Re: [AMBER] Deprotonation of Tyr using Parmed

From: Jason Swails <>
Date: Thu, 24 Aug 2017 05:01:16 -0400

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
AMBER mailing list
Received on Thu Aug 24 2017 - 02:30:03 PDT
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