Before doing any serious modeling, it is very important that the starting model is as correct as possible. Effort spent here in validating the model will save wasting a lot of time later on. Of course, eliminating all errors is practically impossible, but if the number of errors is minimized, then the likelihood of the remaining errors causing problems later on is diminished.
A simple web-page will be written when HTML is used. This web-page allows Firefox to open a Jmol script that can be used easily for examining details of proteins. Two steps need to be done to get this graphical user interface to work. First, JSmol needs to be installed, and second a minor change needs to be done to get Firefox to read local web-pages. But once these are done, using HTML is very easy.
Proteins can have a large number of charged sites. These can be divided into two groups, salt bridges and all other charged sites. This check should be done at least twice. The first time it should be done is after the 1SCF calculation. To check for errors in ionization, start by looking at the output file from the 1SCF calculation. Later on, when the geometry is optimized and before any research work is started, the check should be run again. There are two lists in the output that are relevant, these are headed:
Ion PDB Label Charge Distance PDB label for Salt Bridge Chargeand
Salt Bridges Found (Up to 8.0 Angstroms)
All ionized sites identified by the Lewis structure are shown in the first list but only the salt-bridges are shown in the second list. In the second list the atomic charges are calculated from the electron density.