Re: [AMBER] Deprotonation of Tyr using Parmed

From: Sowmya Indrakumar <>
Date: Thu, 24 Aug 2017 13:04:32 +0000

Hi Jason,
Thanks for the comments. I am following you're tutorial of constant pH MD in explicit solvent. Since the saltconc=0.1, how would I go about doing it at a different salt concentration? In that case, reference energies should be defined at that concentration?

Kindly, could you recommend where I can find information about this.

From: Jason Swails []
Sent: Thursday, August 24, 2017 11:01 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Deprotonation of Tyr using Parmed

On Tue, Aug 22, 2017 at 9:41 AM, Sowmya Indrakumar <>

> Dear Marcos,
> Thanks for you're suggestions.
> This is what I tried. using the parameter and topology files generated
> from H++ at the desired pH, I run parmed "changeProtstate" command to
> change the protonated TYR to deprotonated TYR form.

​As you pointed out in your later email, the `changeProtState` command only
changes the charges of the residues. It "deprotonates" side-chains the
same way that constant pH MD does -- any "deprotonated" atom is simply a
dummy atom with 0 charge. In particular, atom types and parameters remain
unchanged. The charges used are the ones used in CpHMD simulations -- they
are not actually identical to the deprotonated residue charges (that is,
ASH that has been deprotonated using ParmEd has slightly different backbone
charges than ASP​, but the side-chain charges are the same).


Jason M. Swails
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Received on Thu Aug 24 2017 - 06:30:02 PDT
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