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

[Itamar Kass]

  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
============================================

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100927/0e55204c/attachment.html>