On Thu, Jan 28, 2010, Tom Williams wrote:
>
> I am running Sander for protein/water/ions simulation. The protein
> should carry charge although the whole system is neutralized by adding
> the counter ions.
>
> So according to you, in amber, except the manually adjusting protonation
> state, the only way is to run the constant pH molecular first to
> obtain the correct state of each residue and then switch to normal MD
> simulation in Sander.
First, note that there is no "correct [protonation] state". The energetics of
any residue may change with conformation (and hence with time in an MD
simulation), and side chains with a pKa near the solution pH will exist in
more than one state.
Since most calculations assume a single protonation state, there are a number
of tools that can help to assign a "good" choice. H++ and PDB2PQR are two
such tools, that you can get to from the Amber web page,
http://ambermd.org.
You use these before running LEaP, the proceed as usual.
You are welcome to try constant pH simulations, but please be aware that this
is a difficult, advanced and experimental tool.
...hope this helps...dac
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Received on Fri Jan 29 2010 - 05:30:04 PST
