Hello friends, Can you help with telling the algorithm for inferring Hbonds in PDB file. A link of published algo is much appreciated.. Have a nice day!!
Hydrogen bonds are usually detected using a combination of distance and angle criteria. Other fancier methods probably exist, but these geometrical solutions are often good enough.
I won't really look for a hydrogen bond paper, Pubmed exists for that, but I will give the link to the GROMACS manual. Look for the Appendix D.35, it has all the ingredients.
First problem with identifying hydrogen bonbds on a PDB is that, usually, there are no hydrogen atoms included in PDB structures. So your order of operations is:
You can go about this the open-source route -- using PyMol, VMD, GROMACS (as João had mentioned), Simulaid or MODELLER. Or you can also download Schrodinger's Maestro that I use a lot (usually $$$, but free for academics for MD simulations). There it's really trivial to prepare your protein (add hydrogen atoms/minimization/hbond analysis.)
When you decide on a tool, feel free to post another question to get the recipe.