Dear Hosein,
Take a look at these papers, they may be instructive...
+ Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation [
https://doi.org/10.1021/acscentsci.8b00717]
+ Accurate Calculation of Relative Binding Free Energies between Ligands with Different Net Charges [
https://doi.org/10.1021/acs.jctc.8b00825]
Best,
Matias
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Hosein Geraili Daronkola" <geraili.hsn.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Martes, 30 de Julio 2019 5:33:24
Asunto: Re: [AMBER] TI for mutation of charged residues
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.
Best
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07/30/19,
10:30:01 AM
On Mon, Jul 29, 2019 at 9:17 AM Hosein Geraili Daronkola <
geraili.hsn.gmail.com> 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 Mühlenberg 1 OT Golm
14476 Potsdam
Germany
Phone: +49-(0)331 567-9611
Fax: +49-(0)331 567-9602
E-mail: hosein.geraili.mpikg.mpg.de
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Received on Tue Jul 30 2019 - 12:30:02 PDT
