[gmx-users] PH 5.0 ?

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> 
> 
> HI
> How to assign charge for the residue of protein at PH 5.0 ?
> 
> I have Ka values of each residue of protein then i can calculate the 
> overall charge for each residue at PH 5.0 solution.
> 
> However, how to calculate the partial charges of atoms within the 
> residue of protein at PH 5.0?
> 

You shouldn't need to calculate any charges.  Most force fields have each 
relevant residue in both protonated and deprotonated forms already.  See pdb2gmx 
-h for the options used to set these protonation states.

-Justin

> Thank you
> Lin
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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