8.1 Charges & potential
With this dialog, it's possible to assign the atom types and the atomic charges. To open it, select Charge & Pot. from the main menu.
Check and select the Force field type if
you want fix the atom types for molecular mechanics calculations. To assign the atomic
charges, you must check Charges and select the method. Two methods are
available to fix the atom charges: the first one is the Gasteiger-Marsili method
that it's universal and it uses typed atomic charges that are smoothed on the
polar atoms. The second one is less flexible and it uses a fragment/residue
database containing the pre-computed charges. If a residue/fragment is not
included in the database, the atomic charges can't be assigned. To select the
first method, you must choose Gasteiger, to select the second one, you must
choose any other item in the charge list.
If you want fix
atom types and charges to selected atoms only, you must check Consider
selected atoms only. Press Fix to
calculate the atom types and/or the charges, otherwise press Cancel to close the
dialog window. Clicking on the button , it's possible to modify the parameters of the selected
template/data file through the MiniEd:
Please remember to save the changes in order to activate the modifications. The Force Field combo box is populated scanning the ..\VEGA\Data directory every time that the dialog is opened. If a new template is added (click here for more information) and VEGA ZZ is running, you must close and reopen the dialog to refresh the list.