A low pka would mean they are deprotonated at ph 7, so don't change them.
On Aug 6, 2012 9:21 PM, "Zalikha Ibrahim" <zalikha.ibrahim.yahoo.com> wrote:
> Hi to all Amber user,
>
> I have a question about the naming of aspartate and glutamate in PDB.
> Please correct me if I wrong.
> Aspartate and Glutamate are recognized in their deprotonated form by
> default in XLeap (ASP and GLU). If I want to simulate the protein in pH 7,
> should I change the name of all aspartate and glutamate residues that has
> low pKa value at pH 7 as ASH and GLH?
>
> Thanks so much in advance
>
> Zalikha Ibrahim
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Received on Mon Aug 06 2012 - 18:30:03 PDT
