[gmx-users] PH 5.0 ?

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 21 21:35:49 CET 2010

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.


> Thank you
> Lin


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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