From: MEHRAN MB (mb.mehran1_at_gmail.com)
Date: Tue Feb 18 2014 - 10:10:53 CST
Hi Zeynab,
On Sun, Feb 16, 2014 at 10:54 AM, zeynab mohamad hoseyni <
zmhoseyni_at_yahoo.com> wrote:
> Dear all,
> I use pdb2pqr (http://nbcr-222.ucsd.edu/pdb2pqr_1.8/) 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 <http://www.rcsb.org/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columns have been replaced by per-atom charge and radius."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
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