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

[sonali dhindwal]

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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