometry Optimization options 

Option	Description
Full geometry optimization	Optimizes all bonds, angles, and torsion angles.
All bonds only	Optimizes only bond lengths.
All angles only	Optimizes only the bond angles.
All torsion angles only	Optimizes only the torsion angles.
User selected parameters	Opens a palette with selections to control which bond lengths, bond angles, and torsion angles are optimized.
No geometry optimization	Performs no geometry optimization.

Table 53. MOPAC Post Processing options 

Option	Description
Check Output for errors and report results	Checks the .out and.arc files for error messages. Also reports some results. If the MOPAC run fails, some post-processing options are invalid and corresponding results files are not created. If this option detects a fatal error, selected post-process options are not performed. If warning messages are encountered, you are given the choice of continuing or not. Use of this option is strongly recommended.
Make .qmc and dipole file for different conformation	Allows data to be processed to form individual files containing coordinates and charges that can be read into QUANTA MSFs and .qpt files for the corresponding dipole vectors.
Read Coordinates into MSF	Extracts coordinates from the .qmc file and updates the MSF with them.
Read Charges into MSF	Extract the charges from the .qmc file and updates the MSF with them.
Create .csr File	Stores conformers in a .csr file that can be studied later using the Analysis application.
Display Dipole Moment Vector	Retains the dipole moment information in the form of a QUANTA plot file (.qpt), so that the vector can be displayed as a graphical object.
Create MO or Charge Density Map	Processes molecular orbital data for a QUANTA .mbk file containing a contoured map of specified molecular orbitals or the corresponding charge density. If a reaction coordinate study was performed, maps can be generated for the different structures.
Cleanup Files	Presents a list of files created for the MOPAC run and allows their selective deletion. The files are ordered so that the files least likely to be needed again are at the top of the list.

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Comparing MOPAC data

MOPAC AM1 and PM3 data for cyclohexanol, along with similar data from calculations using CHARMm, are reported in Tables 54, 55, and 56. How atom numbers were assigned in these tables depends on how the structure was built, so there may not be a ligand with the data you generate.

Table 54. Comparison of bonds

Bond	CHARMm	AM1	PM3
H-O	0.950	0.964	0.949
O-C1	1.411	1.418	1.409
C1-C2	1.538	1.527	1.537
C2-C3	1.534	1.513	1.520
C3-C4	1.535	1.516	1.520

Table 55. Comparison of angles

Bond	CHARMm	AM1	PM3
H-O-C1	109.7	107.3	107.4
O-C1-C2	111.9	111.0	112.0
C1-C2-C3	110.7	110.6	110.6
C2-C3-C4	111.1	111.3	111.1
C2-C1-C6	111.1	110.9	110.4

Table 56. Comparison of ring torsions

Torsion	CHARMm	AMI	PM3
C1-C2-C3-C4	56.3	56.1	56.8
C2-C3-C4-C5	56.0	56.0	56.4
C3-C4-C5-C6	55.9	56.0	56.1

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Using UHBD

The QUANTA/UHBD interface simplifies the process of creating input for and running the University of Houston Brownian dynamics (UHBD) program. The interface provides access to these UHBD applications such as:

• Electrostatic calculations for macromolecules in solution using the Poisson-Boltzmann equation

• Calculation of diffusion-controlled rate constants using Brownian dynamics

The QUANTA/UHBD interface provides tools for displaying results of UHBD calculations. A 3D contour mesh of the electrostatic potential, the electrostatic potential, and Brownian dynamics trajectories may also be displayed superimposed on the structure. Manipulation of these types of graphic objects is discussed in Chapter 6.

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Summary

QUANTA provides access to several external programs that provide alternative or supplemental approaches to modeling. These include:

• Molecular orbital calculations - CINDO and MOPAC

• Poisson-Boltzmann electrostatics and Brownian dynamics - UHBD

As much as possible, the options available within QUANTA cover all functionality within the original versions of these programs. In addition, the default options in the calculation setup dialog boxes have been specified so that changes are rarely necessary.

External third-party programs are automatically started from QUANTA when a request is made for a calculation. While QUANTA requires a graphics workstation for its interactive graphics and molecular displays, these computationally intensive programs may be run either on the local workstation or on a range of available network hosts.

Following is a brief summary of each program documented in this chapter.

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CINDO

The CINDO program (QCPE Program 141) is a molecular orbital program supplied by the Quantum Chemistry Program Exchange, Department of Chemistry, Indiana University. The program has an upper limit of 200 atoms. Options available within the QUANTA interface cover virtually all functionality within the original version of the external programs.

Charges generated by the program are stored in a quantum mechanical (QM) coordinate file or incorporated directly into the MSF. Once incorporated into the MSF, these charges can be used in subsequent QUANTA and CHARMm calculations or displayed.

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MOPAC

MOPAC (QCPE 445) is a semi-empirical molecular orbital program that is generally used in the study of chemical reactions and molecular structure problems. It is also provided by the Quantum Chemistry Program Exchange, Department of Chemistry, Indiana University.

The semi-empirical Hamiltonians available within MOPAC include:

• PM3

• AM1

• MNDO

• MINDO/3

Available calculations include:

• Vibrational frequencies

• Thermodynamic quantities

• Polarizability

• Isotopic substitution effects

• Geometries

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UHBD

The QUANTA/UHBD interface simplifies the process of creating input for and running the University of Houston Brownian dynamics (UHBD) program and provides tools for displaying results of UHBD calculations. The interface provides access to UHBD applications:

• Electrostatic calculations for macromolecules in solution using the Poisson-Boltzmann equation

• Calculation of diffusion-controlled rate constants using Brownian dynamics

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References

Information on CINDO and MOPAC can be obtained from QCPE documentation obtained from the Quantum Chemistry Program Exchange, Department of Chemistry, Indiana University.

See CINDO calculation methods in Approximate Molecule Orbital Theory, J. A. Pople and D. L. Beveridge, McGraw Hill Inc., New York, 1970.

See MOPAC AM1 calculation methods in Reviews in Computational Chemistry, Chapter 2, K. S. Lipkowitz and D. B. Boyd, VCH Publishers, New York, 1990.

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