Re: Adding hydrogen atoms to the crystall structure

From: Thomas Evangelidis (
Date: Tue Feb 18 2014 - 10:44:56 CST

I have no experience in pdb2pqr, but it seems it is not designed to add
> hydrogen atoms
> "This server enables a user to convert PDB <> files
> into PQR files. PQR files are PDB files where the occupancy and B-factor
> columns have been replaced by per-atom charge and radius."

PDB2PQR does add hydrogens and as a matter of fact it adds them in a way
that the hydrogen bond network in the protein is optimum. It can also
predict the protonation state of titratable amino acids given the pH value.
It can also assign charges using various force fields, including CHARMM,
but I doubt if they correspond to the latest CHARMM protein force field. So
in your case I would safely ignore them and let psfgen assign new charges.

> if you could make psf file (probably using *AutoPSF plugin*) it should
> gave you pdb file including hydrogen atoms too. So I am not sure why you
> are using PQR?1?!

It's been too long since the last time I used psfgen, but I think if
hydrogens are missing, it places all histidine hydrogens to the same
sidechain nitrogen (creates only HID residues) which may be wrong in many

Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens


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