8. I get a warning message about missing AMBER, BIO+, or OPLS parameters.

You have run into the most common problem in molecular mechanics: missing parameters. See Chapter 3 of the HyperChem Computational Chemistry manual (in Part I) for a description of what parameters are. We simply provide published parameters for the published force fields AMBER, CHARMM (which we call BIO+ for trademark reasons) and OPLS. For MM+ we also provide a default parameter scheme for generating parameters when published MM2 parameters are not available, so that you never get warnings about missing parameters.

If you are using a selection so that the atoms with the missing parameters are not selected in the calculation then it is safe to ignore missing stretch, bend or torsion parameters. Otherwise proceeding without parameters can lead to funny optimized geometries, because the program ignores any interactions that it doesn't have parameters for. See the "Warning Messages" part of the Compute Menu section in Chapter 7 of the Reference manual.

If you decide that you need parameters, you can search for them in the literature (we only include parameters from the force field authors and you might find some published by other groups using the force field) or develop your own. At its crudest level this means guessing based on parameters for similar types, but parameter development is an area of active research. Finding or developing parameters for you is beyond the scope of product support for HyperChem.

The following are some basic instructions for adding parameters. You should also see the Parameter Sets and Compiling Parameters sections of the Molecular Mechanics chapter in Part 2 of the Computational Chemistry manual, the Setup/Select Parameter Set and Setup/Compile Parameter File menu item descriptions in Chapter 7 of the Reference manual and Appendices B and F of the Reference manual.

To add new parameters to an existing parameter set you should:

1. Note which parameters are missing.

You should note the kind of interactions (i.e. stretch, bend, non-bonded, etc.) and the atom types involved from the warning messages. You may find it convenient to save a log file so that messages are recorded there. (You can also set WarningType=Log in CHEM.INI or by a script so that warnings from the calculations only go to a log file and not to the screen, but remember to switch it back later or you won't get any warnings unless you save and read a log file!)

The warning messages will probably have much duplication; you just need to identify the unique set of missing parameters.

2. Figure which parameter file to add new parameters to.

First you need to know which force field you are using (MM+, AMBER, BIO+ or OPLS) and which parameter set for that force field (by using the Setup/Select Parameter Set menu and the associated dialog box). You can see which files are used for that parameter set by looking in the CHEM.INI file. For instance, for the AMBER forcefield and amber3 parameter set, you would look in the [amber,amber3] section of the CHEM.INI file using a text editor.

The parameters for each type of interaction (i.e. stretch, bend, non-bonded, etc.) is stored in a different file pointed to by a CHEM.INI keyword. For instance the [amber,amber3] section should have a line like:

QuadraticBend=am89aben.txt

This tells HyperChem to find the bend parameters for the amber3 parameter set in the file am89aben.txt. All the keywords are given in Appendix F of the Reference manual and the formats for the associated files are described in Appendix B.

3. Add new parameters to the appropriate file or files.

It is a good precaution to back up the original before modifying a a parameter file.

Use a text editor to edit the text parameter file or files. (You can also keep parameters in dBASE 3 format files, in which case you would need to use a database program to modify the files.) The file formats are described in Appendix B of the Reference manual and the equations that the parameters are used in are given in the Force Fields section of the Molecular Mechanics chapter in Part 2 of the Computational Chemistry manual.

4. Compile all the parameter sets that use the modified file or files.

Use the Setup/Select Parameter Set and Setup/Compile Parameters menu items to choose and recompile all the parameter sets that use the files you have modified. You can see which sets use which files in the CHEM.INI file.

The Parameter Sets and Compiling Parameters sections of the Molecular Mechanics chapter in Part 2 of the Computational Chemistry manual also describe adding and compiling new parameters or parameter sets. You should use a new set if you want to modify existing parameters or be able to easily switch back and forth between parameter sets.

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