Examples of Data-Sets and Output Files for MOPAC Calculations

Cautions and Warnings

Please send requests for examples to MrMOPAC@ATT.netATT.net
They will be added to this page as quickly as possible.

Getting started

Geometry Optimization Data Set for Formic Acid
Output file for Formic Acid
Data Set for a single-point calculation of Formic Acid
Multiple structures in one job

See also: PDB, TURBOMOLE, Gaussian data set,
   

Working with Proteins

This is an extensive description of how protein chemistry can be modeled using MOPAC. It starts with how to obtain and install MOPAC, and ends with instructions on how to generate the reaction path between two intermediates in enzyme-catalyzed reaction mechanisms.  A complete worked example of the chymotrypsin hydrolysis of a peptide bond is provided.  This would allow a new user to see all the steps and issues involved.  All the files needed for reproducing the entire catalytic cycle are provided.

Relevant Journal Articles



 

MOZYME (Giant Molecules)

Overview and Introduction
Simple MOZYME example
Eigenvectors and eigenvalues in MOZYME
Identifying charged sites
 

Working with proteins (other points)

Factors affecting precision
Generating a PDB file from a MOPAC data set
Automatically correcting net charge on system
Data set for Bacteriorhodopsin
Data set for a short section of DNA
Constrained Geometry Optimization of Crambin, 1CMB structure

C.I. Calculations

States resulting from one-electron excitations

    

Vibrational Frequencies
Docking energy
RMS difference

Simple example: Formaldehyde, data set, output

 

Use of SYMMETRY

In simplifying the geometry optimization of benzene
Benzene data set using symmetry
Output from benzene calculation

Solid State Calculations

How to construct a data-set
Example of a two-dimensional layer system (talc)  as zip file

Using Materials Studio format - An Amorphous Resin

Worked example, Comparison of input data and optimized geometry

   

Generating data for Graphical User Interfaces

Use keyword GRAPH or GRAPHF (for formatted data)

 

Polarizability Calculations

Simple example: p-nitroaniline, data set output

Transition state location

Strategy

 

 

Intrinsic Reaction Coordinates

Diels Alder reaction path