Re: AMBER: questions about run MD at different pH

From: Taufik Al-Sarraj <>
Date: Tue, 15 Apr 2008 11:15:28 -0500

I am curious about the last comment in this communication, how is pH
calculated in AMBER9?

David A. Case wrote:
> On Mon, Mar 03, 2008, Kailee wrote:
>> 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.
>> 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.)
>> 3) Will it be possible that I manually add some H+ or OH- ions to change the
>> pH conditions? and if yes, how should I do it? should I add them in leap or
>> include them in the pdb file? and after the addition of those (H+/OH-),
>> should I still neutralise the system (using PBC)?
> No, this is not possible. Even if you could create a water box big
> enough [**] to allow you to simulate an H+ concentration of 10**-7 M,
> molecular mechanics potentials don't allow chemical changes, so the
> protons could not bond to (or dissociate from) the acids and bases in
> your solute.
> [** Note that if you had one H+ and one OH- ion, you would need about 50
> million water molecules to construct a solution with pH=7.]
> ...dac
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Received on Fri Apr 18 2008 - 21:19:34 PDT
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