[gmx-users] how pdb2gmx calculate the total charge of a protein

Acoot Brett acootbrett at yahoo.com
Sat Apr 7 11:21:42 CEST 2012

Thanks Francesco.
But at any pH value (different protonation state), the H cannot be regarded as fully associated or dissociated. Thus can we further consider whether the total charge calculated by pdb2gmx is really the net charge of the system or not. I regard the net total charge, regardless of positive or negative, can hardly be an integer.
Furthermore, if we do not add couter ions to make the net charge "0" for the whole system and we do the MD, what can occur?

 From: Francesco Oteri <francesco.oteri at gmail.com>
To: gmx-users at gromacs.org 
Sent: Saturday, 7 April 2012 7:14 PM
Subject: Re: [gmx-users] how pdb2gmx calculate the total charge of a protein

Dear Acoot,
the error, I guess, is you assumed the histidines are positive while
    I think they are neutral.
Since the His protonation state is hard to identify at ph7,
    Hystidines are usually neutral.


Il 07/04/2012 09:42, Acoot Brett ha scritto: 

> Dear All, 
>I have a protein, the charged residue numbers in the protein is as following 
>ARG  11
>ASP  19
>glu  25
>his  8
>lys  24 
>asp+glu=   44
>However the total charge of the protein given by pdb2gmx is -9. 
>Will you please introduce to me how pdb2gmx calculate the total charge of the protein? 
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