Re: Adding hydrogen atoms to the crystall structure

From: Thomas Evangelidis (
Date: Tue Feb 18 2014 - 14:56:21 CST

Protein force fields are developed to reproduce experimental observables.
The partial charges of amino acids are part of the force field, therefore
you must not change them. In that respect, you should use PDB2PQR just to
make assumptions about the protonation state of residues like HIS, ASP,
GLU, not to calculate changes for your protein atoms.

On 18 February 2014 22:30, zeynab mohamad hoseyni <>wrote:

> Hi Mehran,
> I used the mentioned server to predict the protonation states of Histidine
> mainly. The server does it according to the Pka values calculated using
> the ProPka server.
> Histidine is one of the polar amino acids who are called titratable amino
> acids (
> Note that in the CHARMM topology file the charges assigned to the atoms of
> each residues are fixed and for example all ARG residues are composed of
> atoms
> with fixed charges and doesn't matter where they are located while in
> reality the Pka values for the ARG residues placing on the surface of
> protein (facing waters)
> are different from those located in the interior of the protein (
> This means that
> the charge distribution has to
> be different for those ARG residues experiencing different environment. PQR
> contain the charge distribution for the atoms of residues according to the
> Pka calculation. So I was trying to use those partiol charges in my psf
> file..
> The HIS case is much more delicate as its Pka is closed to the PH of
> water. So any small changes in the PH could change the protonation state
> of HIS to be one of HSE,
> HSD or HSP. These are all I know...
> All the Best,
> Zeynab
> On Tuesday, February 18, 2014 4:10 PM, MEHRAN MB <>
> wrote:
> Hi Zeynab,
> On Sun, Feb 16, 2014 at 10:54 AM, zeynab mohamad hoseyni <
>> wrote:
> Dear all,
> I use pdb2pqr ( server to add
> hydrogen atoms to the protein structure.
> 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 columns have been replaced by per-atom charge and radius."
> The server produces pqr file containing protein coordinates (including the
> hydrogen atoms) as well as the charges assigned to each atom.
> These charges are different from those provided by topology file
> 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?!
> -mehran

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


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