Many people don’t realize that GaussView can add hydrogen atoms to all or part of a protein input from a PDB file. In doing so, it uses the standard placements for filling out the valences of the various component amino acids. In addition, GaussView can also add hydrogens to any nonstandard residues that may be present in the PDB file.
Various aspects of adding hydrogens to a PDB file are controlled via the Options for Opening Files dialog, accessed via the dialog:
Choosing Yes in the Add Hydrogens popup menu will add hydrogens wherever appropriate as the PDB file atoms are imported. In this case, we want to import a PDB file which already has hydrogen atoms on some residues but not on others. Accordingly, we are using the Options dialog to suppress the automatic adding of hydrogens (which is the default) so that we can be sure that existing residues with hydrogens are not modified. Note that this dialog also allows you to choose whether to import any water molecules that may be present in the PDB file (here we are omitting them).
The next step we will take in importing our PDB file is to locate and select the atoms in the residues to which we want to add hydrogens. The best tool for this job is the PDB Residue Editor, accessed from GaussView’s Edit menu. We proceeded as follows:
We want to limit the display to only the residues we are interested in. We double clicked on the Display column head, which turned the entire column green. Then we selected Hide from the popup menu in any cell, causing the entire molecule to be hidden from display.
Next, we located the residues of interest in the list and set their display status to Show. This causes them to reappear in GaussView’s molecule window (displayed here in tube format for clarity):
Now we want to select all of the displayed atoms. An easy way to do this is to select the Rows=>Select Atoms of Selected Rows menu item in the PDB Residue Editor. This will turn all of the atoms yellow, indicating that they are selected.
- Finally, we select the Edit=>Add Hydrogens to Selected Residues menu item, causing hydrogen atoms to be added to the selected part of the protein.
Last updated on: 15 August 2016.