[gmx-users] apply pH effect on aminoacids

Dallas Warren dallas.warren at monash.edu
Mon May 4 01:32:32 CEST 2020

Protonation state of the amino acids are set during execution of pdb2gmx and
you can choose yourself what their protonation state is using -inter or any
of the other options if you don't want to go through all.


Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a

On Mon, 4 May 2020 at 02:59, azadeh kordzadeh <azadehkordzadeh at gmail.com>

> Hi
> I gave a topology of a protein with pdb2gmx command in next step I change
> protonation some aminoacids but the topology didn't chage. How could I
> create new topology?
> I need to obtain topology protonated aminoacid from other servers?
> Thanks
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