[gmx-users] Query regarding protonation and deprotonation of some residues

[Tsjerk Wassenaar]

Hi Sonali,

First of all, you'll have to find a force field that supports tyrosinate and
serinate. These aren't generally considered titratable and are consequently
not in the list for interactive selections with pdb2gmx. Once you've found a
suitable force field, you'll have to set the protonation states by renaming
the residues. Such simulations are advanced, requiring a thorough knowledge
of simulations and force fields. Do check
http://www.gromacs.org/Documentation/How-tos/Parameterization if you haven't
done so.

Hope it helps,

Tsjerk

On Mon, Sep 27, 2010 at 8:49 AM, sonali dhindwal <
sonali11dhindwal at yahoo.co.in> wrote:

> Thanks Kass for the help.
>
> I want to specifically protonate one of the lysine near the active site and
> deprotonate Tyr and Ser. It will be kind if  you can please help me to know
> how to select that specific residue number.
>
> Regards
> --
> Sonali Dhindwal
>
>
> --- On *Mon, 27/9/10, Itamar Kass <itamar.kass at monash.edu>* wrote:
>
>
> From: Itamar Kass <itamar.kass at monash.edu>
> Subject: Re: [gmx-users] Query regarding protonation and deprotonation of
> some residues
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Monday, 27 September, 2010, 10:07 AM
>
>
> Hi,
>
> You need to define the protonation sate vie pdb2gmx.
>
> pdb2gmx -tyr -lys
>
> On 27/09/10 2:34 PM, sonali dhindwal wrote:
>
>   Hello All,
>
> I came through this research article, in which author has selectively
> deprotonated and protonated some of the residues to simulate the condition
> for electrostatic interaction with the substrate while carrying out
> molecular dynamics simulation.
>
> It will be appreciable, if you could help me regarding the same, how to
> deprotonate Tyr and Ser residue and protonate Lysine residue of the protein
> while preparing the protein topology to be used for molecular dynamics
> simulation in Gromacs.
>
> Thanks and Regards.
>
> --
> Sonali Dhindwal
>
>
> --
>
>
> "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut
>
> ===========================================
> | Itamar Kass, Ph.D.
> | Postdoctoral Research Fellow
> |
> | Department of Biochemistry and Molecular Biology
> | Building 77 Clayton Campus
> | Wellington Road
> | Monash University,
> | Victoria 3800
> | Australia
> |
> | Tel: +61 3 9902 9376
> | Fax: +61 3 9902 9500
> | E-mail: Itamar.Kass at monash.edu <http://mc/compose?to=Itamar.Kass@monash.edu>
> ============================================
>
>
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>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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