Adding hydrogen atoms to the crystall structure

From: zeynab mohamad hoseyni (
Date: Sun Feb 16 2014 - 09:54:40 CST

Dear all, I use pdb2pqr ( server to add hydrogen atoms to the protein structure. 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 and I was wondering how I can change the atomic charges placed in the  psf file to those contained in the pqr file and in fact I'm not sure if I have to do that. Does any body has experience with that?  All the Best, Zeynab

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