[gmx-users] Query regarding protonation and deprotonation of some residues
itamar.kass at monash.edu
Mon Sep 27 06:37:06 CEST 2010
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
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