[gmx-users] apply pH effect on aminoacids

[Dallas Warren]

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.

http://manual.gromacs.org/documentation/current/onlinehelp/gmx-pdb2gmx.html

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
nail.


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

> 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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