AMBER Archive (2007)

Subject: AMBER: Protonation/deprotonation of terminal residues

From: Jesper Soerensen (jes_at_chem.au.dk)
Date: Wed Apr 18 2007 - 07:56:26 CDT

Hi,

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?

Thanks,
Jesper Soerensen

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