When trying to understand protein-ligand interactions it is crucial to understand the precise hydrogen bonding interactions. Just calculating a distance and quoting that in a paper is not enough, AA-A-H and A-H-D angles should be specified as well. WHAT IF, in combination with the topology generator PRODRG, is able to calculate this for you and also expresses the strength of a hydrogen bond with a number between 0 (no hydrogen bond) and 1 (optimal hydrogen bond). To do this, take the following steps.

• Login on one of the PCs and create/change to a suitable directory.
• Edit your protein-ligand-water-other_stuff PDB file so that 1) water molecules have proper PDB names (O HOH rather than TIP OH2) and 2) either no alternate side chains are present OR alternate side chains are defined PRECISELY according to PDB rules.

  Start WHATIF (on one of the PCs !) and type:

  %topolo
  TOPOLOGY.H
  getmol thepdbfile.pdb
  x
  grafic
  shotot
  1
  a
  %center
  hbonds
  hb2ini
  hb2net
  

  Now you can use HB2GRA (showing hydrogens and hydrogen bonds on the graphics (remember to type GO) HB2LIS (will get you the 0-1 geometry factor) and SHOHBO (distances and angles), preferrably in that order. You will probably not be able to operate these commands without some basic WHATIF knowledge - RTFM!

• You can use the table from HB2LIS to generate hydrogen bonds in pymol - remember to also include the ligand-water hydrogen bonds (which HB2LIS will also show). This can be done automatically by transferring the HB2LIS H-bond table into a separate file and then typing:

  cat that_file | ~dava/programs/dava/hb2proc 0.3
  

  You can download the hb2proc.f FORTRAN program here. Compile with f77 hb2proc.f -o hb2proc.

  The 0.3 stands for a cut-off (< 0.3 are poor H-bonds). You will now have a file called 'pymol' in your directory that you can paste into your pymol script (BUT: use the SAME PDB file for your pymol session!).