Re: [AMBER] CpHMD with structurally different protonation states?

From: Adrian Roitberg <>
Date: Wed, 24 Mar 2021 13:22:59 -0400

Hi Anselm.

As Vinicius mentioned, you would need to code inside AMBER to be able to
do this directly.

If you are interesting mostly on the change in pKa of the compound, you
can do Free energy calculations for the molecule in solution and in a
binding pocket for example.


On 3/24/21 7:58 AM, Dr. Anselm Horn wrote:
> [External Email]
> Dear all,
> a question to the CpHMD experts:
> Is it possible to apply the constant-pH simulation approach to systems,
> where the protonated state differs from the deprotonated one in the
> local structure, i.e. atom types and local parameters in addition to
> atomic charges?
> A collegue of mine was interested in investigating such a species, where
> deprotonation results in a different local structure, going from
> all-planar to out-of-plane distorsion.
> As far as I understood the CpHMD approach implemented in Amber, the
> different protonation states are realized by applying different charge
> sets and Hydrogen radii to the titratable residue, keeping the
> perturbation of the system small. And thus, no further change besides
> atomic charges and the presence or absence of H atoms could be taken
> into account.
> Is this correct? Or are there some advanced options, e.g. to switch
> between complete topology files?
> Best regards
> Anselm
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> AMBER mailing list

Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
AMBER mailing list
Received on Wed Mar 24 2021 - 10:30:02 PDT
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