Re: AMBER: questions about run MD at different pH

From: Kailee <>
Date: Tue, 4 Mar 2008 11:40:30 +0000

Dear David,

Thank you very much for your reply. I am still not very clear about some
points in that issue:

> 1) If I protonate my protein (which is solvated in water explicitly) with
> > H++ program at different pHs and then run them in AMBER as normal, at
> which
> > pH will be my protein simulating? will it be the pH value I set in H++
> > program OR there is a fixed pH for all simulations in AMBER?
> There is no "fixed pH for all simulations": you would get behavior
> corresponding to the (fixed) protonations chosen by H++. This might
> roughly
> correspond to a fixed pH, but still involves an unphysical *fixed* set of
> protonation states.

So, in normal MD simulations, there is no 'pH' such parameter, although the
protonation states of amino acids are assigned according to pH, which can be
done beforehand? and can you give a few examples of those unphysical fixed
set of protonation states please?

> >
> > 2) I have read the manual about constant pH calculations, which can be
> used
> > for simulations at different pH, right? however, it's only for implicit
> > solvent simulations, and I would like to ask, is there any other
> differences
> > with this method except it can't be used for explicit solvent, for
> example,
> > I have some non-standard residues ( which I have created frcmod file for
> > them), will these be OK with the method? and are there any differences
> in
> > analysis methods?
> Non-standard residues are a "problem" in the sense that you will have to
> work
> hard to understand the details of how the code works, so that you can
> adapt
> your residues to them; (assuming that your non-standard residues have
> protonataed and de-protonated forms.)

My non-standard residues are those containing metal ions, and I treated
them following the AMBER tutorial with non-standard residues, therefore
those residues contain their neighbouring amino acids. So if the metal ions
and their neighbouring amino acids have fixed protonation states at
different pHs, then the constant pH calculations method should be an easier
choice to compare results at different pHs?

Thanks very much for your help.

Best regards,

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Received on Wed Mar 05 2008 - 06:07:31 PST
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