Molecular mechanics model checking
Several tricks can be useful to control the validity of the constructed model.
First, pay attention to the information panel (Analyze > Information). Check if the boundary conditions have been specified and the parameters are valid. Check the associated Force Field. Check if chemical bonds are specified. Typically, the absence of bonds results from reading a model from a file that lacks them. Usually, the program tries to assign bonds automatically but does not always succeed. Check the number of different molecular types involved in the model. Do their molecular formulas and molecular weights look sensible? Are the charges on the molecules integer? Fractional charges commonly indicate incorrect Force Field association.
Examine the model in mmol format. This format describes both the model and the force field associated with each atom and bond. Of course, it is not easy to check the force field in a large model. It is recommended at least to pay attention to zero force field parameters, which are commonly marked by comments with exclamation points. The torsion angles often have zero values, while the constants of valence angles and bonds can hardly be zero.
After the calculation is started, a warning about missing force field parameters can appear. Usually, such warning appears once for the first missing parameter. The full list of missing parameters can be viewed in the Report/FF_error.txt file.