[gmx-users] charge and ionization state at pH 6.5

Justin A. Lemkul jalemkul at vt.edu
Wed May 16 13:20:31 CEST 2012

On 5/16/12 7:13 AM, Acoot Brett wrote:
> Dear All,
> Will you please tell me how GROMACS calculates the total charge of a protein at
> pH 6.5? And how do we assign the ionization state of the residues, especially
> for HIS at pH 6.5?

Gromacs does not automatically deal with anything aside from pH 7 protonation 
states, though for most residues the difference between 6.5 and 7 is irrelevant. 
  Histidine protonation is assigned based on a hydrogen bonding search.  If you 
need to adjust protonation states, you need to do so yourself, but at pH 6.5 it 
will be very tricky to deal with those histidines.



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


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