AMBER Archive (2009)

Subject: [AMBER] pH calculations

From: Michael Durney (mdurney_at_gmail.com)
Date: Thu Sep 17 2009 - 10:01:08 CDT

I am writing to ask for some general advice on an RNA project.

We have an RNA with a single protonated adenine and have solved the
NMR structure. My next goal
is to use AMBER to refine (or even re-calculate) this structure taking
into account the behaviour of the protonated adenine. Do I need to
create a special residue or library and if so is there a simple way to
do this? What then is the best way to calculate the structure at a
constant solution pH to maintain adenine
protonation and see the effect on the structure?

Further down the line I would like to simulate the system under
different pH conditions to see if any structural transition can be
detected. Is this a reasonable or feasible project to approach using
AMBER and where should I start?

I realize that these are very general questions but any advice would
be appreciated.

Thanks,

Michael.

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