AMBER Archive (2005)

Subject: AMBER: Protonate state of ARG and LYS.

From: Liu, Jingyuan (jliu2_at_iupui.edu)
Date: Thu Feb 10 2005 - 15:56:39 CST

Dear Amber users,

 

I am trying to run GB in combination with the AMBER8 new feature
"Constant pH". The manual mentioned how to deal with acidic amino acids
Asp, Glu and His, but not the basic residues Arg and Lys. I wonder
whether this is due to the carelessness when the manual was prepared, or
we do not need to worry about basic residues in this circumstance. If it
is the first case, what should we do to work with basic residue? If it
is the second case, why? Aren't basic residue positively charged at
neutral pH? Many thanks for your help.

 

Jingyuan

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