Re: [AMBER] TI for mutation of charged residues

From: Hosein Geraili Daronkola <>
Date: Tue, 30 Jul 2019 10:33:24 +0200

One thing that I encountered in these simulations is that, if I disappear
one potassium along with the Asp, mutate to the Asn, in the trajectory the
particular potassium gets very close to the Asp, although there are
thousands more potassium. It means the interaction between these two is
different which makes it unreal.


[image: Mailtrack]
notified by
10:30:01 AM

On Mon, Jul 29, 2019 at 9:17 AM Hosein Geraili Daronkola <> wrote:

> Hi all,
> I am trying to use Ti on pmemd to mutate Aspartate to Asparagine on a
> protein. The problem is that this mutation ends in a charged state because
> I add counterion in the beginning and start from a neutral state. Is there
> an analytical way to remove this effect of ending in a charged state, one
> extra potassium at the end??
> I tried to mutate both Asp and potassium together to Asn, but the problem
> is that they should stay far away to not have a cooperative effect, so I
> could subtract the solvation free energy of potassium from the combination,
> but I cannot increase the box size reasonably enough to get rid of this
> cooperative effect between a negatively charged residue, Asp, and
> positively charge ion, potassium.
> Thanks in advance
> Best

Hosein Geraili Daronkola
Ph.D. student,
Wissenschaftspark Potsdam-Golm
Max Planck Institute of Colloids and Interfaces
Theory and Bio-Systems Department
Office K-1.119
Am M├╝hlenberg 1 OT Golm
14476 Potsdam
Phone: +49-(0)331 567-9611
Fax: +49-(0)331 567-9602
AMBER mailing list
Received on Tue Jul 30 2019 - 02:00:02 PDT
Custom Search