[AMBER] Aspartate and Glutamate naming in PDB

From: Zalikha Ibrahim <zalikha.ibrahim.yahoo.com>
Date: Mon, 6 Aug 2012 18:21:05 -0700 (PDT)

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
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