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

[Peter C. Lai]

Charge assignment is dependent on forcefield. If the forcefield results in 
integral charges for polar residues then that's what you get. (Most classical
FFs do.)

I could be wrong but I don't think gromacs supports polarizable forcefields.

On 2012-04-07 02:21:42AM -0700, Acoot Brett wrote:
> 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?
>  
> Cheers,
>  
> Acoot
>  
> 
> ________________________________
>  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.
> 
> Francesco
> 
> 
> 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
> >arg+his+lys=43 
> >
> >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? 
> >
> >Cheers, 
> >
> >Acoot
>     
> > 
> > 
>  
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