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

[Francesco Oteri]

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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