Re: Problems in setting up low pH systems

From: Giacomo Fiorin (
Date: Wed Jan 11 2012 - 10:03:34 CST

Hello, Zizhang, if you have only a few HIS residues in the system, I think
the best is to rename each of them manually to the residue that you want:
HSD = single protonation in N_delta
HSE = single protonation in N_epsilon
HSP = double protonation (charged Histidine)


On Wed, Jan 11, 2012 at 10:43 AM, Sheng, Zi-Zhang <> wrote:

> Dear all,
> I am a new learner of NAMD. I want to simulate a protein under low pH. I
> used PDB2PQR to assign the protonation state to pH5 first. The .pqr file
> generated by PDB2PQR is used for generating psf file in VMD using autopsf.
> The output of VMD shows that there are two charges in the system, but
> PDB2PQR shows that there are three. It seems VMD will delete the
> protonation state generated by PDB2PQR and reassign them by itself. How can
> i avoid of this? And also, is it appropriate or enough to setup low pH
> system simply by assigning protonation state and adding neutral ions to the
> system? Is it necessary to change HIS to HSE when modeling low pH system?
> Thank you.
> Zizhang sheng

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