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

[Justin A. Lemkul]

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

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Justin A. Lemkul, Ph.D.
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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