Re: AMBER: Protonation/deprotonation of terminal residues

From: FyD <>
Date: Wed, 18 Apr 2007 20:26:47 +0200

Quoting Jesper Soerensen <>:

> I want to simulate two different "pH environments" and to do this I need
> two different protonation states on the terminal residues. So that at
> low pH (~2) the termini are protonated, resulting in a neutral charge on
> the C-term and a positive charge on the N-term, and at higher pH (~9)
> they should be deprotonated, giving C-term a negative charge, and the
> N-term a neutral charge.
> Is this possible, and which is the best way to achieve this? For the
> termini that are charged I can just use the "NXXX" and "CXXX" variants,
> but for the neutral ones, what do I do? Can I just add a hydrogen onto
> the CXXX amino acid, and remove a hydrogen from the NXXX aminoacid? Is
> the effect on the ff paramters severe?

You have examples of neutral terminal aminocid in REDDB...

regard, Francois

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Received on Sun Apr 22 2007 - 06:07:16 PDT
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